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- PDB-5lzu: Structure of the mammalian ribosomal termination complex with acc... -

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Entry
Database: PDB / ID: 5lzu
TitleStructure of the mammalian ribosomal termination complex with accommodated eRF1
Components
  • (40S ribosomal protein ...) x 6
  • (60S ribosomal protein ...) x 5
  • (Ribosomal protein ...) x 3
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • E-site tRNA
  • Eukaryotic peptide chain release factor subunit 1
  • P-site tRNA
  • RACK1Receptor for activated C kinase 1
  • eL13
  • eL14
  • eL18
  • eL19
  • eL20
  • eL21
  • eL22
  • eL24
  • eL28
  • eL29
  • eL30
  • eL31
  • eL32CD59
  • eL33
  • eL34
  • eL38
  • eL39
  • eL40
  • eL42
  • eL43
  • eL8
  • eS10
  • eS17
  • eS19
  • eS21
  • eS24
  • eS25
  • eS26
  • eS28
  • eS30
  • eS31
  • eS7
  • mRNA (UGA stop codon)
  • uL10
  • uL11
  • uL13
  • uL14
  • uL15
  • uL16
  • uL2
  • uL22
  • uL23
  • uL24
  • uL29
  • uL3
  • uL30
  • uL4
  • uL5
  • uL6
  • uS10
  • uS11
  • uS12
  • uS13
  • uS14
  • uS15
  • uS17
  • uS19
  • uS2
  • uS3
  • uS5
  • uS7
  • uS8
  • uS9
KeywordsRIBOSOME / Translation / Elongation
Function / homology
Function and homology information


translation termination factor activity / translation release factor complex / cytoplasmic translational termination / translation release factor activity / regulation of translational termination / translation release factor activity, codon specific / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / regulation of translation involved in cellular response to UV / protein methylation ...translation termination factor activity / translation release factor complex / cytoplasmic translational termination / translation release factor activity / regulation of translational termination / translation release factor activity, codon specific / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / regulation of translation involved in cellular response to UV / protein methylation / positive regulation of base-excision repair / response to TNF agonist / positive regulation of DNA N-glycosylase activity / negative regulation of DNA repair / oxidized pyrimidine DNA binding / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / NF-kappaB complex / cytosolic ribosome / positive regulation of endodeoxyribonuclease activity / oxidized purine DNA binding / sequence-specific mRNA binding / protein kinase A binding / supercoiled DNA binding / ubiquitin-like protein conjugating enzyme binding / positive regulation of T cell receptor signaling pathway / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of activated T cell proliferation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / spindle assembly / positive regulation of JUN kinase activity / ribosomal small subunit biogenesis / polysome / positive regulation of microtubule polymerization / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to leukemia inhibitory factor / Hsp70 protein binding / polysomal ribosome / negative regulation of protein ubiquitination / endodeoxyribonuclease activity / translational termination / positive regulation of interleukin-2 production / rough endoplasmic reticulum / positive regulation of translation / mitotic spindle / ruffle membrane / Hsp90 protein binding / small ribosomal subunit rRNA binding / chromosome segregation / DNA damage response, detection of DNA damage / mRNA 5'-UTR binding / cellular response to gamma radiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / rRNA processing / cellular response to hydrogen peroxide / positive regulation of NIK/NF-kappaB signaling / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / ribosome binding / 5S rRNA binding / cellular response to tumor necrosis factor / cytosolic small ribosomal subunit / small ribosomal subunit / mitochondrial inner membrane / microtubule binding / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / postsynaptic density / positive regulation of NF-kappaB transcription factor activity / mitochondrial matrix / cell differentiation / translation / cell division / synapse / mRNA binding / transcription factor binding / apoptotic process / protein-containing complex binding / nucleolus / protein kinase binding / Golgi apparatus / endoplasmic reticulum / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Ribosomal L28e protein family / Ribosomal protein L2, C-terminal / Ribosomal protein S19/S15, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L24e, conserved site / in:ipr023106: / Ribosomal protein S15P / Ribosomal protein L30e, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 ...Ribosomal L28e protein family / Ribosomal protein L2, C-terminal / Ribosomal protein S19/S15, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L24e, conserved site / in:ipr023106: / Ribosomal protein S15P / Ribosomal protein L30e, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L39e domain superfamily / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein L18e/L15P / Ribosomal protein S19 conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein L31e domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S5 domain 2-type fold / Ubiquitin-like domain superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L7, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / 50S ribosomal protein L30e-like / eRF1, domain 1 / Ribosomal L28e/Mak16 / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L15e core domain superfamily / Ribosomal protein S9, conserved site / G-protein beta WD-40 repeat / Ribosomal protein L32e superfamily / Ribosomal protein L10e/L16 / Ribosomal protein L10e, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein L30, conserved site / WD40-repeat-containing domain / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L22/L17, conserved site / K homology domain-like, alpha/beta / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein L2, domain 3 / Ribosomal protein L2, domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S6, eukaryotic / Ribosomal protein S4e, central region / Ribosomal protein S4e, N-terminal / Ribosomal protein L25/L23 / Ribosomal protein L21e, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L39e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L31e, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L23 / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ubiquitin domain / Ubiquitin conserved site / Ribosomal protein L3, conserved site / WD40 repeat, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L35Ae, conserved site / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / Ribosomal protein L30, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein L21e / Ribosomal protein S13/S18 / Ribosomal S17 / Ribosomal protein S9/S16
40S ribosomal protein S17 / Ribosomal protein L26 / 60S ribosomal protein L12 / 60S ribosomal protein L27a / 40S ribosomal protein S13 / 40S ribosomal protein S3a / 40S ribosomal protein S27a / 60S ribosomal protein L7a / Uncharacterized protein / 40S ribosomal protein S7 ...40S ribosomal protein S17 / Ribosomal protein L26 / 60S ribosomal protein L12 / 60S ribosomal protein L27a / 40S ribosomal protein S13 / 40S ribosomal protein S3a / 40S ribosomal protein S27a / 60S ribosomal protein L7a / Uncharacterized protein / 40S ribosomal protein S7 / 60S ribosomal protein L4 / 60S ribosomal protein L9 / Uncharacterized protein / 60S ribosomal protein L6 / 40S ribosomal protein S20 / WD_REPEATS_REGION domain-containing protein / 60S ribosomal protein L14 / 60S ribosomal protein L35 / 60S ribosomal protein L21 / 60S ribosomal protein L31 / Uncharacterized protein / 60S ribosomal protein L29 / 40S ribosomal protein S12 / 60S ribosomal protein L35a / Ribosomal_L23eN domain-containing protein / Ribosomal protein L24 / 40S ribosomal protein S9 / Ribosomal protein L10 / 60S ribosomal protein L41 / Ribosomal_L18_c domain-containing protein / Ribosomal protein L15 / 60S ribosomal protein L36 / 60S ribosomal protein L8 / 60S ribosomal protein L17 / 60S ribosomal protein L9 / 60S ribosomal protein L27 / 40S ribosomal protein S27 / 60S ribosomal protein L38 / 40S ribosomal protein S15 / Uncharacterized protein / Ribosomal protein L32 / 60S ribosomal protein L28 / 40S ribosomal protein S29 / 60S ribosomal protein L34 / Eukaryotic peptide chain release factor subunit 1 / Ribosomal protein L37 / Uncharacterized protein / 40S ribosomal protein S11 / Uncharacterized protein / 40S ribosomal protein S28 / 60S ribosomal protein L23 / 40S ribosomal protein S30 / 40S ribosomal protein S25 / 60S ribosomal protein L30 / Ribosomal protein S5 / 40S ribosomal protein S15a / 40S ribosomal protein S8 / S10_plectin domain-containing protein / 40S ribosomal protein S4 / Ribosomal protein L3 / 40S ribosomal protein S6 / 40S ribosomal protein S19 / 40S ribosomal protein S3 / 40S ribosomal protein S18 / 60S ribosomal protein L11
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsShao, S. / Murray, J. / Brown, A. / Taunton, J. / Ramakrishnan, V. / Hegde, R.S.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_A022_1007 United Kingdom
Medical Research Council (United Kingdom)MC_U105184332 United Kingdom
Wellcome TrustWT096570 United Kingdom
Citation
Journal: Cell / Year: 2016
Title: Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes.
Authors: Sichen Shao / Jason Murray / Alan Brown / Jack Taunton / V Ramakrishnan / Ramanujan S Hegde /
Abstract: In eukaryotes, accurate protein synthesis relies on a family of translational GTPases that pair with specific decoding factors to decipher the mRNA code on ribosomes. We present structures of the ...In eukaryotes, accurate protein synthesis relies on a family of translational GTPases that pair with specific decoding factors to decipher the mRNA code on ribosomes. We present structures of the mammalian ribosome engaged with decoding factor⋅GTPase complexes representing intermediates of translation elongation (aminoacyl-tRNA⋅eEF1A), termination (eRF1⋅eRF3), and ribosome rescue (Pelota⋅Hbs1l). Comparative analyses reveal that each decoding factor exploits the plasticity of the ribosomal decoding center to differentially remodel ribosomal proteins and rRNA. This leads to varying degrees of large-scale ribosome movements and implies distinct mechanisms for communicating information from the decoding center to each GTPase. Additional structural snapshots of the translation termination pathway reveal the conformational changes that choreograph the accommodation of decoding factors into the peptidyl transferase center. Our results provide a structural framework for how different states of the mammalian ribosome are selectively recognized by the appropriate decoding factor⋅GTPase complex to ensure translational fidelity.
#1: Journal: To Be Published
Title: Decoding mammalian ribosome-mRNA states by translational GTPase complexes
Authors: Shao, S. / Murray, J. / Brown, A. / Taunton, J. / Ramakrishnan, V. / Hegde, R.S.
Validation Report
SummaryFull reportAbout validation report
History
DepositionOct 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Derived calculations
Category: em_software / pdbx_audit_support ...em_software / pdbx_audit_support / pdbx_validate_polymer_linkage / struct_conn
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.2Oct 3, 2018Group: Data collection / Refinement description / Category: refine
Revision 1.3Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / pdbx_validate_polymer_linkage ...pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct_conn / struct_conn_type
Revision 1.4Dec 11, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
A: uL2
B: uL3
C: uL4
D: 60S ribosomal protein L5
E: 60S ribosomal protein L6
F: uL30
G: eL8
H: uL6
I: uL16
J: uL5
L: eL13
M: eL14
N: Ribosomal protein L15
O: uL13
P: uL22
Q: eL18
R: eL19
S: eL20
T: eL21
U: eL22
V: uL14
W: eL24
X: uL23
Y: uL24
Z: 60S ribosomal protein L27
a: uL15
b: eL29
c: eL30
d: eL31
e: eL32
f: eL33
g: eL34
h: uL29
i: 60S ribosomal protein L36
j: Ribosomal protein L37
k: eL38
l: eL39
m: eL40
n: 60s ribosomal protein l41
o: eL42
p: eL43
r: eL28
s: uL10
t: uL11
2: P-site tRNA
3: E-site tRNA
5: 28S ribosomal RNA
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
9: 18S ribosomal RNA
AA: uS2
BB: 40S ribosomal protein S3a
CC: uS5
DD: uS3
EE: 40S ribosomal protein S4
FF: uS7
GG: 40S ribosomal protein S6
HH: eS7
II: 40S ribosomal protein S8
JJ: Ribosomal protein S9 (Predicted)
KK: eS10
LL: uS17
MM: 40S ribosomal protein S12
NN: uS15
OO: uS11
PP: uS19
QQ: uS9
RR: eS17
SS: uS13
TT: eS19
UU: uS10
VV: eS21
WW: uS8
XX: uS12
YY: eS24
ZZ: eS25
aa: eS26
bb: 40S ribosomal protein S27
cc: eS28
dd: uS14
ee: eS30
ff: eS31
gg: RACK1
hh: mRNA (UGA stop codon)
ii: Eukaryotic peptide chain release factor subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,473,136351
Polymers3,466,34285
Non-polymers6,794266
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 64 types, 64 molecules ABCFGHIJLMOPQRSTUVWXYabcdefghk...

#1: Protein uL2


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27
#2: Protein uL3


Mass: 46107.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#3: Protein uL4


Mass: 47727.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5
#6: Protein uL30


Mass: 29201.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SV32
#7: Protein eL8


Mass: 36221.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1STW0
#8: Protein uL6


Mass: 21871.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TX33, UniProt: G1SWI6*PLUS
#9: Protein uL16 / Ribosomal protein L10 (Predicted)


Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#10: Protein uL5


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#11: Protein eL13


Mass: 24331.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#12: Protein eL14


Mass: 23870.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ12
#14: Protein uL13


Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#15: Protein uL22


Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TVT6
#16: Protein eL18


Mass: 21699.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#17: Protein eL19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#18: Protein eL20


Mass: 20827.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#19: Protein eL21 /


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#20: Protein eL22


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#21: Protein uL14


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#22: Protein eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#23: Protein uL23


Mass: 17768.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76
#24: Protein uL24


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#26: Protein uL15


Mass: 16620.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#27: Protein eL29


Mass: 26708.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6
#28: Protein eL30


Mass: 12807.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#29: Protein eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#30: Protein eL32 / CD59


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U437
#31: Protein eL33


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#32: Protein eL34 /


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U945
#33: Protein uL29


Mass: 14566.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#36: Protein eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U001
#37: Protein eL39


Mass: 6455.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#38: Protein eL40


Mass: 11699.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#40: Protein eL42


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U344
#41: Protein eL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#42: Protein eL28


Mass: 15783.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7L1
#43: Protein uL10


Mass: 34380.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#44: Protein uL11


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SMR7
#51: Protein uS2


Mass: 32958.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#53: Protein uS5


Mass: 31327.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#54: Protein uS3


Mass: 26715.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TNM3
#56: Protein uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#58: Protein eS7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#61: Protein eS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#62: Protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#64: Protein uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#65: Protein uS11


Mass: 18133.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T1F0
#66: Protein uS19


Mass: 17049.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#67: Protein uS9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#68: Protein eS17


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#69: Protein uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#70: Protein eS19


Mass: 16106.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN62
#71: Protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIZ2
#72: Protein eS21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#73: Protein uS8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#74: Protein uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#75: Protein eS24


Mass: 15107.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#76: Protein eS25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#77: Protein eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#79: Protein eS28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#80: Protein uS14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#81: Protein eS30


Mass: 14498.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#82: Protein eS31


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#83: Protein RACK1 / Receptor for activated C kinase 1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4
#85: Protein Eukaryotic peptide chain release factor subunit 1 / eRF1 / Protein Cl1 / TB3-1


Mass: 51639.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETF1, ERF1, RF1, SUP45L1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62495

+
60S ribosomal protein ... , 5 types, 5 molecules DEZin

#4: Protein 60S ribosomal protein L5 / / uL18


Mass: 34481.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#5: Protein 60S ribosomal protein L6 / / eL6


Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#25: Protein 60S ribosomal protein L27 / / eL27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#34: Protein 60S ribosomal protein L36 / / eL36


Mass: 12263.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5
#39: Protein/peptide 60s ribosomal protein l41 / / eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4

+
Ribosomal protein ... , 3 types, 3 molecules NjJJ

#13: Protein Ribosomal protein L15 / / eL15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#35: Protein Ribosomal protein L37 / / eL37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#60: Protein Ribosomal protein S9 (Predicted) / Ribosome


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8

+
RNA chain , 7 types, 7 molecules 235789hh

#45: RNA chain P-site tRNA


Mass: 24436.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#46: RNA chain E-site tRNA


Mass: 24102.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#47: RNA chain 28S ribosomal RNA /


Mass: 1148115.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#48: RNA chain 5S ribosomal RNA /


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#49: RNA chain 5.8S ribosomal RNA /


Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#50: RNA chain 18S ribosomal RNA /


Mass: 602778.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#84: RNA chain mRNA (UGA stop codon)


Mass: 4753.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

+
40S ribosomal protein ... , 6 types, 6 molecules BBEEGGIIMMbb

#52: Protein 40S ribosomal protein S3a /


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#55: Protein 40S ribosomal protein S4 /


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17
#57: Protein 40S ribosomal protein S6 /


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#59: Protein 40S ribosomal protein S8 /


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJW1
#63: Protein 40S ribosomal protein S12 /


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#78: Protein 40S ribosomal protein S27 /


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76

+
Non-polymers , 2 types, 266 molecules

#86: Chemical...
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 258 / Source method: obtained synthetically / Formula: Mg
#87: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Affinity-purified 80S ribosome-nascent chain complex reconstituted with eRF1.
Type: RIBOSOME / Entity ID: #1-#85 / Source: NATURAL
Molecular weightValue: 3.3 MDa / Experimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPES1
2100 mMPotassium acetateKOAc1
35 mMMagnessium acetateMg(OAc)21
41 mMDTT1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: 3 ul aliquots were applied to the grid and incubated for 30 s, before blotting for 3s to remove excess solution.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 104478 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 30 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 1611
Image scansMovie frames/image: 16

-
Processing

SoftwareName: REFMAC / Version: 5.8.0124 / Classification: refinement
EM software
IDNameVersionCategory
2RELION1.4particle selection
3EPUimage acquisition
5Gctf0.5CTF correction
8UCSF Chimera1.1model fitting
9Coot5.8model fitting
11REFMAC5.8model refinement
12RELION1.4initial Euler assignment
13RELION1.4final Euler assignment
14RELION1.4classification
15RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 105812
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13852 / Symmetry type: POINT
Atomic model buildingB value: 63.8 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: FSCaverage
RefinementResolution: 3.75→300.16 Å / Cor.coef. Fo:Fc: 0.892 / SU B: 37.363 / SU ML: 0.536 / ESU R: 1.897
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.33253 --
Obs0.33253 971180 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 99.124 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20.31 Å2-0.1 Å2
2--0.58 Å2-0.53 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Total: 219116
Refine LS restraints
Refinement-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.015237786
ELECTRON MICROSCOPYr_bond_other_d0.0030.02157028
ELECTRON MICROSCOPYr_angle_refined_deg1.1021.542344380
ELECTRON MICROSCOPYr_angle_other_deg1.183367581
ELECTRON MICROSCOPYr_dihedral_angle_1_deg29.7187.79822078
ELECTRON MICROSCOPYr_dihedral_angle_2_deg32.90721.5863966
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.681518177
ELECTRON MICROSCOPYr_dihedral_angle_4_deg13.74151108
ELECTRON MICROSCOPYr_chiral_restr0.1330.21238734
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.02177074
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0254229
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it5.10910.35648352
ELECTRON MICROSCOPYr_mcbond_other5.10910.35648351
ELECTRON MICROSCOPYr_mcangle_it9.07515.50160279
ELECTRON MICROSCOPYr_mcangle_other9.07515.50160280
ELECTRON MICROSCOPYr_scbond_it4.3339.903189434
ELECTRON MICROSCOPYr_scbond_other4.3339.902189432
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other7.55314.732284101
ELECTRON MICROSCOPYr_long_range_B_refined23.416698919
ELECTRON MICROSCOPYr_long_range_B_other23.416698920
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.75→3.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.648 71860 -
Rfree-0 -
Obs--100 %

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