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- PDB-6hcq: Structure of the rabbit collided di-ribosome (collided monosome) -

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Entry
Database: PDB / ID: 6hcq
TitleStructure of the rabbit collided di-ribosome (collided monosome)
Components
  • (40S ribosomal protein ...) x 6
  • (60S ribosomal protein ...) x 5
  • (Ribosomal protein ...) x 15
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • A/P tRNA
  • P/E tRNA
  • RACK1Receptor for activated C kinase 1
  • Ribosomal protein
  • eL13
  • eL18
  • eL19
  • eL20
  • eL21
  • eL22
  • eL28
  • eL29
  • eL30
  • eL31
  • eL32CD59
  • eL33
  • eL34
  • eL38
  • eL39
  • eL40
  • eL41
  • eL42
  • eL43
  • eL8
  • eS1
  • eS10
  • eS17
  • eS19
  • eS21
  • eS24
  • eS25
  • eS26
  • eS4
  • eS8
  • mRNAMessenger RNA
  • nascent chain
  • uL10
  • uL13
  • uL15
  • uL22
  • uL23
  • uL29
  • uL3
  • uL30
  • uL4
  • uL6
  • uS10
  • uS11
  • uS12
  • uS13
  • uS14
  • uS15
  • uS19
  • uS2
  • uS3
KeywordsRIBOSOME / Translation / Quality Control
Function / homology
Function and homology information


positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / positive regulation of base-excision repair / positive regulation of DNA N-glycosylase activity / response to TNF agonist / oxidized pyrimidine DNA binding / negative regulation of DNA repair / 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 ...positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / positive regulation of base-excision repair / positive regulation of DNA N-glycosylase activity / response to TNF agonist / oxidized pyrimidine DNA binding / negative regulation of DNA repair / 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 / 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) / spindle assembly / ribosomal large subunit biogenesis / positive regulation of JUN kinase activity / ribosomal small subunit biogenesis / polysome / positive regulation of microtubule polymerization / cellular response to leukemia inhibitory factor / Hsp70 protein binding / polysomal ribosome / negative regulation of protein ubiquitination / endodeoxyribonuclease activity / 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 / 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
Ribosomal L28e protein family / Ribosomal protein L11, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S19 conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L30e, conserved site ...Ribosomal L28e protein family / Ribosomal protein L11, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S19 conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L30e, conserved site / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein L39e, conserved site / Ribosomal protein L31e, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S15P / Ribosomal protein L23 / 30s ribosomal protein S13, C-terminal / Ribosomal L28e/Mak16 / Ribosomal protein S28e conserved site / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S10 domain / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / in:ipr023106: / Ribosomal protein L15e core domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L1-like / Ribosomal protein L1, conserved site / Ribosomal protein L39e domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein S19/S15, superfamily / Ribosomal protein L6, alpha-beta domain / Ribosomal protein S17, conserved site / Ubiquitin-like domain superfamily / Ribosomal protein L2, domain 2 / Ribosomal protein L10e/L16 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L30, ferredoxin-like fold domain / K homology domain-like, alpha/beta / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein L2, domain 3 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S4, conserved site / Ribosomal protein S6, eukaryotic / Ribosomal protein L25/L23 / Ribosomal protein L30, N-terminal / Ribosomal protein L23/L15e core domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein S13/S15, N-terminal / Nucleic acid-binding, OB-fold / WD40-repeat-containing domain / Ribosomal protein L29, conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein S17e, conserved site / Ubiquitin domain / Ubiquitin conserved site / Ribosomal protein L3, conserved site / WD40 repeat, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein L10e, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L21e, conserved site / 50S ribosomal protein L30e-like / Ribosomal protein L5, C-terminal / Ribosomal protein L37ae/L37e / Ribosomal protein S17 / Ribosomal protein S9/S16 / Ribosomal protein S15 / Ribosomal L15 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein L14 / Ribosomal_S17 N-terminal / Plectin/S10 domain / Ribosomal protein S13/S18 / S4 domain / Ribosomal protein S4/S9 N-terminal domain / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L16p/L10e / Ribosomal protein S7e / KH domain / Ribosomal S17 / Ribosomal protein L21e / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L32 / Ribosomal L37ae protein family / Ribosomal protein L37e
40S ribosomal protein S27 / Ribosomal protein L37 / 40S ribosomal protein S29 / 60S ribosomal protein L28 / Ribosomal protein L32 / 40S ribosomal protein S15 / 60S ribosomal protein L17 / 60S ribosomal protein L27 / 40S ribosomal protein S20 / 40S ribosomal protein S3a ...40S ribosomal protein S27 / Ribosomal protein L37 / 40S ribosomal protein S29 / 60S ribosomal protein L28 / Ribosomal protein L32 / 40S ribosomal protein S15 / 60S ribosomal protein L17 / 60S ribosomal protein L27 / 40S ribosomal protein S20 / 40S ribosomal protein S3a / Ribosomal protein L26 / 40S ribosomal protein S13 / 60S ribosomal protein L12 / Ribosomal protein / 60S ribosomal protein L6 / 40S ribosomal protein S27a / WD_REPEATS_REGION domain-containing protein / 60S ribosomal protein L35 / 60S ribosomal protein L9 / 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 / 40S ribosomal protein S9 / Ribosomal protein L10 / 40S ribosomal protein S7 / Uncharacterized protein / 60S ribosomal protein L9 / 40S ribosomal protein S3 / 60S ribosomal protein L11 / Uncharacterized protein / 40S ribosomal protein S17 / 60S ribosomal protein L36 / Uncharacterized protein / 60S ribosomal protein L8 / 40S ribosomal protein S11 / S10_plectin domain-containing protein / 40S ribosomal protein S18 / Ribosomal protein L3 / Ribosomal_L18_c domain-containing protein / 40S ribosomal protein S28 / 40S ribosomal protein S15a / Ribosomal protein S5 / 60S ribosomal protein L30 / 40S ribosomal protein S25 / 40S ribosomal protein S30 / 60S ribosomal protein L23 / Ribosomal protein L15 / 60S ribosomal protein L14 / 40S ribosomal protein S6
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsJuszkiewicz, S. / Chandrasekaran, V. / Lin, Z. / Kraatz, S. / Ramakrishnan, V. / Hegde, R.S.
Funding support United Kingdom, France, 4items
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
Louis-Jeantet Foundation France
CitationJournal: Mol Cell / Year: 2018
Title: ZNF598 Is a Quality Control Sensor of Collided Ribosomes.
Authors: Szymon Juszkiewicz / Viswanathan Chandrasekaran / Zhewang Lin / Sebastian Kraatz / V Ramakrishnan / Ramanujan S Hegde /
Abstract: Aberrantly slow translation elicits quality control pathways initiated by the ubiquitin ligase ZNF598. How ZNF598 discriminates physiologic from pathologic translation complexes and ubiquitinates ...Aberrantly slow translation elicits quality control pathways initiated by the ubiquitin ligase ZNF598. How ZNF598 discriminates physiologic from pathologic translation complexes and ubiquitinates stalled ribosomes selectively is unclear. Here, we find that the minimal unit engaged by ZNF598 is the collided di-ribosome, a molecular species that arises when a trailing ribosome encounters a slower leading ribosome. The collided di-ribosome structure reveals an extensive 40S-40S interface in which the ubiquitination targets of ZNF598 reside. The paucity of 60S interactions allows for different ribosome rotation states, explaining why ZNF598 recognition is indifferent to how the leading ribosome has stalled. The use of ribosome collisions as a proxy for stalling allows the degree of tolerable slowdown to be tuned by the initiation rate on that mRNA; hence, the threshold for triggering quality control is substrate specific. These findings illustrate how higher-order ribosome architecture can be exploited by cellular factors to monitor translation status.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
51: 28S ribosomal RNA
71: 5S ribosomal RNA
81: 5.8S ribosomal RNA
A2: 18S ribosomal RNA
B2: uS2
C2: 40S ribosomal protein S3a
D2: eS1
E2: uS3
F2: eS4
G2: Ribosomal protein S5
H2: 40S ribosomal protein S6
I2: 40S ribosomal protein S7
J2: eS8
K2: Ribosomal protein S9 (Predicted)
L2: eS10
M2: Ribosomal protein S11
N2: 40S ribosomal protein S12
O2: uS15
P2: uS11
Q2: uS19
R2: Ribosomal protein S16
S2: eS17
T2: uS13
U2: eS19
V2: uS10
W2: eS21
X2: Ribosomal protein S15a
Y2: uS12
Z2: eS24
a2: eS25
b2: eS26
c2: 40S ribosomal protein S27
d2: Ribosomal protein S28
e2: uS14
f2: 40S ribosomal protein S30
g2: Ribosomal protein S27a
h2: RACK1
A3: Ribosomal protein L8
B3: uL3
C3: uL4
D3: 60S ribosomal protein L5
E3: 60S ribosomal protein L6
F3: uL30
G3: eL8
H3: uL6
I3: 60S ribosomal protein L10
J3: Ribosomal protein L11
L3: eL13
M3: Ribosomal protein L14
N3: Ribosomal protein L15
O3: uL13
P3: uL22
Q3: eL18
R3: eL19
S3: eL20
T3: eL21
U3: eL22
V3: Ribosomal protein L23
X3: uL23
Y3: Ribosomal protein L26
Z3: 60S ribosomal protein L27
a3: uL15
b3: eL29
c3: eL30
d3: eL31
e3: eL32
f3: eL33
g3: eL34
h3: uL29
i3: 60S ribosomal protein L36
j3: Ribosomal protein L37
k3: eL38
l3: eL39
m3: eL40
n3: eL41
o3: eL42
p3: eL43
r3: eL28
q3: A/P tRNA
t3: uL10
u3: Ribosomal protein L12
v3: mRNA
33: P/E tRNA
w3: Ribosomal protein
1: nascent chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,462,706393
Polymers3,454,89185
Non-polymers7,815308
Water0
1


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

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Components

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RNA chain , 7 types, 7 molecules 517181A2q3v333

#1: RNA chain 28S ribosomal RNA /


Mass: 1177882.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#2: 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)
#3: 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)
#4: RNA chain 18S ribosomal RNA /


Mass: 602779.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#79: RNA chain A/P tRNA


Mass: 23874.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#82: RNA chain mRNA / Messenger RNA


Mass: 6972.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#83: RNA chain P/E tRNA


Mass: 24231.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Protein , 50 types, 50 molecules B2D2E2F2J2L2O2P2Q2S2T2U2V2W2Y2Z2a2b2e2h2B3C3F3G3H3L3O3P3Q3R3...

#5: Protein uS2


Mass: 32958.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#7: Protein eS1


Mass: 31327.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#8: 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
#9: Protein eS4


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#13: Protein eS8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#15: 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
#18: 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
#19: Protein uS11


Mass: 18133.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#20: 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
#22: 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
#23: 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
#24: Protein eS19


Mass: 16106.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#25: 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
#26: Protein eS21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#28: Protein uS12


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


Mass: 15107.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#30: 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
#31: Protein eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#34: 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
#37: 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
#39: 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
#40: Protein uL4


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


Mass: 29201.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB1
#44: Protein eL8


Mass: 36221.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#45: 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
#48: Protein eL13


Mass: 24331.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#51: Protein uL13


Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#52: 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
#53: Protein eL18


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


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


Mass: 20827.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#56: 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
#57: Protein eL22


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#59: 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
#62: Protein uL15


Mass: 16620.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#63: 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
#64: 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
#65: 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
#66: 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
#67: 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
#68: Protein eL34 /


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#69: 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
#72: Protein eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#73: 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
#74: Protein eL40


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


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#77: 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
#78: 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
#80: Protein uL10


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


Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKZ8

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40S ribosomal protein ... , 6 types, 6 molecules C2H2I2N2c2f2

#6: 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
#11: 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
#12: Protein 40S ribosomal protein S7 /


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#17: 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
#32: 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
#35: Protein 40S ribosomal protein S30 /


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

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Ribosomal protein ... , 15 types, 15 molecules G2K2M2R2X2d2g2A3J3M3N3V3Y3j3u3

#10: Protein Ribosomal protein S5 /


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#14: 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
#16: Protein Ribosomal protein S11 /


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#21: Protein Ribosomal protein S16 /


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#27: Protein Ribosomal protein S15a / Ribosome


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#33: Protein Ribosomal protein S28 /


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#36: Protein Ribosomal protein S27a / Ribosome


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#38: Protein Ribosomal protein L8 /


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27
#47: Protein Ribosomal protein L11 /


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#49: Protein Ribosomal protein L14 /


Mass: 23870.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ12
#50: Protein Ribosomal protein L15 /


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#58: Protein Ribosomal protein L23 /


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#60: Protein Ribosomal protein L26 /


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#71: Protein Ribosomal protein L37 /


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#81: Protein Ribosomal protein L12 /


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

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60S ribosomal protein ... , 5 types, 5 molecules D3E3I3Z3i3

#41: Protein 60S ribosomal protein L5 /


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


Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#46: Protein 60S ribosomal protein L10 / / 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
#61: Protein 60S ribosomal protein L27 /


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


Mass: 12263.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5

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Protein/peptide , 2 types, 2 molecules n31

#75: Protein/peptide eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#85: Protein/peptide nascent chain


Mass: 1581.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Non-polymers , 2 types, 308 molecules

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


Mass: 24.305 Da / Num. of mol.: 300 / 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

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Rabbit 80S on globin mRNA in the rotated state with A/P and P/E tRNAs
Type: RIBOSOME / Entity ID: #1-#85 / Source: NATURAL
Molecular weightValue: 4.3 MDa / Experimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 1.79 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14634 / Symmetry type: POINT

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