[English] 日本語
Yorodumi
- PDB-6mtb: Rabbit 80S ribosome with P- and Z-site tRNAs (unrotated state) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mtb
TitleRabbit 80S ribosome with P- and Z-site tRNAs (unrotated state)
Components
  • (40S ribosomal protein ...) x 32
  • (60S ribosomal protein ...) x 43
  • 18S rRNA18S ribosomal RNA
  • 28S rRNA28S ribosomal RNA
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • P-site tRNA
  • Receptor of activated protein C kinase 1
  • Z-site tRNA
  • mRNAMessenger RNA
KeywordsRIBOSOME / translation
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 / cytosolic ribosome / ribosomal large subunit biogenesis / ribosomal small subunit biogenesis / polysomal ribosome / rough endoplasmic reticulum / positive regulation of translation / mRNA 5'-UTR binding ...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 / cytosolic ribosome / ribosomal large subunit biogenesis / ribosomal small subunit biogenesis / polysomal ribosome / rough endoplasmic reticulum / positive regulation of translation / mRNA 5'-UTR binding / cellular response to gamma radiation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / rRNA processing / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / 5S rRNA binding / cytosolic small ribosomal subunit / small ribosomal subunit / ribosome / rRNA binding / structural constituent of ribosome / cell differentiation / translation / synapse / nucleolus / Golgi apparatus / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus
Ribosomal L28e protein family / 30s ribosomal protein S13, C-terminal / Ribosomal protein L24e, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein S19/S15, superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein L39e domain superfamily / Ribosomal protein L1, conserved site / Ribosomal protein L1-like / Ribosomal protein S7 domain ...Ribosomal L28e protein family / 30s ribosomal protein S13, C-terminal / Ribosomal protein L24e, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein S19/S15, superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein L39e domain superfamily / Ribosomal protein L1, conserved site / Ribosomal protein L1-like / Ribosomal protein S7 domain / Ribosomal protein L15e core domain superfamily / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / 60S ribosomal protein L4, C-terminal domain / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein L30e, conserved site / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S28e conserved site / Ribosomal L28e/Mak16 / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 superfamily / Ribosomal protein S15P / Ribosomal protein L5 domain superfamily / Ribosomal L18e/L15P superfamily / Ubiquitin domain / Ribosomal protein L32e, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / WD40 repeat, conserved site / Ribosomal protein L3, conserved site / Ubiquitin conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein S4/S9 / Ribosomal protein S17, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L31e, conserved site / Ribosomal protein L39e, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S7, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L2, C-terminal / Ribosomal protein L29/L35 superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein L22/L17, conserved site / Ribosomal protein L24e / Ribosomal protein L5 / ribosomal L5P family C-terminus / Ribosomal protein S4/S9 N-terminal domain / S4 domain / Ribosomal protein S17 / Ribosomal_S17 N-terminal / Ribosomal protein L14 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal L15 / Ribosomal protein S15 / Ribosomal protein S13/S18 / Ribosomal protein S8 / Ribosomal protein S7e / KOW motif / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal L27e protein family / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein S28e / Ribosomal protein L32 / Ribosomal protein L35Ae / Ribosomal protein S27a / Ribosomal protein L37e / Ribosomal protein L44 / Ribosomal L37ae protein family / Ribosomal protein L16p/L10e / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L32e superfamily / S27a-like superfamily / Winged helix-like DNA-binding domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L21 superfamily / RNA-binding S4 domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein L36e domain superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal L18 C-terminal region / Ribosomal protein L27e superfamily
WD_REPEATS_REGION domain-containing protein / 60S ribosomal protein L35 / 40S ribosomal protein S27a / Ribosomal protein L37 / 60S ribosomal protein L21 / 60S ribosomal protein L31 / Ribosomal protein / 40S ribosomal protein S12 / 60S ribosomal protein L35a / Ribosomal protein L24 ...WD_REPEATS_REGION domain-containing protein / 60S ribosomal protein L35 / 40S ribosomal protein S27a / Ribosomal protein L37 / 60S ribosomal protein L21 / 60S ribosomal protein L31 / Ribosomal protein / 40S ribosomal protein S12 / 60S ribosomal protein L35a / Ribosomal protein L24 / 60S ribosomal protein L17 / 40S ribosomal protein S29 / 40S ribosomal protein S9 / Ribosomal protein L10 / 60S ribosomal protein L14 / 60S ribosomal protein L28 / 60S ribosomal protein L27a / Ribosomal protein S5 / 40S ribosomal protein S13 / Ribosomal protein L26 / 40S ribosomal protein S3a / 40S ribosomal protein S7 / 60S ribosomal protein L4 / 60S ribosomal protein L6 / Uncharacterized protein / Ribosomal_L18_c domain-containing protein / Uncharacterized protein / Ribosomal protein L15 / 60S ribosomal protein L23 / 40S ribosomal protein S30 / 40S ribosomal protein S25 / 60S ribosomal protein L30 / 40S ribosomal protein S15a / Ribosomal protein L32 / 60S ribosomal protein L36 / 40S ribosomal protein S15 / 60S ribosomal protein L27 / 60S ribosomal protein L9 / Uncharacterized protein / 60S ribosomal protein L11 / 40S ribosomal protein S17 / Uncharacterized protein / 40S ribosomal protein S28 / 60S ribosomal protein L8 / 40S ribosomal protein S11 / S10_plectin domain-containing protein / 40S ribosomal protein S18 / 40S ribosomal protein S6 / Ribosomal protein L3 / 60S ribosomal protein L9
Biological speciesOryctolagus cuniculus (rabbit)
unidentified (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBrown, A. / Baird, M.R. / Yip, M.C.J. / Murray, J. / Shao, S.
CitationJournal: Elife / Year: 2018
Title: Structures of translationally inactive mammalian ribosomes.
Authors: Alan Brown / Matthew R Baird / Matthew Cj Yip / Jason Murray / Sichen Shao /
Abstract: The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. ...The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze inactive ribosomes isolated from mammalian reticulocytes, the penultimate stage of red blood cell differentiation. We identify two types of ribosomes that are translationally repressed by protein interactions. The first comprises ribosomes sequestered with elongation factor 2 (eEF2) by SERPINE mRNA binding protein 1 (SERBP1) occupying the ribosomal mRNA entrance channel. The second type are translationally repressed by a novel ribosome-binding protein, interferon-related developmental regulator 2 (IFRD2), which spans the P and E sites and inserts a C-terminal helix into the mRNA exit channel to preclude translation. IFRD2 binds ribosomes with a tRNA occupying a noncanonical binding site, the 'Z site', on the ribosome. These structures provide functional insights into how ribosomal interactions may suppress translation to regulate gene expression.
Validation Report
SummaryFull reportAbout validation report
History
DepositionOct 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Structure summary
Category: pdbx_entry_details / struct_ref ...pdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _struct_ref.db_code / _struct_ref.db_name ..._struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 2.0May 15, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Polymer sequence
Category: atom_site / entity_poly ...atom_site / entity_poly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9237
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: mRNA
2: P-site tRNA
4: Z-site tRNA
5: 28S rRNA
7: 5S rRNA
8: 5.8S rRNA
A: 60S ribosomal protein L8
B: 60S ribosomal protein L3
C: 60S ribosomal protein L4
D: 60S ribosomal protein L5
E: 60S ribosomal protein L6
F: 60S ribosomal protein L7
G: 60S ribosomal protein L7a
H: 60S ribosomal protein L9
I: 60S ribosomal protein L10
J: 60S ribosomal protein L11
L: 60S ribosomal protein L13
M: 60S ribosomal protein L14
N: 60S ribosomal protein L15
O: 60S ribosomal protein L13a
P: 60S ribosomal protein L17
Q: 60S ribosomal protein L18
R: 60S ribosomal protein L19
S: 60S ribosomal protein L18a
T: 60S ribosomal protein L21
U: 60S ribosomal protein L22
V: 60S ribosomal protein L23
W: 60S ribosomal protein L24
X: 60S ribosomal protein L23a
Y: 60S ribosomal protein L26
Z: 60S ribosomal protein L27
a: 60S ribosomal protein L27a
b: 60S ribosomal protein L29
c: 60S ribosomal protein L30
d: 60S ribosomal protein L31
e: 60S ribosomal protein L32
f: 60S ribosomal protein L35a
g: 60S ribosomal protein L34
h: 60S ribosomal protein L35
i: 60S ribosomal protein L36
j: 60S ribosomal protein L37
k: 60S ribosomal protein L38
l: 60S ribosomal protein L39
m: 60S ribosomal protein L40
n: 60S ribosomal protein L41
o: 60S ribosomal protein L36a
p: 60S ribosomal protein L37a
r: 60S ribosomal protein L28
u: 60S ribosomal protein L10a
9: 18S rRNA
AA: 40S ribosomal protein SA
BB: 40S ribosomal protein S3a
CC: 40S ribosomal protein S2
DD: 40S ribosomal protein S3
EE: 40S ribosomal protein S4, X isoform
FF: 40S ribosomal protein S5
GG: 40S ribosomal protein S6
HH: 40S ribosomal protein S7
II: 40S ribosomal protein S8
JJ: 40S ribosomal protein S9
KK: 40S ribosomal protein S10
LL: 40S ribosomal protein S11
MM: 40S ribosomal protein S12
NN: 40S ribosomal protein S13
OO: 40S ribosomal protein S14
PP: 40S ribosomal protein S15
QQ: 40S ribosomal protein S16
RR: 40S ribosomal protein S17
SS: 40S ribosomal protein S18
TT: 40S ribosomal protein S19
UU: 40S ribosomal protein S20
VV: 40S ribosomal protein S21
WW: 40S ribosomal protein S15a
XX: 40S ribosomal protein S23
YY: 40S ribosomal protein S24
ZZ: 40S ribosomal protein S25
aa: 40S ribosomal protein S26
bb: 40S ribosomal protein S27
cc: 40S ribosomal protein S28
dd: 40S ribosomal protein S29
ee: 40S ribosomal protein S30
ff: 40S ribosomal protein S27a
gg: Receptor of activated protein C kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,234,942388
Polymers3,227,20083
Non-polymers7,742305
Water0
1


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

-
Components

+
RNA chain , 7 types, 7 molecules 1245789

#1: RNA chain mRNA / Messenger RNA


Mass: 2205.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#2: 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)
#3: RNA chain Z-site tRNA


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


Mass: 1167366.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#5: RNA chain 5S rRNA / 5S ribosomal RNA


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


Mass: 48559.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#50: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 548638.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

+
60S ribosomal protein ... , 43 types, 43 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...

#7: Protein 60S ribosomal protein L8 /


Mass: 26998.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27
#8: Protein 60S ribosomal protein L3 /


Mass: 45119.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#9: Protein 60S ribosomal protein L4 /


Mass: 41114.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5
#10: Protein 60S ribosomal protein L5 /


Mass: 34077.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#11: 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
#12: Protein 60S ribosomal protein L7 /


Mass: 29201.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#13: Protein 60S ribosomal protein L7a /


Mass: 36221.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#14: Protein 60S ribosomal protein L9 /


Mass: 21627.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TX33, UniProt: G1SWI6*PLUS
#15: Protein 60S ribosomal protein L10 /


Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#16: Protein 60S 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
#17: Protein 60S ribosomal protein L13 /


Mass: 24200.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#18: Protein 60S ribosomal protein L14 /


Mass: 16217.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KNW6
#19: Protein 60S ribosomal protein L15 /


Mass: 24076.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#20: Protein 60S ribosomal protein L13a /


Mass: 23144.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#21: Protein 60S ribosomal protein L17 /


Mass: 17758.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SCJ6
#22: Protein 60S ribosomal protein L18 /


Mass: 21568.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#23: Protein 60S ribosomal protein L19 /


Mass: 21613.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#24: Protein 60S ribosomal protein L18a /


Mass: 20827.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#25: Protein 60S ribosomal protein L21 /


Mass: 18478.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#26: Protein 60S ribosomal protein L22 /


Mass: 11495.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#27: Protein 60S ribosomal protein L23 /


Mass: 13972.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#28: Protein 60S ribosomal protein L24 /


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#29: Protein 60S ribosomal protein L23a /


Mass: 13727.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#30: Protein 60S ribosomal protein L26 /


Mass: 15891.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#31: Protein 60S ribosomal protein L27 /


Mass: 15704.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#32: Protein 60S ribosomal protein L27a /


Mass: 16489.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#33: Protein 60S ribosomal protein L29 /


Mass: 26708.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#34: Protein 60S ribosomal protein L30 /


Mass: 10914.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#35: Protein 60S ribosomal protein L31 /


Mass: 12635.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#36: Protein 60S ribosomal protein L32 /


Mass: 15022.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U437, UniProt: G1TUN8*PLUS
#37: Protein 60S ribosomal protein L35a /


Mass: 12449.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#38: Protein 60S ribosomal protein L34 /


Mass: 12994.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#39: Protein 60S ribosomal protein L35 /


Mass: 14435.403 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#40: Protein 60S ribosomal protein L36 /


Mass: 11888.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5
#41: Protein 60S ribosomal protein L37 /


Mass: 10090.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#42: Protein 60S ribosomal protein L38 /


Mass: 8107.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#43: Protein/peptide 60S ribosomal protein L39 /


Mass: 6324.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#44: Protein 60S ribosomal protein L40 /


Mass: 6212.593 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#45: Protein/peptide 60S ribosomal protein L41 /


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#46: Protein 60S ribosomal protein L36a /


Mass: 12070.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T040
#47: Protein 60S ribosomal protein L37a /


Mass: 10168.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#48: Protein 60S ribosomal protein L28 /


Mass: 14220.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7L1
#49: Protein 60S ribosomal protein L10a /


Mass: 23599.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKZ8

+
40S ribosomal protein ... , 32 types, 32 molecules AABBCCDDEEFFGGHHIIJJKKLLMMNNOOPPQQRRSSTTUUVVWWXXYYZZaabbccddeeff

#51: Protein 40S ribosomal protein SA /


Mass: 24361.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#52: Protein 40S ribosomal protein S3a /


Mass: 24759.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#53: Protein 40S ribosomal protein S2 /


Mass: 24441.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#54: Protein 40S ribosomal protein S3 /


Mass: 25215.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#55: Protein 40S ribosomal protein S4, X isoform / Ribosome


Mass: 29523.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#56: Protein 40S 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
#57: Protein 40S ribosomal protein S6 /


Mass: 27471.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#58: 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
#59: Protein 40S ribosomal protein S8 /


Mass: 24003.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#60: Protein 40S ribosomal protein S9 /


Mass: 21649.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#61: Protein 40S ribosomal protein S10 /


Mass: 11529.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#62: Protein 40S 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
#63: Protein 40S ribosomal protein S12 /


Mass: 13048.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#64: Protein 40S ribosomal protein S13 /


Mass: 17057.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#65: Protein 40S ribosomal protein S14 /


Mass: 14544.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#66: Protein 40S ribosomal protein S15 /


Mass: 14246.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#67: Protein 40S ribosomal protein S16 /


Mass: 16032.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#68: Protein 40S ribosomal protein S17 /


Mass: 15250.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#69: Protein 40S ribosomal protein S18 /


Mass: 16898.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#70: Protein 40S ribosomal protein S19 /


Mass: 15611.003 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#71: Protein 40S ribosomal protein S20 /


Mass: 11395.489 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#72: Protein 40S ribosomal protein S21 /


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#73: Protein 40S ribosomal protein S15a /


Mass: 14734.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#74: Protein 40S ribosomal protein S23 /


Mass: 15626.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#75: Protein 40S ribosomal protein S24 /


Mass: 14432.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#76: Protein 40S ribosomal protein S25 /


Mass: 8526.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#77: Protein 40S ribosomal protein S26 /


Mass: 11645.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#78: Protein 40S ribosomal protein S27 /


Mass: 9348.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#79: Protein 40S ribosomal protein S28 /


Mass: 7007.069 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#80: Protein 40S ribosomal protein S29 /


Mass: 6559.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#81: Protein 40S ribosomal protein S30 /


Mass: 6317.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#82: Protein 40S ribosomal protein S27a / Ribosome


Mass: 7986.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22

+
Protein , 1 types, 1 molecules gg

#83: Protein Receptor of activated protein C kinase 1


Mass: 34669.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4

+
Non-polymers , 2 types, 305 molecules

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


Mass: 24.305 Da / Num. of mol.: 297 / Source method: obtained synthetically / Formula: Mg
#85: Chemical
ChemComp-ZN / ZINC ION / Zinc


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

+
Details

Sequence detailsAccording to the authors the sample sequences cannot include all nucleotides, as the rabbit genome ...According to the authors the sample sequences cannot include all nucleotides, as the rabbit genome is incomplete for the ribosomal RNA.

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Rabbit 80S ribosome with a P- and Z-site tRNA (unrotated state)
Type: RIBOSOME / Entity ID: #1-#83 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Cellular location: cytoplasm
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
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 / Cs: 2.7 mm
Image recordingAverage exposure time: 1.1 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 17 / Used frames/image: 1-17

-
Processing

EM software
IDNameVersionCategory
1RELION2particle selection
2EPUimage acquisition
4GctfCTF correction
7Coot0.8.9model fitting
9RELION2initial Euler assignment
10RELION2final Euler assignment
12RELION23D reconstruction
13PHENIX1.13_2998model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62560 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 5LZV

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more