3J7Q

Structure of the idle mammalian ribosome-Sec61 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structure of the Mammalian ribosome-sec61 complex to 3.4 a resolution.

Voorhees, R.M.Fernandez, I.S.Scheres, S.H.Hegde, R.S.

(2014) Cell 157: 1632-1643

  • DOI: https://doi.org/10.1016/j.cell.2014.05.024
  • Primary Citation of Related Structures:  
    3J7O, 3J7P, 3J7Q, 3J7R

  • PubMed Abstract: 

    Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either transported across or inserted into the membrane via the ribosome-bound Sec61 channel. Here, we report structures of a mammalian ribosome-Sec61 complex in both idle and translating states, determined to 3.4 and 3.9 Å resolution. The data sets permit building of a near-complete atomic model of the mammalian ribosome, visualization of A/P and P/E hybrid-state tRNAs, and analysis of a nascent polypeptide in the exit tunnel. Unprecedented chemical detail is observed for both the ribosome-Sec61 interaction and the conformational state of Sec61 upon ribosome binding. Comparison of the maps from idle and translating complexes suggests how conformational changes to the Sec61 channel could facilitate translocation of a secreted polypeptide. The high-resolution structure of the mammalian ribosome-Sec61 complex provides a valuable reference for future functional and structural studies.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK. Electronic address: voorhees@mrc-lmb.cam.ac.uk.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL2D [auth A]257Sus scrofaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL3E [auth B]394Sus scrofaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL4F [auth C]367Sus scrofaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL18G [auth D]297Sus scrofaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL6H [auth E]236Sus scrofaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL30I [auth F]225Sus scrofaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL8J [auth G]266Sus scrofaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL6K [auth H]192Sus scrofaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL16L [auth I]213Sus scrofaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL5M [auth J]178Sus scrofaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL13N [auth L]211Sus scrofaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL14O [auth M]213Sus scrofaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL15P [auth N]204Sus scrofaMutation(s): 0 
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Find proteins for A0A286ZL65 (Sus scrofa)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL13Q [auth O]201Sus scrofaMutation(s): 2 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL22R [auth P]153Sus scrofaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL18S [auth Q]188Sus scrofaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL19T [auth R]196Sus scrofaMutation(s): 1 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL20U [auth S]224Sus scrofaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL21V [auth T]160Sus scrofaMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL22W [auth U]128Sus scrofaMutation(s): 0 
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Find proteins for P67985 (Sus scrofa)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL14X [auth V]140Sus scrofaMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL24Y [auth W]157Sus scrofaMutation(s): 0 
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Find proteins for A0A4X1SH42 (Sus scrofa)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL23Z [auth X]156Sus scrofaMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL24AA [auth Y]145Sus scrofaMutation(s): 0 
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Find proteins for A0A4X1V977 (Sus scrofa)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL27BA [auth Z]136Sus scrofaMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL15CA [auth a]148Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL29DA [auth b]160Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL30EA [auth c]115Sus scrofaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL31FA [auth d]125Sus scrofaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL32GA [auth e]135Sus scrofaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL33HA [auth f]110Sus scrofaMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL34IA [auth g]117Sus scrofaMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL29JA [auth h]123Sus scrofaMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL36KA [auth i]105Sus scrofaMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL37LA [auth j]86Sus scrofaMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL38MA [auth k]70Sus scrofaMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL39NA [auth l]51Sus scrofaMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL40OA [auth m]128Sus scrofaMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL41PA [auth n]25Sus scrofaMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL42QA [auth o]106Sus scrofaMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL43RA [auth p]91Sus scrofaMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL28SA [auth r]125Sus scrofaMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Sec61 alpha subunitTA [auth 1]476Sus scrofaMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Sec61 gamma subunitUA [auth 2]68Sus scrofaMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Sec61 beta subunitVA [auth 3]36Sus scrofaMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
28S ribosomal RNAA [auth 5]3,722Sus scrofa
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNAB [auth 7]120Sus scrofa
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Entity ID: 3
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAC [auth 8]156Sus scrofa
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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WF [auth j],
XF [auth m],
YF [auth o]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 5]
AC [auth 5]
AD [auth 5]
AE [auth 5]
AF [auth 5]
AB [auth 5],
AC [auth 5],
AD [auth 5],
AE [auth 5],
AF [auth 5],
BB [auth 5],
BC [auth 5],
BD [auth 5],
BE [auth 5],
BF [auth 5],
CB [auth 5],
CC [auth 5],
CD [auth 5],
CE [auth 5],
CF [auth 5],
DB [auth 5],
DC [auth 5],
DD [auth 5],
DE [auth 5],
DF [auth 5],
EB [auth 5],
EC [auth 5],
ED [auth 5],
EE [auth 5],
EF [auth 5],
FB [auth 5],
FC [auth 5],
FD [auth 5],
FE [auth 5],
FF [auth 5],
GB [auth 5],
GC [auth 5],
GD [auth 5],
GE [auth 5],
GF [auth 5],
HB [auth 5],
HC [auth 5],
HD [auth 5],
HE [auth 5],
HF [auth 5],
IB [auth 5],
IC [auth 5],
ID [auth 5],
IE [auth 5],
IF [auth 5],
JB [auth 5],
JC [auth 5],
JD [auth 5],
JE [auth 5],
JF [auth 5],
KB [auth 5],
KC [auth 5],
KD [auth 5],
KE [auth 5],
KF [auth 5],
LB [auth 5],
LC [auth 5],
LD [auth 5],
LE [auth 5],
LF [auth 7],
MB [auth 5],
MC [auth 5],
MD [auth 5],
ME [auth 5],
MF [auth 7],
NB [auth 5],
NC [auth 5],
ND [auth 5],
NE [auth 5],
NF [auth 7],
OB [auth 5],
OC [auth 5],
OD [auth 5],
OE [auth 5],
OF [auth 7],
PB [auth 5],
PC [auth 5],
PD [auth 5],
PE [auth 5],
PF [auth 7],
QB [auth 5],
QC [auth 5],
QD [auth 5],
QE [auth 5],
QF [auth 8],
RB [auth 5],
RC [auth 5],
RD [auth 5],
RE [auth 5],
RF [auth 8],
SB [auth 5],
SC [auth 5],
SD [auth 5],
SE [auth 5],
SF [auth 8],
TB [auth 5],
TC [auth 5],
TD [auth 5],
TE [auth 5],
TF [auth 8],
UB [auth 5],
UC [auth 5],
UD [auth 5],
UE [auth 5],
UF [auth P],
VB [auth 5],
VC [auth 5],
VD [auth 5],
VE [auth 5],
VF [auth V],
WA [auth 5],
WB [auth 5],
WC [auth 5],
WD [auth 5],
WE [auth 5],
XA [auth 5],
XB [auth 5],
XC [auth 5],
XD [auth 5],
XE [auth 5],
YA [auth 5],
YB [auth 5],
YC [auth 5],
YD [auth 5],
YE [auth 5],
ZA [auth 5],
ZB [auth 5],
ZC [auth 5],
ZD [auth 5],
ZE [auth 5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Structure summary
  • Version 1.2: 2014-12-10
    Changes: Other
  • Version 1.3: 2014-12-17
    Changes: Other
  • Version 1.4: 2018-07-18
    Changes: Advisory, Data collection
  • Version 2.0: 2019-10-30
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary