3J7R

Structure of the translating mammalian ribosome-Sec61 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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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Find proteins for A0A4X1W0N5 (Sus scrofa)
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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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Find proteins for P49666 (Sus scrofa)
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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
Find proteins for A0A4X1SN08 (Sus scrofa)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL29DA [auth b]160Sus scrofaMutation(s): 0 
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Find proteins for Q95281 (Sus scrofa)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL30EA [auth c]115Sus scrofaMutation(s): 0 
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Find proteins for A0A4X1TXJ8 (Sus scrofa)
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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
Ribosomal protein uL1TA [auth z]217Sus scrofaMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Sec61 alpha subunitUA [auth 1]393Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Sec61 gamma subunitVA [auth 2]68Sus scrofaMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Sec61 beta subunitWA [auth 3]36Sus scrofaMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS2YA [auth SA]295Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS1ZA [auth SB]264Sus scrofaMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS5AB [auth SC]218Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS3BB [auth SD]243Sus scrofaMutation(s): 0 
EC: 4.2.99.18
Membrane Entity: Yes 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS4CB [auth SE]263Sus scrofaMutation(s): 0 
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Find proteins for A0A287B771 (Sus scrofa)
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS7DB [auth SF]204Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS6EB [auth SG]249Sus scrofaMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS7FB [auth SH]194Sus scrofaMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS8GB [auth SI]208Sus scrofaMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS4HB [auth SJ]194Sus scrofaMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS10IB [auth SK]165Sus scrofaMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS17JB [auth SL]158Sus scrofaMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS12KB [auth SM]124Sus scrofaMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS15LB [auth SN]151Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS11MB [auth SO]151Sus scrofaMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS19NB [auth SP]145Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS9OB [auth SQ]146Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS17PB [auth SR]135Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS13QB [auth SS]152Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS19RB [auth ST]145Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS10SB [auth SU]119Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS21TB [auth SV]83Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS8UB [auth SW]130Sus scrofaMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS12VB [auth SX]143Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS24WB [auth SY]132Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein es25XB [auth SZ]125Sus scrofaMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS26YB [auth Sa]115Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS27ZB [auth Sb]84Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS28AC [auth Sc]69Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS14BC [auth Sd]56Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS30CC [auth Se]133Sus scrofaMutation(s): 0 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS31DC [auth Sf]156Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein RACK1EC [auth Sg]317Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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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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Entity ID: 50
MoleculeChains LengthOrganismImage
18S ribosomal RNAXA [auth S2]1,742Sus scrofa
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Entity ID: 84
MoleculeChains LengthOrganismImage
Messenger RNAFC [auth S4]10Sus scrofa
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Entity ID: 85
MoleculeChains LengthOrganismImage
A/P tRNAGC [auth S5]74Sus scrofa
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Entity ID: 86
MoleculeChains LengthOrganismImage
P/E tRNAHC [auth S6]76Sus scrofa
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
IH [auth j],
JH [auth m],
KH [auth o],
VI [auth Sa]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AD [auth 5]
AE [auth 5]
AF [auth 5]
AG [auth 5]
AH [auth 7]
AD [auth 5],
AE [auth 5],
AF [auth 5],
AG [auth 5],
AH [auth 7],
AI [auth S2],
BD [auth 5],
BE [auth 5],
BF [auth 5],
BG [auth 5],
BH [auth 7],
BI [auth S2],
CD [auth 5],
CE [auth 5],
CF [auth 5],
CG [auth 5],
CH [auth 7],
CI [auth S2],
DD [auth 5],
DE [auth 5],
DF [auth 5],
DG [auth 5],
DH [auth 8],
DI [auth S2],
ED [auth 5],
EE [auth 5],
EF [auth 5],
EG [auth 5],
EH [auth 8],
EI [auth S2],
FD [auth 5],
FE [auth 5],
FF [auth 5],
FG [auth 5],
FH [auth 8],
FI [auth S2],
GD [auth 5],
GE [auth 5],
GF [auth 5],
GG [auth 5],
GH [auth P],
GI [auth S2],
HD [auth 5],
HE [auth 5],
HF [auth 5],
HG [auth 5],
HH [auth V],
HI [auth S2],
IC [auth 5],
ID [auth 5],
IE [auth 5],
IF [auth 5],
IG [auth 5],
II [auth S2],
JC [auth 5],
JD [auth 5],
JE [auth 5],
JF [auth 5],
JG [auth 5],
JI [auth S2],
KC [auth 5],
KD [auth 5],
KE [auth 5],
KF [auth 5],
KG [auth 5],
KI [auth S2],
LC [auth 5],
LD [auth 5],
LE [auth 5],
LF [auth 5],
LG [auth 5],
LH [auth S2],
LI [auth S2],
MC [auth 5],
MD [auth 5],
ME [auth 5],
MF [auth 5],
MG [auth 5],
MH [auth S2],
MI [auth S2],
NC [auth 5],
ND [auth 5],
NE [auth 5],
NF [auth 5],
NG [auth 5],
NH [auth S2],
NI [auth S2],
OC [auth 5],
OD [auth 5],
OE [auth 5],
OF [auth 5],
OG [auth 5],
OH [auth S2],
OI [auth S2],
PC [auth 5],
PD [auth 5],
PE [auth 5],
PF [auth 5],
PG [auth 5],
PH [auth S2],
PI [auth S2],
QC [auth 5],
QD [auth 5],
QE [auth 5],
QF [auth 5],
QG [auth 5],
QH [auth S2],
QI [auth S2],
RC [auth 5],
RD [auth 5],
RE [auth 5],
RF [auth 5],
RG [auth 5],
RH [auth S2],
RI [auth S2],
SC [auth 5],
SD [auth 5],
SE [auth 5],
SF [auth 5],
SG [auth 5],
SH [auth S2],
SI [auth S2],
TC [auth 5],
TD [auth 5],
TE [auth 5],
TF [auth 5],
TG [auth 5],
TH [auth S2],
TI [auth S2],
UC [auth 5],
UD [auth 5],
UE [auth 5],
UF [auth 5],
UG [auth 5],
UH [auth S2],
UI [auth S2],
VC [auth 5],
VD [auth 5],
VE [auth 5],
VF [auth 5],
VG [auth 5],
VH [auth S2],
WC [auth 5],
WD [auth 5],
WE [auth 5],
WF [auth 5],
WG [auth 5],
WH [auth S2],
XC [auth 5],
XD [auth 5],
XE [auth 5],
XF [auth 5],
XG [auth 5],
XH [auth S2],
YC [auth 5],
YD [auth 5],
YE [auth 5],
YF [auth 5],
YG [auth 7],
YH [auth S2],
ZC [auth 5],
ZD [auth 5],
ZE [auth 5],
ZF [auth 5],
ZG [auth 7],
ZH [auth S2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2014-12-17
    Changes: Other
  • Version 1.3: 2015-04-15
    Changes: Non-polymer description
  • 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