4V4N

Structure of the Methanococcus jannaschii ribosome-SecYEBeta channel complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the SecY channel during initiation of protein translocation.

Park, E.Menetret, J.F.Gumbart, J.C.Ludtke, S.J.Li, W.Whynot, A.Rapoport, T.A.Akey, C.W.

(2013) Nature 506: 102-106

  • DOI: 10.1038/nature12720
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Many secretory proteins are targeted by signal sequences to a protein-conducting channel, formed by prokaryotic SecY or eukaryotic Sec61 complexes, and are translocated across the membrane during their synthesis. Crystal structures of the inactive ch ...

    Many secretory proteins are targeted by signal sequences to a protein-conducting channel, formed by prokaryotic SecY or eukaryotic Sec61 complexes, and are translocated across the membrane during their synthesis. Crystal structures of the inactive channel show that the SecY subunit of the heterotrimeric complex consists of two halves that form an hourglass-shaped pore with a constriction in the middle of the membrane and a lateral gate that faces the lipid phase. The closed channel has an empty cytoplasmic funnel and an extracellular funnel that is filled with a small helical domain, called the plug. During initiation of translocation, a ribosome-nascent chain complex binds to the SecY (or Sec61) complex, resulting in insertion of the nascent chain. However, the mechanism of channel opening during translocation is unclear. Here we have addressed this question by determining structures of inactive and active ribosome-channel complexes with cryo-electron microscopy. Non-translating ribosome-SecY channel complexes derived from Methanocaldococcus jannaschii or Escherichia coli show the channel in its closed state, and indicate that ribosome binding per se causes only minor changes. The structure of an active E. coli ribosome-channel complex demonstrates that the nascent chain opens the channel, causing mostly rigid body movements of the amino- and carboxy-terminal halves of SecY. In this early translocation intermediate, the polypeptide inserts as a loop into the SecY channel with the hydrophobic signal sequence intercalated into the open lateral gate. The nascent chain also forms a loop on the cytoplasmic surface of SecY rather than entering the channel directly.


    Organizational Affiliation

    Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, Massachusetts 02118-2526, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Preprotein translocase subunit SecEA767Methanocaldococcus jannaschiiMutation(s): 0 
Find proteins for Q57817 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
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Go to UniProtKB:  Q57817
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L39EAf51Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19EAQ150Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22PAS150Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23PAT84Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24PAU121Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29PAW72Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Protein translocase subunit SecYAX436Methanocaldococcus jannaschiiMutation(s): 0 
Find proteins for Q60175 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
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Go to UniProtKB:  Q60175
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein L7AEAG, B3123Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3AEBA190Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2PBB202Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3PBC186Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4PBD172Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4EBE241Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5PBF217Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6EBG125Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7PBH215Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8PBI129Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8EBJ127Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9PBK135Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11PBM133Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12PBN145Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13PBO148Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14PBP56Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15P/S13EBQ158Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17PBR113Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17EBS67Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19PBT111Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19EBU144Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S24EBV99Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S27EBW63Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S28EBX71Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S27AEBY50Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14EA5, AK81Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1PAA216Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31EAa92Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2AB239Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32EAb127Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3PAC365Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4PAD255Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34EAd89Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5PAE186Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37EAe62Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6PAF184Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L40EAg45Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11PAH134Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L41EAh24Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13PAI142Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37AEAi78Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14PAJ132Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L44EAj94Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein P0/L10EAk212Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15PAL147Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15EAM194Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10E/L16AN168Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18PAO197Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18EAP120Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21EAR95Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24EAV66Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30PAY155Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30EAZ99Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Preprotein translocase subunit SecGA852Methanocaldococcus jannaschiiMutation(s): 0 
Find proteins for P60460 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore P60460 
Go to UniProtKB:  P60460
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10PBL102Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 10
MoleculeChainsLengthOrganism
E-tRNAB177Methanocaldococcus jannaschii

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Entity ID: 11
MoleculeChainsLengthOrganism
16S ribosomal RNAB21495Methanocaldococcus jannaschii

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Entity ID: 38
MoleculeChainsLengthOrganism
23S ribosomal RNAA13049Methanocaldococcus jannaschii

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Entity ID: 39
MoleculeChainsLengthOrganism
5S ribosomal RNAA3126Methanocaldococcus jannaschii
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2015-03-18
    Changes: Other
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2019-12-18
    Changes: Other