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
  • Primary Citation of Related Structures:  
    3J45, 3J46, 4V4N

  • 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 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 ...

    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 LengthOrganismDetailsImage
Preprotein translocase subunit SecEA [auth A7]67Methanocaldococcus jannaschiiMutation(s): 0 
Find proteins for Q57817 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Preprotein translocase subunit SecGB [auth A8]52Methanocaldococcus jannaschiiMutation(s): 0 
Find proteins for P60460 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L39EC [auth Af]51Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19ED [auth AQ]150Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22PE [auth AS]150Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23PF [auth AT]84Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24PG [auth AU]121Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29PH [auth AW]72Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Protein translocase subunit SecYI [auth AX]436Methanocaldococcus jannaschiiMutation(s): 0 
Find proteins for Q60175 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein L7AEYA [auth AG], L [auth B3]123Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3AEM [auth BA]190Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2PN [auth BB]202Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3PO [auth BC]186Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4PP [auth BD]172Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4EQ [auth BE]241Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5PR [auth BF]217Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6ES [auth BG]125Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7PT [auth BH]215Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8PU [auth BI]129Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8EV [auth BJ]127Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9PW [auth BK]135Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10PX [auth BL]102Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11PY [auth BM]133Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12PZ [auth BN]145Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13PAA [auth BO]148Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14PBA [auth BP]56Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15P/S13ECA [auth BQ]158Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17PDA [auth BR]113Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17EEA [auth BS]67Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19PFA [auth BT]111Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19EGA [auth BU]144Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S24EHA [auth BV]99Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S27EIA [auth BW]63Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S28EJA [auth BX]71Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S27AEKA [auth BY]50Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14ENA [auth A5], GB [auth AK]81Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L1POA [auth AA]216Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31EPA [auth Aa]92Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2QA [auth AB]239Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32ERA [auth Ab]127Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3PSA [auth AC]365Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4PTA [auth AD]255Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34EUA [auth Ad]89Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5PVA [auth AE]186Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L37EWA [auth Ae]62Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6PXA [auth AF]184Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L40EZA [auth Ag]45Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11PAB [auth AH]134Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L41EBB [auth Ah]24Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13PCB [auth AI]142Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L37AEDB [auth Ai]78Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14PEB [auth AJ]132Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L44EFB [auth Aj]94Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein P0/L10EHB [auth Ak]212Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15PIB [auth AL]147Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15EJB [auth AM]194Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10E/L16KB [auth AN]168Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18PLB [auth AO]197Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18EMB [auth AP]120Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21ENB [auth AR]95Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24EOB [auth AV]66Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30PPB [auth AY]155Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30EQB [auth AZ]99Methanocaldococcus jannaschiiMutation(s): 0 
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Entity ID: 10
MoleculeChainsLengthOrganismImage
E-tRNAJ [auth B1]77Methanocaldococcus jannaschii
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Entity ID: 11
MoleculeChainsLengthOrganismImage
16S ribosomal RNAK [auth B2]1495Methanocaldococcus jannaschii
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Entity ID: 38
MoleculeChainsLengthOrganismImage
23S ribosomal RNALA [auth A1]3049Methanocaldococcus jannaschii
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Entity ID: 39
MoleculeChainsLengthOrganismImage
5S ribosomal RNAMA [auth A3]126Methanocaldococcus jannaschii
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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