6ITC

Structure of a substrate engaged SecA-SecY protein translocation machine


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the substrate-engaged SecA-SecY protein translocation machine.

Ma, C.Wu, X.Sun, D.Park, E.Catipovic, M.A.Rapoport, T.A.Gao, N.Li, L.

(2019) Nat Commun 10: 2872-2872

  • DOI: 10.1038/s41467-019-10918-2
  • Primary Citation of Related Structures:  
    6ITC

  • PubMed Abstract: 
  • The Sec61/SecY channel allows the translocation of many proteins across the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane. In bacteria, most secretory proteins are transported post-translationally through the SecY chann ...

    The Sec61/SecY channel allows the translocation of many proteins across the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane. In bacteria, most secretory proteins are transported post-translationally through the SecY channel by the SecA ATPase. How a polypeptide is moved through the SecA-SecY complex is poorly understood, as structural information is lacking. Here, we report an electron cryo-microscopy (cryo-EM) structure of a translocating SecA-SecY complex in a lipid environment. The translocating polypeptide chain can be traced through both SecA and SecY. In the captured transition state of ATP hydrolysis, SecA's two-helix finger is close to the polypeptide, while SecA's clamp interacts with the polypeptide in a sequence-independent manner by inducing a short β-strand. Taking into account previous biochemical and biophysical data, our structure is consistent with a model in which the two-helix finger and clamp cooperate during the ATPase cycle to move a polypeptide through the channel.


    Organizational Affiliation

    State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China. long_li@pku.edu.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein translocase subunit SecAA780Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: secAdiv+BSU35300
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Sec, Translocase, and Insertase Proteins
Protein: 
SecA-SecYE complex in nanodiscs, substrate-engaged
Find proteins for P28366 (Bacillus subtilis (strain 168))
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Go to UniProtKB:  P28366
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein translocase subunit SecYY424Geobacillus thermodenitrificans NG80-2Mutation(s): 5 
Gene Names: secYGTNG_0125
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Sec, Translocase, and Insertase Proteins
Protein: 
SecA-SecYE complex in nanodiscs, substrate-engaged
Find proteins for A4IJK8 (Geobacillus thermodenitrificans (strain NG80-2))
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Go to UniProtKB:  A4IJK8
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Protein translocase subunit SecEE70Geobacillus thermodenitrificans NG80-2Mutation(s): 0 
Gene Names: secEGTNG_0091
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Sec, Translocase, and Insertase Proteins
Protein: 
SecA-SecYE complex in nanodiscs, substrate-engaged
Find proteins for A4IJH4 (Geobacillus thermodenitrificans (strain NG80-2))
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Go to UniProtKB:  A4IJH4
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NanobodyV116Lama glamaMutation(s): 0 
Protein Feature View
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Translocating peptideB59Escherichia coliMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Sec, Translocase, and Insertase Proteins
Protein: 
SecA-SecYE complex in nanodiscs, substrate-engaged
Find proteins for P0A910 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Green fluorescent proteinG236Aequorea victoriaMutation(s): 5 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
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  • Reference Sequence
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NanobodyC112Lama glamaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGV
Query on PGV

Download CCD File 
Y
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
 Ligand Interaction
ADP
Query on ADP

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A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
BEF
Query on BEF

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A
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GYS
Query on GYS
GL-PEPTIDE LINKINGC14 H15 N3 O5SER, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2016YFA0500700

Revision History 

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other