6ITC | pdb_00006itc

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 

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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: https://doi.org/10.1038/s41467-019-10918-2
  • Primary Citation 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 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.

Macromolecule Content 

  • Total Structure Weight: 204.08 kDa 
  • Atom Count: 13,844 
  • Modeled Residue Count: 1,739 
  • Deposited Residue Count: 1,797 
  • Unique protein chains: 7

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein translocase subunit SecA780Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: secAdiv+BSU35300
EC: 7.4.2.8
Membrane Entity: Yes 
UniProt
Find proteins for P28366 (Bacillus subtilis (strain 168))
Explore P28366 
Go to UniProtKB:  P28366
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28366
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein translocase subunit SecYB [auth Y]424Geobacillus thermodenitrificans NG80-2Mutation(s): 5 
Gene Names: secYGTNG_0125
Membrane Entity: Yes 
UniProt
Find proteins for A4IJK8 (Geobacillus thermodenitrificans (strain NG80-2))
Explore A4IJK8 
Go to UniProtKB:  A4IJK8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4IJK8
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein translocase subunit SecEC [auth E]70Geobacillus thermodenitrificans NG80-2Mutation(s): 0 
Gene Names: secEGTNG_0091
Membrane Entity: Yes 
UniProt
Find proteins for A4IJH4 (Geobacillus thermodenitrificans (strain NG80-2))
Explore A4IJH4 
Go to UniProtKB:  A4IJH4
Entity Groups
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UniProt GroupA4IJH4
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
NanobodyD [auth V]116Lama glamaMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Translocating peptideE [auth B]59Escherichia coliMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A910 (Escherichia coli (strain K12))
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UniProt GroupP0A910
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Green fluorescent proteinF [auth G]236Aequorea victoriaMutation(s): 5 
Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
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UniProt GroupP42212
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
NanobodyG [auth C]112Lama glamaMutation(s): 0 

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGV

Query on PGV



Download:Ideal Coordinates CCD File
K [auth Y],
L [auth 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
ADP

Query on ADP



Download:Ideal Coordinates CCD File
J [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF

Query on BEF



Download:Ideal Coordinates CCD File
I [auth A]BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG

Query on MG



Download:Ideal Coordinates CCD File
H [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
GYS
Query on GYS
F [auth G]L-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 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • 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
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2025-06-25
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 3.0: 2026-03-18
    Changes: Data collection, Polymer sequence