› 3din

X-ray diffraction
4.5Å resolution

Crystal structure of the protein-translocation complex formed by the SecY channel and the SecA ATPase

Released:
DOI: 10.2210/pdb3din/pdb
PDB entry 3din coloured by chain, front view.
PDB entry 3din coloured by chain, side view.
PDB entry 3din coloured by chain, top view.
Source organisms:
Primary publication:
Structure of a complex of the ATPase SecA and the protein-translocation channel.
Zimmer J, Nam Y, Rapoport TA
Nature 455 936-43 (2008)
PMID: 18923516

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O + cellular protein(Side 1) = ADP + phosphate + cellular protein(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-101252 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Protein translocase subunit SecA Chains: A, B
Molecule details ›
Chains: A, B
Length: 871 amino acids
Theoretical weight: 100.64 KDa
Source organism: Thermotoga maritima MSB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9X1R4 (Residues: 1-871; Coverage: 100%)
Gene names: TM_1578, secA
Sequence domains:
Protein translocase subunit SecY Chains: C, F
Molecule details ›
Chains: C, F
Length: 431 amino acids
Theoretical weight: 48.22 KDa
Source organism: Thermotoga maritima MSB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9X1I9 (Residues: 1-431; Coverage: 100%)
Gene names: TM_1480, secY
Sequence domains: SecY
Protein translocase subunit SecE Chains: D, G
Molecule details ›
Chains: D, G
Length: 65 amino acids
Theoretical weight: 7.32 KDa
Source organism: Thermotoga maritima MSB8
Expression system: Escherichia coli
UniProt:
  • Canonical: P35874 (Residues: 1-65; Coverage: 100%)
Gene names: TM_0452, secE
Sequence domains: SecE/Sec61-gamma subunits of protein translocation complex
Protein-export membrane protein SecG Chains: E, H
Molecule details ›
Chains: E, H
Length: 76 amino acids
Theoretical weight: 8.25 KDa
Source organism: Thermotoga sp. RQ2
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A0F6AK20 (Residues: 1-76; Coverage: 100%)
Gene name: TRQ2_0456
Sequence domains: Preprotein translocase SecG subunit

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand ADP 2 x ADP
Ligand BEF 2 x BEF
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID, APS BEAMLINE 24-ID-C, NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 101.616Å b: 156.003Å c: 358.155Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.279 0.279 0.303
Expression system: Escherichia coli

Quick links

Citations

61 review citations

The bacterial cell envelope.
Silhavy et al. (2010)
60 more

59 mentions without citation

The bacterial Sec-translocase: structure and mechanism.
Lycklama A Nijeholt et al. (2012)
58 more