3K5B | pdb_00003k5b

Crystal structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.288 (Depositor), 0.299 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.252 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3K5B

This is version 1.3 of the entry. See complete history

Literature

The structure of the peripheral stalk of Thermus thermophilus H(+)-ATPase/synthase.

Lee, L.K.Stewart, A.G.Donohoe, M.Bernal, R.A.Stock, D.

(2010) Nat Struct Mol Biol 17: 373-378

  • DOI: https://doi.org/10.1038/nsmb.1761
  • Primary Citation Related Structures: 
    3K5B

  • PubMed Abstract: 

    Proton-translocating ATPases are ubiquitous protein complexes that couple ATP catalysis with proton translocation via a rotary catalytic mechanism. The peripheral stalks are essential components that counteract torque generated from proton translocation during ATP synthesis or from ATP hydrolysis during proton pumping. Despite their essential role, the peripheral stalks are the least conserved component of the complexes, differing substantially between subtypes in composition and stoichiometry. We have determined the crystal structure of the peripheral stalk of the A-type ATPase/synthase from Thermus thermophilus consisting of subunits E and G. The structure contains a heterodimeric right-handed coiled coil, a protein fold never observed before. We have fitted this structure into the 23 A resolution EM density of the intact A-ATPase complex, revealing the precise location of the peripheral stalk and new implications for the function and assembly of proton-translocating ATPases.


  • Organizational Affiliation
    • Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, Australia.

Macromolecule Content 

  • Total Structure Weight: 65.11 kDa 
  • Atom Count: 4,056 
  • Modeled Residue Count: 569 
  • Deposited Residue Count: 584 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type ATP synthase, subunit (VAPC-THERM)A [auth G],
C [auth B]
104Thermus thermophilus HB8Mutation(s): 0 
Gene Names: 55981248TTHA1279
UniProt
Find proteins for Q5SIT5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SIT5 
Go to UniProtKB:  Q5SIT5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SIT5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit EB [auth E],
D [auth A]
188Thermus thermophilus HB8Mutation(s): 3 
Gene Names: 55981245atpETTHA1276vatE
UniProt
Find proteins for P74901 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P74901 
Go to UniProtKB:  P74901
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP74901
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A [auth G],
C [auth B]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.288 (Depositor), 0.299 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.252 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.781α = 90
b = 79.755β = 97.64
c = 75.796γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
BioCARSdata collection
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-10-09
    Changes: Data collection, Structure summary