3A5C

Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.51 Å
  • R-Value Free: 0.437 
  • R-Value Work: 0.429 

wwPDB Validation 3D Report Full Report


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Literature

Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase

Numoto, N.Hasegawa, Y.Takeda, K.Miki, K.

(2009) EMBO Rep 10: 1228-1234

  • DOI: 10.1038/embor.2009.202
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • V-type ATPases (V-ATPases) are categorized as rotary ATP synthase/ATPase complexes. The V-ATPases are distinct from F-ATPases in terms of their rotation scheme, architecture and subunit composition. However, there is no detailed structural informatio ...

    V-type ATPases (V-ATPases) are categorized as rotary ATP synthase/ATPase complexes. The V-ATPases are distinct from F-ATPases in terms of their rotation scheme, architecture and subunit composition. However, there is no detailed structural information on V-ATPases despite the abundant biochemical and biophysical research. Here, we report a crystallographic study of V1-ATPase, from Thermus thermophilus, which is a soluble component consisting of A, B, D and F subunits. The structure at 4.5 A resolution reveals inter-subunit interactions and nucleotide binding. In particular, the structure of the central stalk composed of D and F subunits was shown to be characteristic of V1-ATPases. Small conformational changes of respective subunits and significant rearrangement of the quaternary structure observed in the three AB pairs were related to the interaction with the straight central stalk. The rotation mechanism is discussed based on a structural comparison between V1-ATPases and F1-ATPases.


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
V-type ATP synthase beta chainD, E, F, L, M, N478Thermus thermophilus HB8Mutation(s): 0 
Gene Names: atpBTTHA1272
EC: 3.6.3.14
Find proteins for Q56404 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q56404 
Go to UniProtKB:  Q56404
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
V-type ATP synthase subunit DG, O223Thermus thermophilus HB8Mutation(s): 0 
Gene Names: atpDvatDTTHA1271
EC: 3.6.3.14
Find proteins for O87880 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  O87880
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
V-type ATP synthase subunit FH, P104Thermus thermophilus HB8Mutation(s): 0 
Gene Names: atpFvatFTTHA1274
EC: 3.6.3.14
Find proteins for P74903 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P74903 
Go to UniProtKB:  P74903
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V-type ATP synthase alpha chainA, B, C, I, J, K578Thermus thermophilus HB8Mutation(s): 0 
Gene Names: atpATTHA1273
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
Find proteins for Q56403 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q56403 
Go to UniProtKB:  Q56403
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A, C, I, K
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.51 Å
  • R-Value Free: 0.437 
  • R-Value Work: 0.429 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 381.578α = 90
b = 381.578β = 90
c = 147.672γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance