3W3A

Crystal structure of V1-ATPase at 3.9 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.381 
  • R-Value Work: 0.328 
  • R-Value Observed: 0.328 

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This is version 1.2 of the entry. See complete history


Literature

Origin of Asymmetry at the Intersubunit Interfaces of V1-ATPase from Thermusthermophilus

Nagamatsu, Y.Takeda, K.Kuranaga, T.Numoto, N.Miki, K.

(2013) J Mol Biol 425: 2699-2708

  • DOI: 10.1016/j.jmb.2013.04.022
  • Primary Citation of Related Structures:  
    3W3A

  • PubMed Abstract: 
  • V-type ATPase (V-ATPase) is one of the rotary ATPase complexes that mediate energy conversion between the chemical energy of ATP and the ion gradient across the membrane through a rotary catalytic mechanism. Because V-ATPase has structural features similar to those of well-studied F-type ATPase, the structure is expected to highlight the common essence of the torque generation of rotary ATPases ...

    V-type ATPase (V-ATPase) is one of the rotary ATPase complexes that mediate energy conversion between the chemical energy of ATP and the ion gradient across the membrane through a rotary catalytic mechanism. Because V-ATPase has structural features similar to those of well-studied F-type ATPase, the structure is expected to highlight the common essence of the torque generation of rotary ATPases. Here, we report a complete model of the extra-membrane domain of the V-ATPase (V1-ATPase) of a thermophilic bacterium, Thermus thermophilus, consisting of three A subunits, three B subunits, one D subunit, and one F subunit. The X-ray structure at 3.9Å resolution provides detailed information about the interactions between A3B3 and DF subcomplexes as well as interactions among the respective subunits, which are defined by the properties of side chains. Asymmetry at the intersubunit interfaces was detected from the structural differences among the three AB pairs in the different reaction states, while the large interdomain motion in the catalytic A subunits was not observed unlike F1 from various species and V1 from Enterococcus hirae. Asymmetry is mainly realized by rigid-body rearrangements of the relative position between A and B subunits. This is consistent with the previous observations by the high-resolution electron microscopy for the whole V-ATPase complexes. Therefore, our result plausibly implies that the essential motion for the torque generation is not the large interdomain movement of the catalytic subunits but the rigid-body rearrangement of subunits.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
V-type ATP synthase alpha chainA, B, C, I, J, K577Thermus 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))
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Go to UniProtKB:  Q56403
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
V-type ATP synthase beta chainD, E, F, L, M, N457Thermus thermophilus HB8Mutation(s): 0 
Gene Names: atpBTTHA1272
EC: 3.6.3.14
Find proteins for Q56404 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q56404
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
V-type ATP synthase subunit DG, O210Thermus 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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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
V-type ATP synthase subunit FH, P100Thermus thermophilus HB8Mutation(s): 0 
Gene Names: atpFvatFTTHA1274
EC: 3.6.3.14
Find proteins for P74903 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  P74903
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
Q [auth A], R [auth C], S [auth I], T [auth K]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.381 
  • R-Value Work: 0.328 
  • R-Value Observed: 0.328 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 382.144α = 90
b = 382.144β = 90
c = 148.248γ = 120
Software Package:
Software NamePurpose
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description