5Y5Z

V/A-type ATPase/synthase from Thermus thermophilus, rotational state 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryo EM structure of intact rotary H+-ATPase/synthase from Thermus thermophilus

Nakanishi, A.Kishikawa, J.I.Tamakoshi, M.Mitsuoka, K.Yokoyama, K.

(2018) Nat Commun 9: 89-89

  • DOI: https://doi.org/10.1038/s41467-017-02553-6
  • Primary Citation of Related Structures:  
    5Y5X, 5Y5Y, 5Y5Z, 5Y60

  • PubMed Abstract: 

    Proton translocating rotary ATPases couple ATP hydrolysis/synthesis, which occurs in the soluble domain, with proton flow through the membrane domain via a rotation of the common central rotor complex against the surrounding peripheral stator apparatus. Here, we present a large data set of single particle cryo-electron micrograph images of the V/A type H + -rotary ATPase from the bacterium Thermus thermophilus, enabling the identification of three rotational states based on the orientation of the rotor subunit. Using masked refinement and classification with signal subtractions, we obtain homogeneous reconstructions for the whole complexes and soluble V 1 domains. These reconstructions are of higher resolution than any EM map of intact rotary ATPase reported previously, providing a detailed molecular basis for how the rotary ATPase maintains structural integrity of the peripheral stator apparatus, and confirming the existence of a clear proton translocation path from both sides of the membrane.


  • Organizational Affiliation

    Department of Molecular Biosciences, Kyoto Sangyo University, Motoyama Kamigamo, Kita-ku, Kyoto, 603-8555, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase alpha chain
A, B, C
578Thermus thermophilus HB8Mutation(s): 0 
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
UniProt
Find proteins for Q56403 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ56403
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase beta chain
D, E, F
478Thermus thermophilus HB8Mutation(s): 0 
UniProt
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UniProt GroupQ56404
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit D223Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for O87880 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit F104Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase, subunit (VAPC-THERM)
I, K
120Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SIT5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SIT5
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit E
J, L
188Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit C323Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit I652Thermus thermophilus HB8Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q5SIT6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase, subunit K
O, P, Q, R, S
O, P, Q, R, S, T, U, V, W, X, Y, Z
99Thermus thermophilus HB8Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q5SIT7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1b

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Science and Culture of JapanJapan17H03648
Ministry of Education, Science and Culture of JapanJapan16K21472

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references