5Y5X

V/A-type ATPase/synthase from Thermus thermophilus, rotational state 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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. yokoken@cc.kyoto-su.ac.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
V-type ATP synthase alpha chainA, B, C578Thermus thermophilus HB8Mutation(s): 0 
Gene Names: atpATTHA1273
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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Go to UniProtKB:  Q56403
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UniProt GroupQ56403
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
V-type ATP synthase beta chainD, E, F478Thermus thermophilus HB8Mutation(s): 0 
Gene Names: atpBTTHA1272
UniProt
Find proteins for Q56404 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ56404
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
V-type ATP synthase subunit DG223Thermus thermophilus HB8Mutation(s): 0 
Gene Names: atpDvatDTTHA1271
UniProt
Find proteins for O87880 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupO87880
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
V-type ATP synthase subunit FH104Thermus thermophilus HB8Mutation(s): 0 
Gene Names: atpFvatFTTHA1274
UniProt
Find proteins for P74903 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupP74903
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
V-type ATP synthase, subunit (VAPC-THERM)I, K120Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1279
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
MoleculeChainsSequence LengthOrganismDetailsImage
V-type ATP synthase subunit EJ, L188Thermus thermophilus HB8Mutation(s): 0 
Gene Names: atpEvatETTHA1276
UniProt
Find proteins for P74901 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
V-type ATP synthase subunit CM323Thermus thermophilus HB8Mutation(s): 0 
Gene Names: atpCTTHA1275
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
V-type ATP synthase subunit IN652Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1278
Membrane Entity: Yes 
UniProt
Find proteins for Q5SIT6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
V-type ATP synthase, subunit K
O, P, Q, R, S, T, U, V, W, X, Y, Z
O, P, Q, R, S, T, U, V, W, X, Y, Z
99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1277
Membrane Entity: Yes 
UniProt
Find proteins for Q5SIT7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SIT7
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth A],
BA [auth C]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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