8GXX

3 nucleotide-bound V1EG of V/A-ATPase from Thermus thermophilus.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryo-EM analysis of V/A-ATPase intermediates reveals the transition of the ground-state structure to steady-state structures by sequential ATP binding.

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

(2023) J Biol Chem 299: 102884-102884

  • DOI: https://doi.org/10.1016/j.jbc.2023.102884
  • Primary Citation of Related Structures:  
    8GXU, 8GXW, 8GXX, 8GXY, 8GXZ

  • PubMed Abstract: 

    Vacuolar/archaeal-type ATPase (V/A-ATPase) is a rotary ATPase that shares a common rotary catalytic mechanism with F o F 1 ATP synthase. Structural images of V/A-ATPase obtained by single-particle cryo-electron microscopy during ATP hydrolysis identified several intermediates, revealing the rotary mechanism under steady-state conditions. However, further characterization is needed to understand the transition from the ground state to the steady state. Here, we identified the cryo-electron microscopy structures of V/A-ATPase corresponding to short-lived initial intermediates during the activation of the ground state structure by time-resolving snapshot analysis. These intermediate structures provide insights into how the ground-state structure changes to the active, steady state through the sequential binding of ATP to its three catalytic sites. All the intermediate structures of V/A-ATPase adopt the same asymmetric structure, whereas the three catalytic dimers adopt different conformations. This is significantly different from the initial activation process of F o F 1 , where the overall structure of the F 1 domain changes during the transition from a pseudo-symmetric to a canonical asymmetric structure (PNAS NEXUS, pgac116, 2022). In conclusion, our findings provide dynamical information that will enhance the future prospects for studying the initial activation processes of the enzymes, which have unknown intermediate structures in their functional pathway.


  • Organizational Affiliation

    Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan; Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Osaka, 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: 7.1.2.2
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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  • Reference Sequence
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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
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
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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UniProt GroupO87880
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit F104Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P74903 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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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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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit E
J, L
188Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P74901 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan20H03231
Japan Society for the Promotion of Science (JSPS)Japan20J00162
Japan Society for the Promotion of Science (JSPS)Japan20K06514
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanJPMXP09A21OS0008
Japan Agency for Medical Research and Development (AMED)JapanJP17am0101001

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references
  • Version 1.2: 2023-02-15
    Changes: Database references
  • Version 1.3: 2024-07-03
    Changes: Data collection, Refinement description