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 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 : 102884-102884

  • DOI: 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 (cryo-EM) during ATP hydrolysis identified several intermediates, revealing the rotary mechanism under steady-state conditions ...

    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 (cryo-EM) 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-EM 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. Electronic address: 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: 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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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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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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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

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O [auth B],
P [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
M [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
N [auth A],
Q [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION--
IMAGE ACQUISITIONSerialEM--
CTF CORRECTIONCTFFIND--
MODEL FITTINGCoot--
MODEL REFINEMENTPHENIX--
INITIAL EULER ASSIGNMENTcryoSPARC--
FINAL EULER ASSIGNMENTRELION--
CLASSIFICATIONRELION--
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