7XKQ

F1 domain of FoF1-ATPase with the down form of epsilon subunit from Bacillus PS3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

Structural basis of unisite catalysis of bacterial F 0 F 1 -ATPase.

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

(2022) PNAS Nexus 1: pgac116-pgac116

  • DOI: https://doi.org/10.1093/pnasnexus/pgac116
  • Primary Citation of Related Structures:  
    7XKH, 7XKO, 7XKP, 7XKQ, 7XKR

  • PubMed Abstract: 

    Adenosine triphosphate (ATP) synthases (F 0 F 1 -ATPases) are crucial for all aerobic organisms. F 1 , a water-soluble domain, can catalyze both the synthesis and hydrolysis of ATP with the rotation of the central γε rotor inside a cylinder made of α 3 β 3 in three different conformations (referred to as β E , β TP , and β DP ). In this study, we determined multiple cryo-electron microscopy structures of bacterial F 0 F 1 exposed to different reaction conditions. The structures of nucleotide-depleted F 0 F 1 indicate that the ε subunit directly forces β TP to adopt a closed form independent of the nucleotide binding to β TP . The structure of F 0 F 1 under conditions that permit only a single catalytic β subunit per enzyme to bind ATP is referred to as unisite catalysis and reveals that ATP hydrolysis unexpectedly occurs on β TP instead of β DP , where ATP hydrolysis proceeds in the steady-state catalysis of F 0 F 1 . This indicates that the unisite catalysis of bacterial F 0 F 1 significantly differs from the kinetics of steady-state turnover with continuous rotation of the shaft.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha
A, B, C
502Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncAatpA
EC: 7.1.2.2
UniProt
Find proteins for A0A0M3VGF9 (Bacillus sp. (strain PS3))
Explore A0A0M3VGF9 
Go to UniProtKB:  A0A0M3VGF9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3VGF9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta
D, E, F
484Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncDatpD
EC: 7.1.2.2
UniProt
Find proteins for P07677 (Bacillus sp. (strain PS3))
Explore P07677 
Go to UniProtKB:  P07677
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07677
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase gamma chain285Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncGatpG
UniProt
Find proteins for A0A0M4TPJ7 (Bacillus sp. (strain PS3))
Explore A0A0M4TPJ7 
Go to UniProtKB:  A0A0M4TPJ7
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UniProt GroupA0A0M4TPJ7
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase epsilon chain133Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncCatpC
UniProt
Find proteins for A0A0M5MQR7 (Bacillus sp. (strain PS3))
Explore A0A0M5MQR7 
Go to UniProtKB:  A0A0M5MQR7
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UniProt GroupA0A0M5MQR7
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
M [auth C]
Q [auth E]
S [auth F]
I [auth A],
L [auth B],
M [auth C],
Q [auth E],
S [auth F],
U [auth H]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

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

Download Ideal Coordinates CCD File 
J [auth A]
K [auth B]
N [auth C]
O [auth D]
R [auth E]
J [auth A],
K [auth B],
N [auth C],
O [auth D],
R [auth E],
T [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION4.0

Structure Validation

View Full Validation Report



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)Japan20K06514
Japan Agency for Medical Research and Development (AMED)JapanJP17am0101001
Japan Society for the Promotion of Science (JSPS)Japan20J00162

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description