2XOK

Refined structure of yeast F1c10 ATPase complex to 3 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2XOK/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2010-08-18 Released: 2010-09-22 
• Deposition Author(s): Stock, D., W Leslie, A.G., Walker, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 0.253 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 

Starting Model: experimental

Literature

Molecular architecture of the rotary motor in ATP synthase.

Stock, D., Leslie, A.G., Walker, J.E.

(1999) Science 286: 1700-1705

• PubMed: 10576729 
• DOI: https://doi.org/10.1126/science.286.5445.1700
• Primary Citation of Related Structures:  
  1QO1, 2XOK


• PubMed Abstract: 
  

  Adenosine triphosphate (ATP) synthase contains a rotary motor involved in biological energy conversion. Its membrane-embedded F0 sector has a rotation generator fueled by the proton-motive force, which provides the energy required for the synthesis of ATP by the F1 domain. An electron density map obtained from crystals of a subcomplex of yeast mitochondrial ATP synthase shows a ring of 10 c subunits. Each c subunit forms an alpha-helical hairpin. The interhelical loops of six to seven of the c subunits are in close contact with the gamma and delta subunits of the central stalk. The extensive contact between the c ring and the stalk suggests that they may rotate as an ensemble during catalysis.

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Organizational Affiliation: 

Medical Research Council Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 19-mer - A10B3C3D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 19-mer - A10B6C1D1E1 

Local Symmetry: Cyclic - C10  (Explore in 3D)
Local Stoichiometry: Homo 10-mer - A10 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - B3C3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 478.95 kDa 
• Atom Count: 30,113 
• Modelled Residue Count: 4,032 
• Deposited Residue Count: 4,460 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL	A, B, C	545	Saccharomyces cerevisiae	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P07251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07251  Go to UniProtKB:  P07251

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL	D, E, F	511	Saccharomyces cerevisiae	Mutation(s): 0  EC: 7.1.2.2 Membrane Entity: Yes
UniProt
Find proteins for P00830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00830  Go to UniProtKB:  P00830

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL	G	311	Saccharomyces cerevisiae	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P38077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38077  Go to UniProtKB:  P38077

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP SYNTHASE	H	160	Saccharomyces cerevisiae	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q12165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12165  Go to UniProtKB:  Q12165

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP SYNTHASE CATALYTIC SECTOR F1 EPSILON SUBUNIT	I	61	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for E9P9X4 (Saccharomyces cerevisiae) Explore E9P9X4  Go to UniProtKB:  E9P9X4

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL	J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q], Q [auth R], R [auth S], S [auth T]	76	Saccharomyces cerevisiae	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P61829 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P61829  Go to UniProtKB:  P61829

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	BA [auth F], T [auth A], V [auth B], X [auth C], Z [auth D]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	AA [auth D], CA [auth F], U [auth A], W [auth B], Y [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 0.253 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.352	α = 90
b = 173.711	β = 91.77
c = 137.889	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Stock, D., W Leslie, A.G., Walker, J.E.

Revision History  

• Version 1.0: 2010-09-22
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-10-09
  Changes: Data collection, Database references, Other
• Version 1.5: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description