5BPS | pdb_00005bps

Structure of the yeast F1FO ATPase C10 ring with oligomycin A

• PDB DOI: https://doi.org/10.2210/pdb5BPS/pdb

• Classification: MEMBRANE PROTEIN/ANTIBIOTIC
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2015-05-28 Released: 2015-08-26 
• Deposition Author(s): Symersky, J., Xu, T., Mueller, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Structure of the yeast F1FO ATPase C10 ring with oligomycin A

Mueller, D.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C10  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C10  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 83.44 kDa 
• Atom Count: 6,011 
• Modeled Residue Count: 747 
• Deposited Residue Count: 760 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit 9, mitochondrial	A, B, C, D, E, F [auth K], G [auth L], H [auth M], I [auth N], J [auth O]	76	Saccharomyces cerevisiae	Mutation(s): 0  EC: 3.6 Membrane Entity: Yes
UniProt
Find proteins for P61829 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P61829  Go to UniProtKB:  P61829

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EFO	K [auth B], L [auth B], M [auth E], N [auth K], O [auth L], P [auth M], Q [auth O]	Oligomycin A C45 H74 O11 MNULEGDCPYONBU-AWJDAWNUSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME	A, B, C, D, E, F [auth K], G [auth L], H [auth M], I [auth N], J [auth O]	L-PEPTIDE LINKING	C6 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.216	α = 90
b = 76.216	β = 90
c = 489.19	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-26 
Deposition Author(s): Symersky, J., Xu, T., Mueller, D.M.

Revision History  

• Version 1.0: 2015-08-26
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary