5BPS

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.239
R-Value Work: 0.201
R-Value Observed: 0.203

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structure of the yeast F1FO ATPase C10 ring with oligomycin A

Mueller, D.M.

To be published.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit 9, mitochondrial	A B C D E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61829
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EFO Query on EFO Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain M [auth E] SDF format, chain N [auth K] SDF format, chain Q [auth O] SDF format, chain L [auth B] SDF format, chain O [auth L] SDF format, chain P [auth M] MOL2 format, chain K [auth B] MOL2 format, chain M [auth E] MOL2 format, chain N [auth K] MOL2 format, chain Q [auth O] MOL2 format, chain L [auth B] MOL2 format, chain O [auth L] MOL2 format, chain P [auth M] mmCIF format, chain K [auth B] mmCIF format, chain M [auth E] mmCIF format, chain N [auth K] mmCIF format, chain Q [auth O] mmCIF format, chain L [auth B] mmCIF format, chain O [auth L] mmCIF format, chain P [auth M]	K [auth B] L [auth B] M [auth E] N [auth K] O [auth L] 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		Interactions Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth E] Focus chain N [auth K] Focus chain O [auth L] Focus chain P [auth M] Focus chain Q [auth O] Interactions & Density Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth E] Focus chain N [auth K] Focus chain O [auth L] Focus chain P [auth M] Focus chain Q [auth O]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	A B C D E 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
R-Value Work: 0.201
R-Value Observed: 0.203
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-08-26

Deposition Author(s):

Symersky, J.

Xu, T.

Mueller, D.M.

Revision History (Full details and data files)

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

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Help and Resources

5BPS

Structure of the yeast F1FO ATPase C10 ring with oligomycin A

Structure of the yeast F1FO ATPase C10 ring with oligomycin A

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)