8B4O | pdb_00008b4o

Cryo-EM structure of cytochrome bd oxidase from C. glutamicum

• PDB DOI: https://doi.org/10.2210/pdb8B4O/pdb
• EM Map EMD-15851: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Corynebacterium glutamicum
• Expression System: Corynebacterium glutamicum
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTM


• Deposited: 2022-09-20 Released: 2022-12-28 
• Deposition Author(s): Grund, T.N., Kusumoto, T., Michel, H., Sakamoto, J., Safarian, S.
• Funding Organization(s): Max Planck Society

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of cytochrome bd oxidase from C. glutamicum

Grund, T.N., Michel, H., Safarian, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 94.81 kDa 
• Atom Count: 6,156 
• Modeled Residue Count: 772 
• Deposited Residue Count: 846 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome bd-type quinol oxidase subunit II	A [auth B]	333	Corynebacterium glutamicum	Mutation(s): 0  Gene Names: cydB, CS176_1127 EC: 1.10.3 Membrane Entity: Yes
UniProt
Find proteins for Q8NRA3 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NRA3  Go to UniProtKB:  Q8NRA3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome BD ubiquinol oxidase subunit I	B [auth A]	513	Corynebacterium glutamicum	Mutation(s): 0  Gene Names: cydA, BBD29_06150 Membrane Entity: Yes
UniProt
Find proteins for Q9KWL8 (Corynebacterium glutamicum) Explore Q9KWL8  Go to UniProtKB:  Q9KWL8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HDD (Subject of Investigation/LOI)	C [auth A]	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE C34 H32 Fe N4 O5 HMYRFFHHXXPRDI-XCVPDAMTSA-M
HEB (Subject of Investigation/LOI)	D [auth A], E [auth A]	HEME B/C C34 H34 Fe N4 O4 NEGHHAJBRZGUAY-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-28 
Deposition Author(s): Grund, T.N., Kusumoto, T., Michel, H., Sakamoto, J., Safarian, S.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2022-12-28
  Type: Initial release
  
• Version 1.1: 2024-07-24
  Changes: Data collection
• Version 1.2: 2026-09-02
  Type: Remediation
  Reason: Metalloprotein remediation
  Changes: Data collection, Derived calculations, Structure summary