9HWK | pdb_00009hwk

Structure of the Cytochrome o ubiquinol oxidase embedded in the nanodisc

• PDB DOI: https://doi.org/10.2210/pdb9HWK/pdb
• EM Map EMD-52451: EMDB EMDataResource

• Classification: ELECTRON TRANSPORT
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-05 Released: 2026-01-14 
• Deposition Author(s): Mim, C., Zhang, Q., Murthy, A.V.
• Funding Organization(s): Carl Trygger Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.72 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

In silico classification and identification co-purified protein complexes yield new structures and multiple MSP assembly states

Zhang, Q., Murthy, A.V., Mim, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 145.64 kDa 
• Atom Count: 9,584 
• Modeled Residue Count: 1,202 
• Deposited Residue Count: 1,291 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome bo(3) ubiquinol oxidase subunit 1	A [auth F]	663	Escherichia coli	Mutation(s): 0  EC: 7.1.1.3
UniProt
Find proteins for P0ABI8 (Escherichia coli (strain K12)) Explore P0ABI8  Go to UniProtKB:  P0ABI8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome bo(3) ubiquinol oxidase subunit 2	B [auth G]	315	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ABJ1 (Escherichia coli (strain K12)) Explore P0ABJ1  Go to UniProtKB:  P0ABJ1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome bo(3) ubiquinol oxidase subunit 3	C [auth H]	204	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ABJ3 (Escherichia coli (strain K12)) Explore P0ABJ3  Go to UniProtKB:  P0ABJ3

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome bo(3) ubiquinol oxidase subunit 4	D [auth I]	109	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ABJ6 (Escherichia coli (strain K12)) Explore P0ABJ6  Go to UniProtKB:  P0ABJ6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEO (Subject of Investigation/LOI)	E [auth F]	HEME O C49 H58 Fe N4 O5 FRKORVCRVCLRBA-BZKSIRDQSA-L
HEM (Subject of Investigation/LOI)	F	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
ZN (Subject of Investigation/LOI)	H [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)	G [auth F]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.72 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	Servalcat

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-14 
Deposition Author(s): Mim, C., Zhang, Q., Murthy, A.V.

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Funding Organization	Location	Grant Number
Carl Trygger Foundation	Sweden	CTS 21:1630

Revision History  

• Version 1.0: 2026-01-14
  Type: Initial release