8XIW | pdb_00008xiw

Cryo-EM complex structure between hydroxylase and regulatory component from soluble methane monooxygenase

• PDB DOI: https://doi.org/10.2210/pdb8XIW/pdb
• EM Map EMD-38391: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Methylosinus sporium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-20 Released: 2025-06-25 
• Deposition Author(s): Hwang, Y., Ryu, B., Pozharski, E., Lee, S.J.
• Funding Organization(s): National Research Foundation (NRF, Korea), Ministry of Education (MoE, Korea)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Heartbeat-like dynamics drives oxygen activation in methane monooxygenase

Hwang, Y., Ryu, B., Lee, D.H., Hong, H.J., Na, J.G., Song, C.G., Kang, H.G., Pozharski, E., Lee, S.J.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2025.01.28.635075

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A2B2C2D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A4B2C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A2B2C2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 264.34 kDa 
• Atom Count: 18,397 
• Modeled Residue Count: 2,266 
• Deposited Residue Count: 2,318 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methane monooxygenase	A, E	526	Methylosinus sporium	Mutation(s): 0
UniProt
Find proteins for Q27RN7 (Methylosinus sporium) Explore Q27RN7  Go to UniProtKB:  Q27RN7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methane monooxygenase	B, F	395	Methylosinus sporium	Mutation(s): 0
UniProt
Find proteins for Q27RN6 (Methylosinus sporium) Explore Q27RN6  Go to UniProtKB:  Q27RN6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Methane monooxygenase	C, G	169	Methylosinus sporium	Mutation(s): 0
UniProt
Find proteins for Q27RN4 (Methylosinus sporium) Explore Q27RN4  Go to UniProtKB:  Q27RN4

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Methane monooxygenase	D	138	Methylosinus sporium	Mutation(s): 0  Gene Names: mmoB, C5689_05360, FM996_19905
UniProt
Find proteins for Q27RN5 (Methylosinus sporium) Explore Q27RN5  Go to UniProtKB:  Q27RN5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE (Subject of Investigation/LOI)	H [auth A], I [auth A], J [auth E], K [auth E]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.19.2-4158

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Hwang, Y., Ryu, B., Pozharski, E., Lee, S.J.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2015M3D3A1A01064876
Ministry of Education (MoE, Korea)	Korea, Republic Of	2017R1A6A1A03015876

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release