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)

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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

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

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q27RN7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q27RN6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q27RN4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q27RN5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain K [auth E] SDF format, chain J [auth E] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain K [auth E] MOL2 format, chain J [auth E] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain K [auth E] mmCIF format, chain J [auth E] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], J [auth E], K [auth E]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth E] Focus chain K [auth E] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth E] Focus chain K [auth E]

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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-25

Deposition Author(s):

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