8ZGO | pdb_00008zgo

CryoEM structure of monomeric quinol dependent nitric oxide reductase from Neisseria meningitidis

• PDB DOI: https://doi.org/10.2210/pdb8ZGO/pdb
• EM Map EMD-60085: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Neisseria meningitidis alpha14
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2024-05-09 Released: 2025-05-14 
• Deposition Author(s): Gopalasingam, C.C., Shiro, Y., Tosha, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

CryoEM structure of monomeric quinol dependent nitric oxide reductase from Neisseria meningitidis

Gopalasingam, C.C., Shiro, Y., Tosha, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 85.72 kDa 
• Atom Count: 5,980 
• Modeled Residue Count: 742 
• Deposited Residue Count: 751 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitric-oxide reductase	A	751	Neisseria meningitidis alpha14	Mutation(s): 0  Gene Names: norB, NMO_1451 EC: 1.7.99.7 Membrane Entity: Yes
UniProt
Find proteins for C6S880 (Neisseria meningitidis (strain alpha14)) Explore C6S880  Go to UniProtKB:  C6S880

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A], C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
FE	D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.1.1
MODEL REFINEMENT	PHENIX	1.20

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Gopalasingam, C.C., Shiro, Y., Tosha, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H05761
Japan Society for the Promotion of Science (JSPS)	Japan	JP20K22633

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release