8ZGP | pdb_00008zgp

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

PDB DOI: https://doi.org/10.2210/pdb8ZGP/pdb
EM Map EMD-60086: 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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 1.89 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

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

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

To be published.

Macromolecule Content

Total Structure Weight: 171.44 kDa
Atom Count: 12,156
Modeled Residue Count: 1,484
Deposited Residue Count: 1,502
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitric-oxide reductase	A, B	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C6S880
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], G [auth B], H [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]