8KEI

Cryo-EM structure of NADPH oxidase 2 in complex with p22phox and EROS

PDB DOI: https://doi.org/10.2210/pdb8KEI/pdb
EM Map EMD-37159: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Oryctolagus cuniculus
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2023-08-11 Released: 2024-05-22
Deposition Author(s): Liang, S.Y., Liu, A.J., Liu, Y.Z., Ye, R.D.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.56 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of NADPH oxidase 2 in complex with p22phox and EROS

Liang, S.Y., Liu, A.J., Liu, Y.Z., Ye, R.D.

To be published.

Macromolecule Content

Total Structure Weight: 149.16 kDa
Atom Count: 10,209
Modelled Residue Count: 1,272
Deposited Residue Count: 1,303
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-245 light chain	A	133	Homo sapiens	Mutation(s): 0 Gene Names: CYBA Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P13498 (Homo sapiens) Explore P13498 Go to UniProtKB: P13498
PHAROS: P13498 GTEx: ENSG00000051523
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13498
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-245 heavy chain	B	565	Homo sapiens	Mutation(s): 0 Gene Names: CYBB, NOX2 EC: 1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P04839 (Homo sapiens) Explore P04839 Go to UniProtKB: P04839
PHAROS: P04839 GTEx: ENSG00000165168
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04839
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B	Go to GlyGen: P04839-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
monoclonal antibody 7G5 heavy chain	C	224	Oryctolagus cuniculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-245 chaperone 1	D	164	Homo sapiens	Mutation(s): 0 Gene Names: CYBC1, C17orf62, EROS Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQA9 (Homo sapiens) Explore Q9BQA9 Go to UniProtKB: Q9BQA9
PHAROS: Q9BQA9 GTEx: ENSG00000178927
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BQA9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
monoclonal antibody 7G5 light chain	E	217	Oryctolagus cuniculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G	3		N-Glycosylation	Interactions Focus chain F Focus chain G Interactions & Density Focus chain F Focus chain G
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LBN Query on LBN Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-VYOBOKEXSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
POV (Subject of Investigation/LOI) Query on POV Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	I [auth B], J [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]