9CG3 | pdb_00009cg3

Human kidney respiratory complex III

PDB DOI: https://doi.org/10.2210/pdb9CG3/pdb
EM Map EMD-45567: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2024-06-28 Released: 2025-08-06
Deposition Author(s): Zhang, Z., Lyu, M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.96 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Human kidney respiratory complex III

Zhang, Z., Lyu, M.

To be published.

Macromolecule Content

Total Structure Weight: 518.55 kDa
Atom Count: 31,844
Modeled Residue Count: 3,995
Deposited Residue Count: 4,630
Unique protein chains: 10

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 8	A, T [auth N]	82	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O14949 (Homo sapiens) Explore O14949 Go to UniProtKB: O14949
PHAROS: O14949 GTEx: ENSG00000164405
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14949
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	B [auth C], K [auth P]	274	Homo sapiens	Mutation(s): 0 EC: 7.1.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P47985 (Homo sapiens) Explore P47985 Go to UniProtKB: P47985
PHAROS: P47985 GTEx: ENSG00000169021
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P47985
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 9	C [auth D], L [auth Q]	63	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UDW1 (Homo sapiens) Explore Q9UDW1 Go to UniProtKB: Q9UDW1
PHAROS: Q9UDW1 GTEx: ENSG00000184076
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UDW1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 6, mitochondrial	D [auth E], M [auth R]	91	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P07919 (Homo sapiens) Explore P07919 Go to UniProtKB: P07919
PHAROS: P07919 GTEx: ENSG00000173660
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07919
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 7	E [auth F], N [auth S]	111	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P14927 (Homo sapiens) Explore P14927 Go to UniProtKB: P14927
PHAROS: P14927 GTEx: ENSG00000156467
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14927
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 10	F [auth G], O [auth T]	56	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O14957 (Homo sapiens) Explore O14957 Go to UniProtKB: O14957
PHAROS: O14957 GTEx: ENSG00000127540
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14957
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1, heme protein, mitochondrial	G [auth H], P [auth U]	325	Homo sapiens	Mutation(s): 0 EC: 7.1.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P08574 (Homo sapiens) Explore P08574 Go to UniProtKB: P08574
PHAROS: P08574 GTEx: ENSG00000179091
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08574
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	H [auth J], Q [auth V]	380	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P00156 (Homo sapiens) Explore P00156 Go to UniProtKB: P00156
PHAROS: P00156 GTEx: ENSG00000198727
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00156
Sequence Annotations Expand
Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 2, mitochondrial	I [auth K], R [auth W]	453	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P22695 (Homo sapiens) Explore P22695 Go to UniProtKB: P22695
PHAROS: P22695 GTEx: ENSG00000140740
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22695
Sequence Annotations Expand
Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 1, mitochondrial	J [auth L], S [auth Y]	480	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P31930 (Homo sapiens) Explore P31930 Go to UniProtKB: P31930
PHAROS: P31930 GTEx: ENSG00000010256
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31930
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain V [auth H] SDF format, chain Z [auth U] MOL2 format, chain V [auth H] MOL2 format, chain Z [auth U] mmCIF format, chain V [auth H] mmCIF format, chain Z [auth U]	V [auth H], Z [auth U]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain V [auth H] Focus chain Z [auth U] Interactions & Density Focus chain V [auth H] Focus chain Z [auth U]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain AA [auth V] SDF format, chain BA [auth V] SDF format, chain W [auth J] SDF format, chain X [auth J] MOL2 format, chain AA [auth V] MOL2 format, chain BA [auth V] MOL2 format, chain W [auth J] MOL2 format, chain X [auth J] mmCIF format, chain AA [auth V] mmCIF format, chain BA [auth V] mmCIF format, chain W [auth J] mmCIF format, chain X [auth J]	AA [auth V], BA [auth V], W [auth J], X [auth J]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AA [auth V] Focus chain BA [auth V] Focus chain W [auth J] Focus chain X [auth J] Interactions & Density Focus chain AA [auth V] Focus chain BA [auth V] Focus chain W [auth J] Focus chain X [auth J]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain Y [auth P] SDF format, chain U [auth C] MOL2 format, chain Y [auth P] MOL2 format, chain U [auth C] mmCIF format, chain Y [auth P] mmCIF format, chain U [auth C]	U [auth C], Y [auth P]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain U [auth C] Focus chain Y [auth P] Interactions & Density Focus chain U [auth C] Focus chain Y [auth P]