9HZL | pdb_00009hzl

High resolution cryo-EM structure of human complex III in mitochondria

PDB DOI: https://doi.org/10.2210/pdb9HZL/pdb
EM Map EMD-52525: EMDB EMDataResource

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

Deposited: 2025-01-14 Released: 2025-11-12
Deposition Author(s): Nguyen, M.D., Khajawa, A., Rorbach, J.
Funding Organization(s): Knut and Alice Wallenberg Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.52 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

Structural basis for late maturation steps of mitochondrial respiratory chain complex IV within the human respirasome

Nguyen, M.D., Khajawa, A., Rorbach, J.

To be published.

Macromolecule Content

Total Structure Weight: 602.15 kDa
Atom Count: 34,614
Modeled Residue Count: 4,209
Deposited Residue Count: 5,178
Unique protein chains: 10

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 8	A, L [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, C, M [auth O], N [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
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 9	D, O [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
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 6, mitochondrial	E, P [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
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 7	F, Q [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
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 10	G, R [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
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1, heme protein, mitochondrial	H, S [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	I [auth J], T [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
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 2, mitochondrial	J [auth K], U [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
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 1, mitochondrial	K [auth L], V [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
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Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL (Subject of Investigation/LOI) Query on CDL Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain DA [auth H] SDF format, chain HA [auth J] SDF format, chain KA [auth J] SDF format, chain OA [auth T] SDF format, chain SA [auth U] SDF format, chain W [auth A] SDF format, chain YA [auth V] SDF format, chain ZA [auth Y] MOL2 format, chain BA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain HA [auth J] MOL2 format, chain KA [auth J] MOL2 format, chain OA [auth T] MOL2 format, chain SA [auth U] MOL2 format, chain W [auth A] MOL2 format, chain YA [auth V] MOL2 format, chain ZA [auth Y] mmCIF format, chain BA [auth G] mmCIF format, chain DA [auth H] mmCIF format, chain HA [auth J] mmCIF format, chain KA [auth J] mmCIF format, chain OA [auth T] mmCIF format, chain SA [auth U] mmCIF format, chain W [auth A] mmCIF format, chain YA [auth V] mmCIF format, chain ZA [auth Y]	BA [auth G] DA [auth H] HA [auth J] KA [auth J] OA [auth T] BA [auth G], DA [auth H], HA [auth J], KA [auth J], OA [auth T], SA [auth U], W [auth A], YA [auth V], ZA [auth Y]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain BA [auth G] Focus chain DA [auth H] Focus chain HA [auth J] Focus chain KA [auth J] Focus chain OA [auth T] Focus chain SA [auth U] Focus chain W [auth A] Focus chain YA [auth V] Focus chain ZA [auth Y] Interactions & Density Focus chain BA [auth G] Focus chain DA [auth H] Focus chain HA [auth J] Focus chain KA [auth J] Focus chain OA [auth T] Focus chain SA [auth U] Focus chain W [auth A] Focus chain YA [auth V] Focus chain ZA [auth Y]
U10 (Subject of Investigation/LOI) Query on U10 Download Ideal Coordinates CCD File SDF format, chain IA [auth J] SDF format, chain JA [auth J] SDF format, chain VA [auth V] SDF format, chain WA [auth V] MOL2 format, chain IA [auth J] MOL2 format, chain JA [auth J] MOL2 format, chain VA [auth V] MOL2 format, chain WA [auth V] mmCIF format, chain IA [auth J] mmCIF format, chain JA [auth J] mmCIF format, chain VA [auth V] mmCIF format, chain WA [auth V]	IA [auth J], JA [auth J], VA [auth V], WA [auth V]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain IA [auth J] Focus chain JA [auth J] Focus chain VA [auth V] Focus chain WA [auth V] Interactions & Density Focus chain IA [auth J] Focus chain JA [auth J] Focus chain VA [auth V] Focus chain WA [auth V]
PC1 Query on PC1 Download Ideal Coordinates CCD File SDF format, chain NA [auth P] MOL2 format, chain NA [auth P] mmCIF format, chain NA [auth P]	NA [auth P]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain NA [auth P] Interactions & Density Focus chain NA [auth P]
PLX Query on PLX Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain PA [auth T] MOL2 format, chain AA [auth D] MOL2 format, chain PA [auth T] mmCIF format, chain AA [auth D] mmCIF format, chain PA [auth T]	AA [auth D], PA [auth T]	(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL C₄₂ H₈₉ N O₈ P YVNJQRQLQPWVSQ-IWSHAHEXSA-O		Interactions Focus chain AA [auth D] Focus chain PA [auth T] Interactions & Density Focus chain AA [auth D] Focus chain PA [auth T]
3PE Query on 3PE Download Ideal Coordinates CCD File SDF format, chain AB [auth Y] SDF format, chain LA [auth L] SDF format, chain QA [auth U] SDF format, chain X [auth C] SDF format, chain XA [auth V] SDF format, chain Z [auth C] MOL2 format, chain AB [auth Y] MOL2 format, chain LA [auth L] MOL2 format, chain QA [auth U] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth V] MOL2 format, chain Z [auth C] mmCIF format, chain AB [auth Y] mmCIF format, chain LA [auth L] mmCIF format, chain QA [auth U] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth V] mmCIF format, chain Z [auth C]	AB [auth Y] LA [auth L] QA [auth U] X [auth C] XA [auth V] AB [auth Y], LA [auth L], QA [auth U], X [auth C], XA [auth V], Z [auth C]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain AB [auth Y] Focus chain LA [auth L] Focus chain QA [auth U] Focus chain X [auth C] Focus chain XA [auth V] Focus chain Z [auth C] Interactions & Density Focus chain AB [auth Y] Focus chain LA [auth L] Focus chain QA [auth U] Focus chain X [auth C] Focus chain XA [auth V] Focus chain Z [auth C]
PEE Query on PEE Download Ideal Coordinates CCD File SDF format, chain GA [auth J] MOL2 format, chain GA [auth J] mmCIF format, chain GA [auth J]	GA [auth J]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain GA [auth J] Interactions & Density Focus chain GA [auth J]
HEC (Subject of Investigation/LOI) Query on HEC Download Ideal Coordinates CCD File SDF format, chain CA [auth H] SDF format, chain RA [auth U] MOL2 format, chain CA [auth H] MOL2 format, chain RA [auth U] mmCIF format, chain CA [auth H] mmCIF format, chain RA [auth U]	CA [auth H], RA [auth U]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain CA [auth H] Focus chain RA [auth U] Interactions & Density Focus chain CA [auth H] Focus chain RA [auth U]
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain EA [auth J] SDF format, chain FA [auth J] SDF format, chain TA [auth V] SDF format, chain UA [auth V] MOL2 format, chain EA [auth J] MOL2 format, chain FA [auth J] MOL2 format, chain TA [auth V] MOL2 format, chain UA [auth V] mmCIF format, chain EA [auth J] mmCIF format, chain FA [auth J] mmCIF format, chain TA [auth V] mmCIF format, chain UA [auth V]	EA [auth J], FA [auth J], TA [auth V], UA [auth V]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain EA [auth J] Focus chain FA [auth J] Focus chain TA [auth V] Focus chain UA [auth V] Interactions & Density Focus chain EA [auth J] Focus chain FA [auth J] Focus chain TA [auth V] Focus chain UA [auth V]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain MA [auth P] SDF format, chain Y [auth C] MOL2 format, chain MA [auth P] MOL2 format, chain Y [auth C] mmCIF format, chain MA [auth P] mmCIF format, chain Y [auth C]	MA [auth P], Y [auth C]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain MA [auth P] Focus chain Y [auth C] Interactions & Density Focus chain MA [auth P] Focus chain Y [auth C]