9I7U | pdb_00009i7u

Cryo-EM structure of NDUFA4 bound complex IV within the respirasome complex

PDB DOI: https://doi.org/10.2210/pdb9I7U/pdb
EM Map EMD-52662: EMDB EMDataResource

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

Deposited: 2025-02-02 Released: 2025-12-03
Deposition Author(s): Nguyen, M.D., Singh, V., Rorbach, J.
Funding Organization(s): Knut and Alice Wallenberg Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.15 Å
Aggregation State: CELL
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., Rorbach, J.

To be published.

Macromolecule Content

Total Structure Weight: 243.96 kDa
Atom Count: 15,296
Modeled Residue Count: 1,848
Deposited Residue Count: 2,095
Unique protein chains: 14

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	A	513	Homo sapiens	Mutation(s): 0 EC: 7.1.1.9
UniProt & NIH Common Fund Data Resources
Find proteins for P00395 (Homo sapiens) Explore P00395 Go to UniProtKB: P00395
PHAROS: P00395 GTEx: ENSG00000198804
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00395
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	B	227	Homo sapiens	Mutation(s): 0 EC: 7.1.1.9
UniProt & NIH Common Fund Data Resources
Find proteins for P00403 (Homo sapiens) Explore P00403 Go to UniProtKB: P00403
PHAROS: P00403 GTEx: ENSG00000198712
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00403
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 3	C	261	Homo sapiens	Mutation(s): 0 EC: 7.1.1.9
UniProt & NIH Common Fund Data Resources
Find proteins for P00414 (Homo sapiens) Explore P00414 Go to UniProtKB: P00414
PHAROS: P00414 GTEx: ENSG00000198938
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00414
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial	D	169	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P13073 (Homo sapiens) Explore P13073 Go to UniProtKB: P13073
PHAROS: P13073 GTEx: ENSG00000131143
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13073
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5A, mitochondrial	E	150	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P20674 (Homo sapiens) Explore P20674 Go to UniProtKB: P20674
PHAROS: P20674 GTEx: ENSG00000178741
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20674
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5B, mitochondrial	F	129	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P10606 (Homo sapiens) Explore P10606 Go to UniProtKB: P10606
PHAROS: P10606 GTEx: ENSG00000135940
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10606
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6A1, mitochondrial	G	109	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P12074 (Homo sapiens) Explore P12074 Go to UniProtKB: P12074
PHAROS: P12074 GTEx: ENSG00000111775
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12074
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6B1	H	86	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P14854 (Homo sapiens) Explore P14854 Go to UniProtKB: P14854
PHAROS: P14854 GTEx: ENSG00000126267
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14854
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6C	I	75	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P09669 (Homo sapiens) Explore P09669 Go to UniProtKB: P09669
PHAROS: P09669 GTEx: ENSG00000164919
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09669
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7A2, mitochondrial	J	83	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P14406 (Homo sapiens) Explore P14406 Go to UniProtKB: P14406
PHAROS: P14406 GTEx: ENSG00000112695
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14406
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7B, mitochondrial	K	80	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P24311 (Homo sapiens) Explore P24311 Go to UniProtKB: P24311
PHAROS: P24311 GTEx: ENSG00000131174
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24311
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7C, mitochondrial	L	63	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P15954 (Homo sapiens) Explore P15954 Go to UniProtKB: P15954
PHAROS: P15954 GTEx: ENSG00000127184
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15954
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 8A, mitochondrial	M	69	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P10176 (Homo sapiens) Explore P10176 Go to UniProtKB: P10176
PHAROS: P10176 GTEx: ENSG00000176340
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10176
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit NDUFA4	N	81	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O00483 (Homo sapiens) Explore O00483 Go to UniProtKB: O00483
PHAROS: O00483 GTEx: ENSG00000189043
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00483
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 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 AA [auth N] MOL2 format, chain AA [auth N] mmCIF format, chain AA [auth N]	AA [auth N]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain AA [auth N] Interactions & Density Focus chain AA [auth N]
HEA (Subject of Investigation/LOI) Query on HEA Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A]	R [auth A], S [auth A]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain R [auth A] Focus chain S [auth A]
PGV Query on PGV Download Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C₄₀ H₇₇ O₁₀ P ADYWCMPUNIVOEA-GPJPVTGXSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
PEE (Subject of Investigation/LOI) Query on PEE Download Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C]	V [auth C], W [auth C], X [auth C], Y [auth C]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain Z [auth F] MOL2 format, chain Z [auth F] mmCIF format, chain Z [auth F]	Z [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain Z [auth F] Interactions & Density Focus chain Z [auth F]
CU (Subject of Investigation/LOI) Query on CU Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain O [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain O [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	O [auth A], T [auth B], U [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain O [auth A] Focus chain T [auth B] Focus chain U [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]