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› 8ugi

Electron Microscopy
2.1Å resolution

High resolution in-situ structure of typeA supercomplex in respiratory chain (I1III2IV1,composite)

Released:
DOI: 10.2210/pdb8ugi/pdb
PDB entry 8ugi coloured by chain, front view.
PDB entry 8ugi coloured by chain, side view.
PDB entry 8ugi coloured by chain, top view.
Source organism: Sus scrofa
Primary publication:
High-resolution in situ structures of mammalian respiratory supercomplexes.
Zheng W, Chai P, Zhu J, Zhang K
OpenAccess logo Nature (2024)
PMID: 38811722
Related structures: EMD-42226

Function and Biology Details

Reactions catalysed: 
a ubiquinone + NADH + 5 H(+)(in) = a ubiquinol + NAD(+) + 4 H(+)(out).
a quinol + 2 Fe(III)-[cytochrome c](out) = a quinone + 2 Fe(II)-[cytochrome c](out) + 2 H(+)(out).
4 Fe(II)-[cytochrome c] + O2 + 8 H(+)(in) = 4 Fe(III)-[cytochrome c] +2 H2O + 4 H(+)(out).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 81-mer (preferred)
PDBe Complex ID:
PDB-CPX-283014 (preferred)
Entry contents:
68 distinct polypeptide molecules
Macromolecules (68 distinct):
NADH-ubiquinone oxidoreductase chain 3 Chain: 1A
Molecule details ›
Chain: 1A
Length: 115 amino acids
Theoretical weight: 13.03 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: O79880 (Residues: 1-115; Coverage: 100%)
Gene names: MT-ND3, MTND3, NADH3, ND3
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial Chain: 1B
Molecule details ›
Chain: 1B
Length: 258 amino acids
Theoretical weight: 28.5 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VVS8 (Residues: 1-258; Coverage: 100%)
Gene name: NDUFS7
Sequence domains: NADH ubiquinone oxidoreductase, 20 Kd subunit
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial Chain: 1C
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial Chain: 1D
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial Chain: 1E
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Chain: 1F
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial Chain: 1G
NADH-ubiquinone oxidoreductase chain 1 Chain: 1H
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial Chain: 1I
NADH-ubiquinone oxidoreductase chain 6 Chain: 1J
NADH-ubiquinone oxidoreductase chain 4L Chain: 1K
NADH-ubiquinone oxidoreductase chain 5 Chain: 1L
NADH-ubiquinone oxidoreductase chain 4 Chain: 1M
NADH-ubiquinone oxidoreductase chain 2 Chain: 1N
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial Chain: 1O
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial Chain: 1P
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial Chain: 1Q
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial Chain: 1R
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 Chain: 1S
Acyl carrier protein Chains: 1T, 1U
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 Chain: 1V
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 Chain: 1W
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 Chain: 1X
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 Chain: 1Y
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 Chain: 1Z
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 Chain: 1a
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 Chain: 1b
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial Chain: 1c
NADH dehydrogenase [ubiquinone] 1 subunit C2 Chain: 1d
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 Chain: 1e
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 Chain: 1f
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial Chain: 1g
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial Chain: 1h
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 Chain: 1i
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial Chain: 1j
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 Chain: 1k
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial Chain: 1l
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 Chain: 1m
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 Chain: 1n
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 Chain: 1o
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 Chain: 1p
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 Chain: 1q
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 Chain: 1r
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial Chain: 1s
Cytochrome b-c1 complex subunit 1, mitochondrial Chains: 3A, 3N
Cytochrome b-c1 complex subunit 2, mitochondrial Chains: 3B, 3O
Cytochrome b Chains: 3C, 3P
Cytochrome c1, heme protein, mitochondrial Chains: 3D, 3Q
Cytochrome b-c1 complex subunit Rieske, mitochondrial Chains: 3E, 3I, 3R, 3V
Cytochrome b-c1 complex subunit 7 Chains: 3F, 3S
Cytochrome b-c1 complex subunit 8 Chains: 3G, 3T
Cytochrome b-c1 complex subunit 6 Chains: 3H, 3U
Complex III subunit 9 Chains: 3J, 3W
Cytochrome b-c1 complex subunit 10 Chains: 3X, 3Y
Cytochrome c oxidase subunit 1 Chain: 4A
Cytochrome c oxidase subunit 2 Chain: 4B
Cytochrome c oxidase subunit 3 Chain: 4C
Cytochrome c oxidase subunit 4 Chain: 4D
Cytochrome c oxidase subunit 5A, mitochondrial Chain: 4E
Cytochrome c oxidase subunit 5B, mitochondrial Chain: 4F
Cytochrome c oxidase subunit Chain: 4G
Cytochrome c oxidase subunit Chain: 4H
Cytochrome c oxidase subunit 6C Chain: 4I
Cytochrome c oxidase subunit 7A1, mitochondrial Chain: 4J
Cytochrome c oxidase subunit 7B, mitochondrial Chain: 4K
Cytochrome c oxidase subunit 7C, mitochondrial Chain: 4L
Cytochrome c oxidase subunit 8 Chain: 4M
Cytochrome c oxidase subunit NDUFA4 Chain: 4N

Ligands and Environments

24 bound ligands:
Ligand 3PE 27 x 3PE
Ligand PC1 15 x PC1
Ligand SF4 6 x SF4
Ligand FES 4 x FES
Ligand FMN 1 x FMN
Ligand K 1 x K
Ligand CDL 15 x CDL
Ligand GTP 1 x GTP
Ligand MG 2 x MG
Ligand NDP 1 x NDP
Ligand ZN 2 x ZN
Ligand EHZ 2 x EHZ
Ligand AME 1 x AME
Ligand MYR 1 x MYR
Ligand HEM 4 x HEM
Ligand HEC 2 x HEC
Ligand PGV 15 x PGV
Ligand HEA 2 x HEA
Ligand CU 1 x CU
Ligand NA 1 x NA
Ligand CUA 1 x CUA
Ligand PSC 1 x PSC
Ligand PEK 2 x PEK
Ligand PO4 1 x PO4
1 modified residue:
Ligand FME 7 x FME

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 2.1Å
Relevant EMDB volumes: EMD-42226

Quick links

Citations

4 citation in other articles

Structure of the flotillin complex in a native membrane environment.
Fu et al. (2024)
3 more