› 5xti

Electron Microscopy
17.4Å resolution

Cryo-EM architecture of human respiratory chain megacomplex-I2III2IV2

Released:
DOI: 10.2210/pdb5xti/pdb
PDB entry 5xti coloured by chain, front view.
PDB entry 5xti coloured by chain, side view.
PDB entry 5xti coloured by chain, top view.
Source organisms:
Primary publication:
Architecture of Human Mitochondrial Respiratory Megacomplex I2III2IV2.
Guo R, Zong S, Wu M, Gu J, Yang M
Cell 170 1247-1257.e12 (2017)
PMID: 28844695
Related structures: EMD-6776

Function and Biology Details

Reactions catalysed: 
NADH + ubiquinone + 5 H(+)(Side 1) = NAD(+) + ubiquinol + 4 H(+)(Side 2)
4 ferrocytochrome c + O(2) + 8 H(+)(Side 1) = 4 ferricytochrome c + 4 H(2)O(Side 2)
Quinol + 2 ferricytochrome c(Side 2) = quinone + 2 ferrocytochrome c(Side 2) + 2 H(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 138-mer (preferred)
PDBe Complex ID:
PDB-CPX-110814 (preferred)
Entry contents:
68 distinct polypeptide molecules
Macromolecules (68 distinct):
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Chains: A, BA
Molecule details ›
Chains: A, BA
Length: 431 amino acids
Theoretical weight: 47.32 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P49821 (Residues: 27-457; Coverage: 93%)
Gene names: NDUFV1, UQOR1
Sequence domains:
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial Chains: B, BB
Molecule details ›
Chains: B, BB
Length: 176 amino acids
Theoretical weight: 20.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O00217 (Residues: 35-210; Coverage: 84%)
Gene name: NDUFS8
Sequence domains: 4Fe-4S dicluster domain
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial Chains: BC, C
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 Chains: BE, E
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 Chains: BF, F
Acyl carrier protein, mitochondrial Chains: BG, BX, G, X
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 Chains: BH, H
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 Chains: BI, I
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial Chains: BJ, J
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial Chains: BK, K
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial Chains: BL, L
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial Chains: BM, M
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 Chains: BN, N
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial Chains: BO, O
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial Chains: BP, P
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial Chains: BQ, Q
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 Chains: BS, S
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial Chains: BT, T
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 Chains: BU, U
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 Chains: BV, V
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 Chains: BW, W
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial Chains: BY, Y
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 Chains: BZ, Z
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial Chains: Ba, a
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 Chains: Bb, b
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial Chains: Bc, c
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 Chains: Bd, d
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial Chains: Be, e
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial Chains: Bf, f
NADH dehydrogenase [ubiquinone] 1 subunit C2 Chains: Bg, g
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 Chains: Bh, h
NADH-ubiquinone oxidoreductase chain 2 Chains: Bi, i
NADH-ubiquinone oxidoreductase chain 3 Chains: Bj, j
NADH-ubiquinone oxidoreductase chain 4L Chains: Bk, k
NADH-ubiquinone oxidoreductase chain 5 Chains: Bl, l
NADH-ubiquinone oxidoreductase chain 6 Chains: Bm, m
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 Chains: Bn, n
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 Chains: Bo, o
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 Chains: Bp, p
NADH-ubiquinone oxidoreductase chain 4 Chains: Br, r
NADH-ubiquinone oxidoreductase chain 1 Chains: Bs, s
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 Chains: Bu, u
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 Chains: Bv, v
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial Chains: Bw, w
Cytochrome c oxidase subunit 1 Chains: Bx, x
Cytochrome c oxidase subunit 2 Chains: By, y
Cytochrome c oxidase subunit 3 Chains: Bz, z
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial Chains: 0, B0
Cytochrome c oxidase subunit 5A, mitochondrial Chains: 1, B1
Cytochrome c oxidase subunit 5B, mitochondrial Chains: 2, B2
Cytochrome c oxidase subunit 6A2, mitochondrial Chains: 3, B3
Cytochrome c oxidase subunit 6B1 Chains: 4, B4
Cytochrome c oxidase subunit 6C Chains: 5, B5
Cytochrome c oxidase subunit 7A1, mitochondrial Chains: 6, B6
Cytochrome c oxidase subunit 7B, mitochondrial Chains: 7, B7
Cytochrome c oxidase subunit 7C, mitochondrial Chains: 8, B8
Cytochrome c oxidase subunit 8B, mitochondrial Chains: 9, B9
Cytochrome b-c1 complex subunit 8 Chains: AA, AN
Cytochrome b-c1 complex subunit 9 Chains: AB, AO
Cytochrome b-c1 complex subunit Rieske, mitochondrial Chains: AC, AP
Cytochrome b-c1 complex subunit 9 Chains: AD, AQ
Cytochrome b-c1 complex subunit 6, mitochondrial Chains: AE, AR
Cytochrome b-c1 complex subunit 7 Chains: AF, AS
Cytochrome b-c1 complex subunit 10 Chains: AG, AT
Cytochrome c1, heme protein, mitochondrial Chains: AH, AU
Cytochrome b Chains: AJ, AV
Cytochrome b-c1 complex subunit 2, mitochondrial Chains: AK, AW
Cytochrome b-c1 complex subunit 1, mitochondrial Chains: AL, AY

Ligands and Environments

14 bound ligands:
Ligand SF4 12 x SF4
Ligand FMN 2 x FMN
Ligand PLX 21 x PLX
Ligand 8Q1 4 x 8Q1
Ligand NDP 2 x NDP
Ligand FES 6 x FES
Ligand CDL 19 x CDL
Ligand PEE 14 x PEE
Ligand CU 6 x CU
Ligand MG 2 x MG
Ligand HEA 4 x HEA
Ligand ZN 2 x ZN
Ligand HEC 2 x HEC
Ligand HEM 4 x HEM
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 17.4Å
Relevant EMDB volumes: EMD-6776

Quick links

Citations

73 review citations

The assembly, regulation and function of the mitochondrial respiratory chain.
Vercellino et al. (2022)
72 more

9 mentions without citation

Structure and Mechanism of Respiratory III-IV Supercomplexes in Bioenergetic Membranes.
Brzezinski et al. (2021)
8 more