› 8bpx

Electron Microscopy
2.09Å resolution

Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete composition)

Released:
DOI: 10.2210/pdb8bpx/pdb
PDB entry 8bpx coloured by chain, front view.
PDB entry 8bpx coloured by chain, side view.
PDB entry 8bpx coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Cryo-EM structure of the respiratory I + III2 supercomplex from Arabidopsis thaliana at 2 Å resolution.
Klusch N, Dreimann M, Senkler J, Rugen N, Kühlbrandt W, Braun HP
OpenAccess logo Nat Plants (2022)
PMID: 36585502
Related structures: EMD-16168

Function and Biology Details

Reactions catalysed: 
NADH + ubiquinone + 5 H(+)(Side 1) = NAD(+) + ubiquinol + 4 H(+)(Side 2)
Release of N-terminal targeting peptides from precursor proteins imported into the mitochondrion, typically with Arg in position P2.
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 67-mer (preferred)
PDBe Complex ID:
PDB-CPX-123483 (preferred)
Entry contents:
57 distinct polypeptide molecules
Macromolecules (57 distinct):
NADH-ubiquinone oxidoreductase chain 3 Chain: A
Molecule details ›
Chain: A
Length: 119 amino acids
Theoretical weight: 13.97 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P92533 (Residues: 1-119; Coverage: 100%)
Gene names: AtMg00990, NAD3, ND3
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 218 amino acids
Theoretical weight: 24.07 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q42577 (Residues: 1-218; Coverage: 100%)
Gene names: At5g11770, T22P22_160
Sequence domains: NADH ubiquinone oxidoreductase, 20 Kd subunit
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 Chain: C
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 Chain: D
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial Chain: E
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Chain: F
NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial Chain: G
NADH-ubiquinone oxidoreductase chain 1 Chain: H
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial Chain: I
NADH-ubiquinone oxidoreductase chain 6 Chain: J
NADH-ubiquinone oxidoreductase chain 4L Chain: K
NADH-ubiquinone oxidoreductase chain 5 Chain: L
NADH-ubiquinone oxidoreductase chain 4 Chain: M
NADH-ubiquinone oxidoreductase chain 2 Chain: N
F21O3.19 protein Chain: O
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial Chain: P
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial Chain: Q
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial Chain: R
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 Chain: S
Acyl carrier protein 1, mitochondrial Chain: T
Acyl carrier protein 2, mitochondrial Chain: U
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial Chain: V
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 Chain: W
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B Chain: X
Outer envelope pore protein 16-3, chloroplastic/mitochondrial Chain: Y
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A Chain: Z
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 Chain: a
Expressed protein Chain: b
Transmembrane protein Chain: c
Excitatory amino acid transporter Chain: d
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B Chain: e
NADH-ubiquinone oxidoreductase 21kDa subunit N-terminal domain-containing protein Chain: f
ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein Chain: g
F1N21.17 Chain: i
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 Chain: j
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A Chain: k
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial Chain: l
Expressed protein Chain: m
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 Chain: n
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 Chain: o
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B Chain: p
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 Chain: q
Transmembrane protein Chain: u
Uncharacterized protein At2g27730, mitochondrial Chain: v
Gamma carbonic anhydrase-like 2, mitochondrial Chain: x
Gamma carbonic anhydrase 2, mitochondrial Chain: y
Gamma carbonic anhydrase 1, mitochondrial Chain: z
Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrial Chains: AA, BA
Probable mitochondrial-processing peptidase subunit beta, mitochondrial Chains: AB, BB
Cytochrome b Chains: AC, BC
Cytochrome b-c1 complex subunit Rieske-1, mitochondrial Chains: AD, BD
Cytochrome c1 2, heme protein, mitochondrial Chains: AE, BE
Cytochrome b-c1 complex subunit 7-2, mitochondrial Chains: AF, BF
Cytochrome b-c1 complex subunit 8-1, mitochondrial Chains: AG, BG
Cytochrome b-c1 complex subunit 6-1, mitochondrial Chains: AH, BH
Cytochrome b-c1 complex subunit 9, mitochondrial Chains: AI, BI
Cytochrome b-c1 complex subunit 10, mitochondrial Chains: AJ, BJ

Ligands and Environments

18 bound ligands:
Ligand PGT 10 x PGT
Ligand SF4 6 x SF4
Ligand PTY 14 x PTY
Ligand FES 4 x FES
Ligand FMN 1 x FMN
Ligand UQ9 1 x UQ9
Ligand Q7G 6 x Q7G
Ligand 3PH 11 x 3PH
Ligand PC7 9 x PC7
Ligand UQ5 4 x UQ5
Ligand FE 1 x FE
Ligand NDP 1 x NDP
Ligand ZN 4 x ZN
Ligand 8Q1 2 x 8Q1
Ligand CDL 9 x CDL
Ligand COO 1 x COO
Ligand HEM 6 x HEM
Ligand UQ7 1 x UQ7
1 modified residue:
Ligand FME 3 x FME

Experiments and Validation Details

Entry percentile scores
Resolution: 2.09Å
Relevant EMDB volumes: EMD-16168

Quick links

Citations

2 review citations

An evolving view of complex II-noncanonical complexes, megacomplexes, respiration, signaling, and beyond.
Iverson et al. (2023)
1 more

4 mentions without citation

The biogenesis and regulation of the plant oxidative phosphorylation system.
Ghifari et al. (2023)
3 more