› 7aqq

Electron Microscopy
3.06Å resolution

Cryo-EM structure of Arabidopsis thaliana Complex-I (membrane core)

Released:
DOI: 10.2210/pdb7aqq/pdb
PDB entry 7aqq coloured by chain, front view.
PDB entry 7aqq coloured by chain, side view.
PDB entry 7aqq coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
A ferredoxin bridge connects the two arms of plant mitochondrial complex I.
Klusch N, Senkler J, Yildiz Ö, Kühlbrandt W, Braun HP
OpenAccess logo Plant Cell 33 2072-2091 (2021)
PMID: 33768254
Related structures: EMD-11872

Function and Biology Details

Reaction catalysed: 
NADH + ubiquinone + 5 H(+)(Side 1) = NAD(+) + ubiquinol + 4 H(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 21-mer (preferred)
PDBe Complex ID:
PDB-CPX-126463 (preferred)
Entry contents:
21 distinct polypeptide molecules
Macromolecules (21 distinct):
NADH-ubiquinone oxidoreductase chain 3 Chain: A
Molecule details ›
Chain: A
Length: 119 amino acids
Theoretical weight: 13.94 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-ubiquinone oxidoreductase chain 1 Chain: H
Molecule details ›
Chain: H
Length: 325 amino acids
Theoretical weight: 36.02 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P92558 (Residues: 1-325; Coverage: 100%)
Gene names: At2g07785, At2g07786, AtMg00516/AtMg01120/AtMg01275, NAD1, ND1
Sequence domains: NADH dehydrogenase
NADH-ubiquinone oxidoreductase chain 6 Chain: J
Molecule details ›
Chain: J
Length: 205 amino acids
Theoretical weight: 23.69 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P60497 (Residues: 1-205; Coverage: 100%)
Gene names: AtMg00270, NAD6, ND6
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 6
NADH-ubiquinone oxidoreductase chain 4L Chain: K
Molecule details ›
Chain: K
Length: 100 amino acids
Theoretical weight: 11.17 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q04614 (Residues: 1-100; Coverage: 100%)
Gene names: AtMg00650, NAD4L, ND4L
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
NADH-ubiquinone oxidoreductase chain 5 Chain: L
Molecule details ›
Chain: L
Length: 669 amino acids
Theoretical weight: 74.5 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P29388 (Residues: 1-669; Coverage: 100%)
Gene names: AtMg00060/AtMg00513/AtMg00665, NAD5, NAD5C, ND5
Sequence domains:
NADH-ubiquinone oxidoreductase chain 4 Chain: M
Molecule details ›
Chain: M
Length: 495 amino acids
Theoretical weight: 56.06 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P93313 (Residues: 1-495; Coverage: 100%)
Gene names: AtMg00580, NAD4, ND4
Sequence domains: Proton-conducting membrane transporter
NADH-ubiquinone oxidoreductase chain 2 Chain: N
Molecule details ›
Chain: N
Length: 499 amino acids
Theoretical weight: 55.49 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: O05000 (Residues: 1-499; Coverage: 100%)
Gene names: AtMg00285/AtMg01320, NAD2, ND2
Sequence domains: Proton-conducting membrane transporter
F21O3.19 protein Chain: O
Molecule details ›
Chain: O
Length: 159 amino acids
Theoretical weight: 17.63 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SRR8 (Residues: 1-159; Coverage: 100%)
Gene names: At3g07480, F21O3.19
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B Chain: X
Molecule details ›
Chain: X
Length: 106 amino acids
Theoretical weight: 11.99 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q8LGE7 (Residues: 1-106; Coverage: 100%)
Gene names: At5g18800, F17K4.50
Sequence domains: CHCH domain
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A Chain: Z
Molecule details ›
Chain: Z
Length: 143 amino acids
Theoretical weight: 16.15 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q8RWA7 (Residues: 1-143; Coverage: 100%)
Gene names: At1g04630, MEE4, T1G11.12
Sequence domains: GRIM-19 protein
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 Chain: a
Molecule details ›
Chain: a
Length: 65 amino acids
Theoretical weight: 7.35 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9C9Z5 (Residues: 1-65; Coverage: 100%)
Gene names: At3g08610, F17O14.8
Sequence domains: NADH-ubiquinone oxidoreductase MWFE subunit
At2g46540/F11C10.23 Chain: b
Molecule details ›
Chain: b
Length: 65 amino acids
Theoretical weight: 6.81 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9ZPY5 (Residues: 1-65; Coverage: 100%)
Gene names: At2g46540, F13A10.7, F13A10_7
Excitatory amino acid transporter Chain: d
Molecule details ›
Chain: d
Length: 81 amino acids
Theoretical weight: 9.22 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q94AL6 (Residues: 1-81; Coverage: 100%)
Gene names: At4g20150, F1C12.70, F1C12_70
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B Chain: e
Molecule details ›
Chain: e
Length: 83 amino acids
Theoretical weight: 9.91 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9LZI6 (Residues: 1-83; Coverage: 100%)
Gene names: At3g62790, F26K9_220
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFS5-15kDa
NADH-ubiquinone oxidoreductase 21kDa subunit N-terminal domain-containing protein Chain: f
Molecule details ›
Chain: f
Length: 106 amino acids
Theoretical weight: 11.36 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q84W12 (Residues: 1-106; Coverage: 100%)
Gene names: At4g16450, DL4250W, FCAALL.388
Sequence domains: NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit
F1N21.17 Chain: i
Molecule details ›
Chain: i
Length: 98 amino acids
Theoretical weight: 11.81 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9FYF8 (Residues: 1-98; Coverage: 100%)
Gene names: At1g67350, F1N21.17
Sequence domains: NADH-ubiquinone oxidoreductase 11 kDa subunit
unknown Chain: u
Molecule details ›
Chain: u
Length: 30 amino acids
Theoretical weight: 2.57 KDa
Source organism: Arabidopsis thaliana
Uncharacterized protein At2g27730, mitochondrial Chain: v
Molecule details ›
Chain: v
Length: 113 amino acids
Theoretical weight: 11.97 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9ZUX4 (Residues: 1-113; Coverage: 100%)
Gene names: At2g27730, F15K20.17
Gamma carbonic anhydrase-like 2, mitochondrial Chain: x
Molecule details ›
Chain: x
Length: 256 amino acids
Theoretical weight: 27.99 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SMN1 (Residues: 1-256; Coverage: 100%)
Gene names: At3g48680, GAMMACAL2, T8P19.190
Gamma carbonic anhydrase 2, mitochondrial Chain: y
Molecule details ›
Chain: y
Length: 278 amino acids
Theoretical weight: 30.1 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9C6B3 (Residues: 1-278; Coverage: 100%)
Gene names: APFI, At1g47260, F8G22.2, GAMMACA2
Sequence domains: Bacterial transferase hexapeptide (six repeats)
Gamma carbonic anhydrase 1, mitochondrial Chain: z
Molecule details ›
Chain: z
Length: 275 amino acids
Theoretical weight: 30.01 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9FWR5 (Residues: 1-275; Coverage: 100%)
Gene names: At1g19580, F14P1.8, F18O14.34, GAMMACA1

Ligands and Environments

9 bound ligands:
Ligand UQ9 1 x UQ9
Ligand PTY 2 x PTY
Ligand LMN 1 x LMN
Ligand FE 1 x FE
Ligand PC7 1 x PC7
Ligand ZN 1 x ZN
Ligand PGT 1 x PGT
Ligand PSF 1 x PSF
Ligand T7X 1 x T7X
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.06Å
Relevant EMDB volumes: EMD-11872

Quick links

Citations

11 review citations

Structure of respiratory complex I - An emerging blueprint for the mechanism.
Kampjut et al. (2022)
10 more