› 6khi

Electron Microscopy
3Å resolution

Supercomplex for cylic electron transport in cyanobacteria

Released:
DOI: 10.2210/pdb6khi/pdb
PDB entry 6khi coloured by chain, front view.
PDB entry 6khi coloured by chain, side view.
PDB entry 6khi coloured by chain, top view.
Source organism: Thermosynechococcus vestitus BP-1
Primary publication:
Structural basis for electron transport mechanism of complex I-like photosynthetic NAD(P)H dehydrogenase.
Pan X, Cao D, Xie F, Xu F, Su X, Mi H, Zhang X, Li M
Nat Commun 11 610 (2020)
PMID: 32001694
Related structures: EMD-9989

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero icosamer (preferred)
PDBe Complex ID:
PDB-CPX-141199 (preferred)
Entry contents:
20 distinct polypeptide molecules
Macromolecules (20 distinct):
NAD(P)H-quinone oxidoreductase subunit 1 Chain: A
Molecule details ›
Chain: A
Length: 372 amino acids
Theoretical weight: 40.57 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DL32 (Residues: 1-372; Coverage: 100%)
Gene names: ndhA, tlr0667
Sequence domains: NADH dehydrogenase
NAD(P)H-quinone oxidoreductase subunit 2 Chain: B
Molecule details ›
Chain: B
Length: 515 amino acids
Theoretical weight: 55.17 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DMR6 (Residues: 1-515; Coverage: 100%)
Gene names: ndhB, tll0045
Sequence domains:
NAD(P)H-quinone oxidoreductase subunit 3 Chain: C
Molecule details ›
Chain: C
Length: 132 amino acids
Theoretical weight: 15.01 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DJ02 (Residues: 1-132; Coverage: 100%)
Gene names: ndhC, tlr1429
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
NAD(P)H-quinone oxidoreductase chain 4 1 Chain: D
Molecule details ›
Chain: D
Length: 529 amino acids
Theoretical weight: 57.85 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DKY0 (Residues: 1-529; Coverage: 100%)
Gene names: ndhD1, tll0719
Sequence domains: Proton-conducting membrane transporter
NAD(P)H-quinone oxidoreductase subunit 4L Chain: E
Molecule details ›
Chain: E
Length: 101 amino acids
Theoretical weight: 11.14 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DL29 (Residues: 1-101; Coverage: 100%)
Gene name: ndhE
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
NADH dehydrogenase subunit 5 Chain: F
Molecule details ›
Chain: F
Length: 656 amino acids
Theoretical weight: 72.03 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DKX9 (Residues: 1-656; Coverage: 100%)
Gene name: ndhF1
Sequence domains:
NADH-quinone oxidoreductase subunit J Chain: G
Molecule details ›
Chain: G
Length: 200 amino acids
Theoretical weight: 21.58 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DL30 (Residues: 1-200; Coverage: 100%)
Gene name: ndhG
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 6
NAD(P)H-quinone oxidoreductase subunit H Chain: H
Molecule details ›
Chain: H
Length: 394 amino acids
Theoretical weight: 45.27 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DJD9 (Residues: 1-394; Coverage: 100%)
Gene names: ndhH, tlr1288
Sequence domains: Respiratory-chain NADH dehydrogenase, 49 Kd subunit
NAD(P)H-quinone oxidoreductase subunit I Chain: I
Molecule details ›
Chain: I
Length: 196 amino acids
Theoretical weight: 22.44 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DL31 (Residues: 1-196; Coverage: 100%)
Gene names: ndhI, tlr0668
Sequence domains: 4Fe-4S dicluster domain
NAD(P)H-quinone oxidoreductase subunit J Chain: J
Molecule details ›
Chain: J
Length: 168 amino acids
Theoretical weight: 19.36 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DJ01 (Residues: 1-168; Coverage: 100%)
Gene names: ndhJ, tlr1430
Sequence domains: Respiratory-chain NADH dehydrogenase, 30 Kd subunit
NAD(P)H-quinone oxidoreductase subunit K Chain: K
Molecule details ›
Chain: K
Length: 237 amino acids
Theoretical weight: 25.77 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DKZ4 (Residues: 1-237; Coverage: 100%)
Gene names: ndhK, tlr0705
Sequence domains: NADH ubiquinone oxidoreductase, 20 Kd subunit
NAD(P)H-quinone oxidoreductase subunit L Chain: L
Molecule details ›
Chain: L
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DKZ3 (Residues: 1-76; Coverage: 100%)
Gene names: ndhL, tsr0706
Sequence domains: NADH dehydrogenase transmembrane subunit
NAD(P)H-quinone oxidoreductase subunit M Chain: M
Molecule details ›
Chain: M
Length: 111 amino acids
Theoretical weight: 12.58 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DLN5 (Residues: 1-111; Coverage: 100%)
Gene names: ndhM, tll0447
Sequence domains: Cyanobacterial and plastid NDH-1 subunit M
NAD(P)H-quinone oxidoreductase subunit N Chain: N
Molecule details ›
Chain: N
Length: 150 amino acids
Theoretical weight: 16.66 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DJU2 (Residues: 1-150; Coverage: 100%)
Gene names: ndhN, tlr1130
Sequence domains: NADH-quinone oxidoreductase cyanobacterial subunit N
NAD(P)H-quinone oxidoreductase subunit O Chain: O
Molecule details ›
Chain: O
Length: 70 amino acids
Theoretical weight: 7.88 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DMU4 (Residues: 1-70; Coverage: 100%)
Gene names: ndhO, tsl0017
Sequence domains: Cyanobacterial and plant NDH-1 subunit O
Proton-translocating NADH-quinone dehydrogenase subunit P NdhP Chain: P
Molecule details ›
Chain: P
Length: 44 amino acids
Theoretical weight: 4.88 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: V5V507 (Residues: 1-44; Coverage: 100%)
Gene names: NK55_02900, ndhP
Proton-translocating NADH-quinone dehydrogenase subunit Q NdhQ Chain: Q
Molecule details ›
Chain: Q
Length: 45 amino acids
Theoretical weight: 4.86 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: V5V791 (Residues: 1-45; Coverage: 100%)
Gene names: NK55_09855, ndhQ
DUF3252 domain-containing protein Chain: S
Molecule details ›
Chain: S
Length: 110 amino acids
Theoretical weight: 12.46 KDa
Source organism: Thermosynechococcus vestitus BP-1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8DL61 (Residues: 1-110; Coverage: 100%)
Gene name: tlr0636
Sequence domains: NAD(P)H dehydrogenase subunit S
DUF2996 domain-containing protein Chain: V
Molecule details ›
Chain: V
Length: 146 amino acids
Theoretical weight: 16.02 KDa
Source organism: Thermosynechococcus vestitus BP-1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8DLL4 (Residues: 1-146; Coverage: 100%)
Gene name: tlr0472
Sequence domains: Protein of unknown function (DUF2996)
Ferredoxin-1 Chain: 1
Molecule details ›
Chain: 1
Length: 98 amino acids
Theoretical weight: 10.85 KDa
Source organism: Thermosynechococcus vestitus BP-1
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A3C9 (Residues: 1-98; Coverage: 100%)
Gene names: petF, petF1, tsl1009
Sequence domains: 2Fe-2S iron-sulfur cluster binding domain

Ligands and Environments

7 bound ligands:
Ligand DGD 2 x DGD
Ligand LHG 6 x LHG
Ligand SQD 3 x SQD
Ligand BCR 2 x BCR
Ligand LMG 2 x LMG
Ligand SF4 3 x SF4
Ligand FES 1 x FES
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3Å
Relevant EMDB volumes: EMD-9989
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Architecture of bacterial respiratory chains.
Kaila et al. (2021)
6 more

2 mentions without citation

Structural basis for electron transport mechanism of complex I-like photosynthetic NAD(P)H dehydrogenase.
Pan et al. (2020)
1 more