› 7eu3

Electron Microscopy
3.7Å resolution

Chloroplast NDH complex

Released:
DOI: 10.2210/pdb7eu3/pdb
PDB entry 7eu3 coloured by chain, front view.
PDB entry 7eu3 coloured by chain, side view.
PDB entry 7eu3 coloured by chain, top view.
Source organisms:
Primary publication:
Architecture of the chloroplast PSI-NDH supercomplex in Hordeum vulgare.
Shen L, Tang K, Wang W, Wang C, Wu H, Mao Z, An S, Chang S, Kuang T, Shen JR, Han G, Zhang X
Nature 601 649-654 (2022)
PMID: 34879391
Related structures: EMD-31307

Function and Biology Details

Reaction catalysed: 
Peptidylproline (omega=180) = peptidylproline (omega=0)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 25-mer (preferred)
PDBe Complex ID:
PDB-CPX-105901 (preferred)
Entry contents:
25 distinct polypeptide molecules
Macromolecules (25 distinct):
NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic Chain: A
Molecule details ›
Chain: A
Length: 346 amino acids
Theoretical weight: 38.54 KDa
Source organism: Hordeum vulgare
UniProt:
  • Canonical: P92432 (Residues: 15-360; Coverage: 96%)
Gene name: ndhA
Sequence domains: NADH dehydrogenase
NAD(P)H-quinone oxidoreductase subunit 2 A, chloroplastic Chain: B
Molecule details ›
Chain: B
Length: 483 amino acids
Theoretical weight: 53.45 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: P0CC72 (Residues: 28-510; Coverage: 95%)
Gene name: ndhB1
Sequence domains:
NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic Chain: C
Molecule details ›
Chain: C
Length: 117 amino acids
Theoretical weight: 13.3 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: A1E9J6 (Residues: 4-120; Coverage: 98%)
Gene name: ndhC
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
NAD(P)H-quinone oxidoreductase chain 4, chloroplastic Chain: D
Molecule details ›
Chain: D
Length: 499 amino acids
Theoretical weight: 56.22 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: O03060 (Residues: 2-500; Coverage: 100%)
Gene name: ndhD
Sequence domains: Proton-conducting membrane transporter
NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic Chain: E
Molecule details ›
Chain: E
Length: 100 amino acids
Theoretical weight: 11.2 KDa
Source organism: Hordeum vulgare
UniProt:
  • Canonical: P69378 (Residues: 1-100; Coverage: 99%)
Gene names: ndh4L, ndhE
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic Chain: F
Molecule details ›
Chain: F
Length: 777 amino acids
Theoretical weight: 87.55 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: A0A7T7JN26 (Residues: 1-777; Coverage: 100%)
Gene name: ndhF
Sequence domains:
NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic Chain: G
Molecule details ›
Chain: G
Length: 176 amino acids
Theoretical weight: 19.59 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: O98693 (Residues: 1-176; Coverage: 100%)
Gene name: ndhG
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 6
NAD(P)H-quinone oxidoreductase subunit H, chloroplastic Chain: H
Molecule details ›
Chain: H
Length: 383 amino acids
Theoretical weight: 44.56 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: O98691 (Residues: 11-393; Coverage: 98%)
Gene name: ndhH
Sequence domains: Respiratory-chain NADH dehydrogenase, 49 Kd subunit
NAD(P)H-quinone oxidoreductase subunit I, chloroplastic Chain: I
Molecule details ›
Chain: I
Length: 165 amino acids
Theoretical weight: 19.27 KDa
Source organism: Hordeum vulgare
UniProt:
  • Canonical: O98692 (Residues: 3-167; Coverage: 92%)
Gene name: ndhI
Sequence domains: 4Fe-4S dicluster domain
NAD(P)H-quinone oxidoreductase subunit J, chloroplastic Chain: J
Molecule details ›
Chain: J
Length: 159 amino acids
Theoretical weight: 18.73 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: Q7GT16 (Residues: 1-159; Coverage: 100%)
Gene name: ndhJ
Sequence domains: Respiratory-chain NADH dehydrogenase, 30 Kd subunit
NAD(P)H-quinone oxidoreductase subunit K, chloroplastic Chain: K
Molecule details ›
Chain: K
Length: 245 amino acids
Theoretical weight: 27.57 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: S4Z232 (Residues: 1-245; Coverage: 100%)
Gene name: ndhK
Sequence domains: NADH ubiquinone oxidoreductase, 20 Kd subunit
NAD(P)H-quinone oxidoreductase subunit L, chloroplastic Chain: L
Molecule details ›
Chain: L
Length: 192 amino acids
Theoretical weight: 22.24 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: F2CUR7 (Residues: 1-192; Coverage: 100%)
Sequence domains: NADH dehydrogenase transmembrane subunit
NAD(P)H-quinone oxidoreductase subunit M, chloroplastic Chain: M
Molecule details ›
Chain: M
Length: 213 amino acids
Theoretical weight: 24.05 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: F2D138 (Residues: 1-213; Coverage: 100%)
Sequence domains: Cyanobacterial and plastid NDH-1 subunit M
NAD(P)H-quinone oxidoreductase subunit N Chain: N
Molecule details ›
Chain: N
Length: 233 amino acids
Theoretical weight: 25.93 KDa
Source organism: Hordeum vulgare subsp. spontaneum
Unidentified stromal protein Chain: T
Molecule details ›
Chain: T
Length: 61 amino acids
Theoretical weight: 5.21 KDa
Source organism: Hordeum vulgare subsp. spontaneum
PsbP C-terminal domain-containing protein Chain: 1
Molecule details ›
Chain: 1
Length: 154 amino acids
Theoretical weight: 17.84 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: A0A8I6Y1Z8 (Residues: 76-229; Coverage: 67%)
Sequence domains: PsbP
Photosynthetic NDH subunit of lumenal location 2, chloroplastic Chain: 2
Molecule details ›
Chain: 2
Length: 216 amino acids
Theoretical weight: 23.95 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: F2CTW7 (Residues: 1-216; Coverage: 100%)
Sequence domains: Oxygen evolving enhancer protein 3
Photosynthetic NDH subunit of subcomplex L3 Chain: 3
Molecule details ›
Chain: 3
Length: 227 amino acids
Theoretical weight: 24.73 KDa
Source organism: Hordeum vulgare subsp. spontaneum
Photosynthetic NDH subunit of subcomplex L4 Chain: 4
Molecule details ›
Chain: 4
Length: 130 amino acids
Theoretical weight: 13.95 KDa
Source organism: Hordeum vulgare subsp. spontaneum
Peptidyl-prolyl cis-trans isomerase Chain: 5
Molecule details ›
Chain: 5
Length: 243 amino acids
Theoretical weight: 25.82 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: F2CTD7 (Residues: 1-243; Coverage: 100%)
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
Photosynthetic NDH subunit of subcomplex B 1, chloroplastic Chain: 6
Molecule details ›
Chain: 6
Length: 469 amino acids
Theoretical weight: 51.68 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: F2D3G1 (Residues: 1-469; Coverage: 100%)
Photosynthetic NDH subunit of subcomplex B 2, chloroplastic Chain: 7
Molecule details ›
Chain: 7
Length: 361 amino acids
Theoretical weight: 38.08 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: F2D932 (Residues: 1-361; Coverage: 100%)
Photosynthetic NDH subunit of subcomplex B3 Chain: 8
Molecule details ›
Chain: 8
Length: 119 amino acids
Theoretical weight: 13.31 KDa
Source organism: Hordeum vulgare subsp. spontaneum
Photosynthetic NDH subunit of subcomplex B 4, chloroplastic Chain: 9
Molecule details ›
Chain: 9
Length: 83 amino acids
Theoretical weight: 9.76 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: F2CPQ4 (Residues: 70-110, 111-148; Coverage: 44%)
Photosynthetic NDH subunit of subcomplex B 5, chloroplastic Chain: 0
Molecule details ›
Chain: 0
Length: 155 amino acids
Theoretical weight: 18.15 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: F2DWH9 (Residues: 61-215; Coverage: 70%)

Ligands and Environments

4 bound ligands:
Ligand LHG 1 x LHG
Ligand BCR 1 x BCR
Ligand SQD 2 x SQD
Ligand SF4 1 x SF4
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-31307

Quick links

Citations

2 review citations

Cyanobacterial NDH-1 Complexes.
Hualing M. (2022)
1 more