› 7f9o

Electron Microscopy
4.5Å resolution

PSI-NDH supercomplex of Barley

Released:
DOI: 10.2210/pdb7f9o/pdb
PDB entry 7f9o coloured by chain, front view.
PDB entry 7f9o coloured by chain, side view.
PDB entry 7f9o coloured by chain, top view.
Source organism: Hordeum vulgare subsp. spontaneum
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-31498

Function and Biology Details

Reactions catalysed: 
Reduced plastocyanin + oxidized ferredoxin + light = oxidized plastocyanin + reduced ferredoxin
NADH + ubiquinone + 5 H(+)(Side 1) = NAD(+) + ubiquinol + 4 H(+)(Side 2)
Peptidylproline (omega=180) = peptidylproline (omega=0)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 55-mer (preferred)
PDBe Complex ID:
PDB-CPX-103928 (preferred)
Entry contents:
42 distinct polypeptide molecules
Macromolecules (42 distinct):
Photosystem I P700 chlorophyll a apoprotein A1 Chains: A, e
Molecule details ›
Chains: A, e
Length: 750 amino acids
Theoretical weight: 83.22 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: S4Z1K7 (Residues: 1-750; Coverage: 100%)
Gene name: psaA
Sequence domains: Photosystem I psaA/psaB protein
Photosystem I P700 chlorophyll a apoprotein A2 Chains: B, f
Molecule details ›
Chains: B, f
Length: 734 amino acids
Theoretical weight: 82.69 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: S4Z289 (Residues: 1-734; Coverage: 100%)
Gene name: psaB
Sequence domains: Photosystem I psaA/psaB protein
Photosystem I iron-sulfur center Chains: C, g
Molecule details ›
Chains: C, g
Length: 81 amino acids
Theoretical weight: 8.91 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: S4YZ47 (Residues: 1-81; Coverage: 100%)
Gene name: psaC
Sequence domains: 4Fe-4S dicluster domain
Photosystem I reaction center subunit II, chloroplastic Chains: D, h
Molecule details ›
Chains: D, h
Length: 205 amino acids
Theoretical weight: 21.96 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: P36213 (Residues: 1-205; Coverage: 100%)
Gene name: psaD
Sequence domains: PsaD
Photosystem I reaction center subunit IV, chloroplastic Chains: E, i
Molecule details ›
Chains: E, i
Length: 147 amino acids
Theoretical weight: 15.48 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: P13194 (Residues: 1-147; Coverage: 100%)
Gene name: PSAE
Sequence domains: Photosystem I reaction centre subunit IV / PsaE
Photosystem I reaction center subunit III, chloroplastic Chains: F, j
Molecule details ›
Chains: F, j
Length: 235 amino acids
Theoretical weight: 24.87 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: P13192 (Residues: 1-235; Coverage: 100%)
Gene name: PSAF
Sequence domains: Photosystem I reaction centre subunit III
Photosystem I reaction center subunit VI, chloroplastic Chains: H, k
Molecule details ›
Chains: H, k
Length: 143 amino acids
Theoretical weight: 14.9 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: P20143 (Residues: 1-143; Coverage: 100%)
Gene name: PSAH
Sequence domains: Photosystem I reaction centre subunit VI
Photosystem I reaction center subunit VIII Chains: I, l
Molecule details ›
Chains: I, l
Length: 36 amino acids
Theoretical weight: 4.01 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: S4Z1D9 (Residues: 1-36; Coverage: 100%)
Gene name: psaI
Sequence domains: Photosystem I reaction centre subunit VIII
Photosystem I reaction center subunit IX Chains: J, m
Molecule details ›
Chains: J, m
Length: 42 amino acids
Theoretical weight: 4.75 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: S4Z1E9 (Residues: 1-42; Coverage: 100%)
Gene name: psaJ
Sequence domains: Photosystem I reaction centre subunit IX / PsaJ
Photosystem I reaction center subunit psaK, chloroplastic Chains: K, n
Molecule details ›
Chains: K, n
Length: 131 amino acids
Theoretical weight: 13.74 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: P36886 (Residues: 1-131; Coverage: 100%)
Gene name: PSAK
Sequence domains: Photosystem I psaG / psaK
Photosystem I reaction center subunit XI, chloroplastic Chains: L, o
Molecule details ›
Chains: L, o
Length: 209 amino acids
Theoretical weight: 22.23 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: P23993 (Residues: 1-209; Coverage: 100%)
Gene name: PSAL
Sequence domains: Photosystem I reaction centre subunit XI
Chlorophyll a-b binding protein Lhca1 Chains: 1, p
Molecule details ›
Chains: 1, p
Length: 247 amino acids
Theoretical weight: 26.69 KDa
Source organism: Hordeum vulgare subsp. spontaneum
Chlorophyll a-b binding protein, chloroplastic Chain: 2
Molecule details ›
Chain: 2
Length: 255 amino acids
Theoretical weight: 27.32 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: Q43485 (Residues: 1-255; Coverage: 100%)
Gene name: Lhca2
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chains: 3, q
Molecule details ›
Chains: 3, q
Length: 269 amino acids
Theoretical weight: 29.37 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: F2DAN8 (Residues: 1-269; Coverage: 100%)
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein Lhca5 Chain: 5
Molecule details ›
Chain: 5
Length: 257 amino acids
Theoretical weight: 27.62 KDa
Source organism: Hordeum vulgare subsp. spontaneum
NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic Chain: G
Molecule details ›
Chain: G
Length: 346 amino acids
Theoretical weight: 38.54 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: P92432 (Residues: 15-360; Coverage: 96%)
Gene name: ndhA
Sequence domains: NADH dehydrogenase
NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic Chain: M
Molecule details ›
Chain: M
Length: 483 amino acids
Theoretical weight: 53.45 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: S4Z268 (Residues: 28-510; Coverage: 95%)
Gene name: ndhB
Sequence domains:
NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic Chain: N
Molecule details ›
Chain: N
Length: 117 amino acids
Theoretical weight: 13.3 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: S4Z1L1 (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: O
Molecule details ›
Chain: O
Length: 499 amino acids
Theoretical weight: 56.22 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: S4Z8N2 (Residues: 2-500; Coverage: 100%)
Gene name: ndhD
Sequence domains: Proton-conducting membrane transporter
NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic Chain: P
Molecule details ›
Chain: P
Length: 100 amino acids
Theoretical weight: 11.2 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: S4Z1I1 (Residues: 1-100; Coverage: 99%)
Gene name: ndhE
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic Chain: Q
Molecule details ›
Chain: Q
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: R
Molecule details ›
Chain: R
Length: 176 amino acids
Theoretical weight: 19.59 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: A0A4Y5SEJ9 (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: S
Molecule details ›
Chain: S
Length: 383 amino acids
Theoretical weight: 44.56 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: S4Z272 (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: T
Molecule details ›
Chain: T
Length: 165 amino acids
Theoretical weight: 19.27 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: A0A218LNN1 (Residues: 3-167; Coverage: 92%)
Gene name: ndhI
Sequence domains: 4Fe-4S dicluster domain
NAD(P)H-quinone oxidoreductase subunit J, chloroplastic Chain: U
Molecule details ›
Chain: U
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: V
Molecule details ›
Chain: V
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: W
Molecule details ›
Chain: W
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: X
Molecule details ›
Chain: X
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, chloroplastic Chain: Y
Molecule details ›
Chain: Y
Length: 233 amino acids
Theoretical weight: 25.93 KDa
Source organism: Hordeum vulgare subsp. spontaneum
Unidentified stromal protein Chain: Z
Molecule details ›
Chain: Z
Length: 61 amino acids
Theoretical weight: 5.21 KDa
Source organism: Hordeum vulgare subsp. spontaneum
Photosynthetic NDH subunit of subcomplex L1 Chain: a
Molecule details ›
Chain: a
Length: 154 amino acids
Theoretical weight: 17.84 KDa
Source organism: Hordeum vulgare subsp. spontaneum
Photosynthetic NDH subunit of lumenal location 2, chloroplastic Chain: b
Molecule details ›
Chain: b
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 L2 Chain: c
Molecule details ›
Chain: c
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: d
Molecule details ›
Chain: d
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%)
2Fe-2S ferredoxin-type domain-containing protein Chain: 8
Molecule details ›
Chain: 8
Length: 119 amino acids
Theoretical weight: 13.31 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: F2DD79 (Residues: 78-196; Coverage: 61%)
Sequence domains: 2Fe-2S iron-sulfur cluster binding domain
Photosynthetic NDH subunit of subcomplex B4 Chain: 9
Molecule details ›
Chain: 9
Length: 83 amino acids
Theoretical weight: 9.76 KDa
Source organism: Hordeum vulgare subsp. spontaneum
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%)
Chlorophyll a-b binding protein, chloroplastic Chain: r
Molecule details ›
Chain: r
Length: 197 amino acids
Theoretical weight: 21.98 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: Q9LKC7 (Residues: 29-225; Coverage: 86%)
Gene name: Lhca4
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chain: s
Molecule details ›
Chain: s
Length: 211 amino acids
Theoretical weight: 23.9 KDa
Source organism: Hordeum vulgare subsp. spontaneum
UniProt:
  • Canonical: F2D0D5 (Residues: 56-266; Coverage: 78%)
Sequence domains: Chlorophyll A-B binding protein

Ligands and Environments

12 bound ligands:
Ligand CL0 2 x CL0
Ligand CLA 273 x CLA
Ligand PQN 4 x PQN
Ligand LHG 11 x LHG
Ligand BCR 51 x BCR
Ligand SF4 7 x SF4
Ligand DGD 4 x DGD
Ligand LMG 7 x LMG
Ligand LUT 12 x LUT
Ligand CHL 23 x CHL
Ligand XAT 4 x XAT
Ligand SQD 2 x SQD
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.5Å
Relevant EMDB volumes: EMD-31498

Quick links

Citations

2 review citations

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