› 7wg5

Electron Microscopy
3.89Å resolution

Cyclic electron transport supercomplex NDH-PSI from Arabidopsis

Released:
DOI: 10.2210/pdb7wg5/pdb
PDB entry 7wg5 coloured by chain, front view.
PDB entry 7wg5 coloured by chain, side view.
PDB entry 7wg5 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Supramolecular assembly of chloroplast NADH dehydrogenase-like complex with photosystem I from Arabidopsis thaliana.
Su X, Cao D, Pan X, Shi L, Liu Z, Dall'Osto L, Bassi R, Zhang X, Li M
Mol Plant 15 454-467 (2022)
PMID: 35123031
Related structures: EMD-32477

Function and Biology Details

Reactions catalysed: 
Reduced plastocyanin + oxidized ferredoxin + light = oxidized plastocyanin + reduced ferredoxin
Peptidylproline (omega=180) = peptidylproline (omega=0)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 58-mer (preferred)
PDBe Complex ID:
PDB-CPX-103144 (preferred)
Entry contents:
44 distinct polypeptide molecules
Macromolecules (44 distinct):
Photosystem I P700 chlorophyll a apoprotein A1 Chains: AA, BA
Molecule details ›
Chains: AA, BA
Length: 750 amino acids
Theoretical weight: 83.32 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P56766 (Residues: 1-750; Coverage: 100%)
Gene names: AtCg00350, psaA
Sequence domains: Photosystem I psaA/psaB protein
Photosystem I P700 chlorophyll a apoprotein A2 Chains: AB, BB
Molecule details ›
Chains: AB, BB
Length: 734 amino acids
Theoretical weight: 82.56 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P56767 (Residues: 1-734; Coverage: 100%)
Gene names: AtCg00340, psaB
Sequence domains: Photosystem I psaA/psaB protein
Photosystem I iron-sulfur center Chains: AC, BC
Molecule details ›
Chains: AC, BC
Length: 81 amino acids
Theoretical weight: 9.05 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P62090 (Residues: 1-81; Coverage: 100%)
Gene names: AtCg01060, frxA, psaC
Sequence domains: 4Fe-4S dicluster domain
Photosystem I reaction center subunit II-2, chloroplastic Chains: AD, BD
Molecule details ›
Chains: AD, BD
Length: 204 amino acids
Theoretical weight: 22.34 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SA56 (Residues: 1-204; Coverage: 100%)
Gene names: At1g03130, F10O3_4, PSAD2
Sequence domains: PsaD
Photosystem I reaction center subunit IV A, chloroplastic Chains: AE, BE
Molecule details ›
Chains: AE, BE
Length: 143 amino acids
Theoretical weight: 14.98 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9S831 (Residues: 1-143; Coverage: 100%)
Gene names: At4g28750, F16A16.140, PSAE1
Sequence domains: Photosystem I reaction centre subunit IV / PsaE
Photosystem I reaction center subunit III, chloroplastic Chains: AF, BF
Molecule details ›
Chains: AF, BF
Length: 221 amino acids
Theoretical weight: 24.2 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SHE8 (Residues: 1-221; Coverage: 100%)
Gene names: At1g31330, PSAF, T19E23.12
Sequence domains: Photosystem I reaction centre subunit III
Photosystem I reaction center subunit V, chloroplastic Chains: AG, BG
Molecule details ›
Chains: AG, BG
Length: 160 amino acids
Theoretical weight: 17.1 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9S7N7 (Residues: 1-160; Coverage: 100%)
Gene names: At1g55670, F20N2.21, F20N2.33, F20N2_3, PSAG
Sequence domains: Photosystem I psaG / psaK
Photosystem I reaction center subunit VI-2, chloroplastic Chains: AH, BH
Molecule details ›
Chains: AH, BH
Length: 145 amino acids
Theoretical weight: 15.29 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SUI6 (Residues: 1-145; Coverage: 100%)
Gene names: At1g52230, F9I5.11, PSAH2
Sequence domains: Photosystem I reaction centre subunit VI
Photosystem I reaction center subunit VIII Chains: AI, BI
Molecule details ›
Chains: AI, BI
Length: 37 amino acids
Theoretical weight: 4.14 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P56768 (Residues: 1-37; Coverage: 100%)
Gene names: AtCg00510, psaI
Sequence domains: Photosystem I reaction centre subunit VIII
Photosystem I reaction center subunit IX Chains: AJ, BJ
Molecule details ›
Chains: AJ, BJ
Length: 44 amino acids
Theoretical weight: 5.01 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P56769 (Residues: 1-44; Coverage: 100%)
Gene names: AtCg00630, psaJ
Sequence domains: Photosystem I reaction centre subunit IX / PsaJ
Photosystem I reaction center subunit psaK, chloroplastic Chains: AK, BK
Molecule details ›
Chains: AK, BK
Length: 130 amino acids
Theoretical weight: 13.22 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SUI5 (Residues: 1-130; Coverage: 100%)
Gene names: At1g30380, PSAK, T4K22.2
Sequence domains: Photosystem I psaG / psaK
Photosystem I reaction center subunit XI, chloroplastic Chains: AL, BL
Molecule details ›
Chains: AL, BL
Length: 219 amino acids
Theoretical weight: 23.07 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SUI4 (Residues: 1-219; Coverage: 100%)
Gene names: At4g12800, PSAL, T20K18.150
Sequence domains: Photosystem I reaction centre subunit XI
Chlorophyll a-b binding protein 6, chloroplastic Chains: A1, B1
Molecule details ›
Chains: A1, B1
Length: 241 amino acids
Theoretical weight: 26.02 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q01667 (Residues: 1-241; Coverage: 100%)
Gene names: At3g54890, CAB6, F28P10.130, LHCA1
Sequence domains: Chlorophyll A-B binding protein
Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic Chains: A3, B3
Molecule details ›
Chains: A3, B3
Length: 273 amino acids
Theoretical weight: 29.21 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SY97 (Residues: 1-273; Coverage: 100%)
Gene names: At1g61520, LHCA3, T25B24.12
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein 4, chloroplastic Chain: A4
Molecule details ›
Chain: A4
Length: 251 amino acids
Theoretical weight: 27.76 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P27521 (Residues: 1-251; Coverage: 100%)
Gene names: At3g47470, CAB4, F1P2.20, LHCA4
Sequence domains: Chlorophyll A-B binding protein
Photosystem I chlorophyll a/b-binding protein 6, chloroplastic Chain: A6
Molecule details ›
Chain: A6
Length: 270 amino acids
Theoretical weight: 29.97 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q8LCQ4 (Residues: 1-270; Coverage: 100%)
Gene names: At1g19150, LHCA6, T29M8.2
Sequence domains: Chlorophyll A-B binding protein
Photosystem I chlorophyll a/b-binding protein 2, chloroplastic Chain: B2
Molecule details ›
Chain: B2
Length: 257 amino acids
Theoretical weight: 27.78 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SYW8 (Residues: 1-257; Coverage: 100%)
Gene names: At3g61470, F2A19.70, LHCA2
Sequence domains: Chlorophyll A-B binding protein
Photosystem I chlorophyll a/b-binding protein 5, chloroplastic Chain: B5
Molecule details ›
Chain: B5
Length: 256 amino acids
Theoretical weight: 27.83 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9C639 (Residues: 1-256; Coverage: 100%)
Gene names: At1g45474, F2G19.4, LHCA5
Sequence domains: Chlorophyll A-B binding protein
NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic Chain: A
Molecule details ›
Chain: A
Length: 360 amino acids
Theoretical weight: 40.04 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q37165 (Residues: 1-360; Coverage: 100%)
Gene names: AtCg01100, ndhA
Sequence domains: NADH dehydrogenase
NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic Chain: B
Molecule details ›
Chain: B
Length: 512 amino acids
Theoretical weight: 57.02 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: A0A1B1W4Z4 (Residues: 1-512; Coverage: 100%)
Gene name: ndhB
Sequence domains:
NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic Chain: C
Molecule details ›
Chain: C
Length: 120 amino acids
Theoretical weight: 13.85 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P56751 (Residues: 1-120; Coverage: 100%)
Gene names: AtCg00440, ndhC
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
NAD(P)H-quinone oxidoreductase chain 4, chloroplastic Chain: D
Molecule details ›
Chain: D
Length: 506 amino acids
Theoretical weight: 56.99 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: A0A1B1W4Z0 (Residues: 1-506; 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: 101 amino acids
Theoretical weight: 11.3 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P26289 (Residues: 1-101; Coverage: 100%)
Gene names: AtCg01070, ndhE
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic Chain: F
Molecule details ›
Chain: F
Length: 746 amino acids
Theoretical weight: 85.3 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P56752 (Residues: 1-746; Coverage: 100%)
Gene names: AtCg01010, ndhF
Sequence domains:
NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic Chain: G
Molecule details ›
Chain: G
Length: 176 amino acids
Theoretical weight: 19.22 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q95695 (Residues: 1-176; Coverage: 100%)
Gene names: AtCg01080, ndhG
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 6
Photosynthetic NDH subunit of subcomplex B 1, chloroplastic Chain: a
Molecule details ›
Chain: a
Length: 461 amino acids
Theoretical weight: 51.08 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9S9N6 (Residues: 1-461; Coverage: 100%)
Gene names: At1g15980, GT9, NDF1, NDH48, PNSB1, T24D18.8
Photosynthetic NDH subunit of subcomplex B 2, chloroplastic Chain: b
Molecule details ›
Chain: b
Length: 348 amino acids
Theoretical weight: 38.05 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q94AQ8 (Residues: 1-348; Coverage: 100%)
Gene names: At1g64770, F13O11.8, NDF2, NDH45, PNSB2
Photosynthetic NDH subunit of subcomplex B 3, chloroplastic Chain: c
Molecule details ›
Chain: c
Length: 204 amino acids
Theoretical weight: 22.45 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9LU21 (Residues: 1-204; Coverage: 100%)
Gene names: At3g16250, MYA6.6, NDF4, PNSB3
Sequence domains: 2Fe-2S iron-sulfur cluster binding domain
NDH dependent flow 6 Chain: d
Molecule details ›
Chain: d
Length: 161 amino acids
Theoretical weight: 18.7 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: B3H6Z4 (Residues: 1-161; Coverage: 100%)
Gene names: At1g18730, F6A14.16, F6A14_16, NDF6, NDH dependent flow 6, PNSB4, PnsB4
Photosynthetic NDH subunit of subcomplex B 5, chloroplastic Chain: e
Molecule details ›
Chain: e
Length: 212 amino acids
Theoretical weight: 23.77 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9FG89 (Residues: 1-212; Coverage: 100%)
Gene names: At5g43750, MQD19.9, NDH18, PNSB5
Photosynthetic NDH subunit of lumenal location 1, chloroplastic Chain: f
Molecule details ›
Chain: f
Length: 238 amino acids
Theoretical weight: 27 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: O80634 (Residues: 1-238; Coverage: 100%)
Gene names: At2g39470, F12L6.13, PNSL1, PPL2
Sequence domains: PsbP
Photosynthetic NDH subunit of lumenal location 2, chloroplastic Chain: g
Molecule details ›
Chain: g
Length: 190 amino acids
Theoretical weight: 22.18 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9XI73 (Residues: 1-190; Coverage: 100%)
Gene names: At1g14150, F7A19.23, PNSL2, PQL1, PQL2
Sequence domains: Oxygen evolving enhancer protein 3
Photosynthetic NDH subunit of lumenal location 3, chloroplastic Chain: h
Molecule details ›
Chain: h
Length: 220 amino acids
Theoretical weight: 24.81 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SGH4 (Residues: 1-220; Coverage: 100%)
Gene names: At3g01440, PNSL3, PQL1, PQL2, T13O15.8
Sequence domains: Oxygen evolving enhancer protein 3
Photosynthetic NDH subunit of lumenal location 4, chloroplastic Chain: i
Molecule details ›
Chain: i
Length: 217 amino acids
Theoretical weight: 23.28 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SCY3 (Residues: 1-217; Coverage: 100%)
Gene names: At4g39710, FKBP16-2, FKBP22-2, FKBP23I, PNSL4, T19P19.100
Sequence domains: FKBP-type peptidyl-prolyl cis-trans isomerase
Photosynthetic NDH subunit of lumenal location 5, chloroplastic Chain: j
Molecule details ›
Chain: j
Length: 255 amino acids
Theoretical weight: 27.92 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9ASS6 (Residues: 1-259; Coverage: 99%)
  • Best match: Q9ASS6-2 (Residues: 1-255)
Gene names: At5g13120, CYP20-2, PNSL5, T19L5_80
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
NAD(P)H-quinone oxidoreductase subunit H, chloroplastic Chain: H
Molecule details ›
Chain: H
Length: 393 amino acids
Theoretical weight: 45.55 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P56753 (Residues: 1-393; Coverage: 100%)
Gene names: AtCg01110, 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: 172 amino acids
Theoretical weight: 20.11 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P56755 (Residues: 1-172; Coverage: 100%)
Gene names: AtCg01090, ndhI
Sequence domains: 4Fe-4S dicluster domain
NAD(P)H-quinone oxidoreductase subunit J, chloroplastic Chain: J
Molecule details ›
Chain: J
Length: 158 amino acids
Theoretical weight: 18.58 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P56754 (Residues: 1-158; Coverage: 100%)
Gene names: AtCg00420, 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: 225 amino acids
Theoretical weight: 25.4 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P56756 (Residues: 1-225; Coverage: 100%)
Gene names: AtCg00430, ndhK, psbG
Sequence domains: NADH ubiquinone oxidoreductase, 20 Kd subunit
NAD(P)H-quinone oxidoreductase subunit L, chloroplastic Chain: L
Molecule details ›
Chain: L
Length: 191 amino acids
Theoretical weight: 21.99 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9CAC5 (Residues: 1-191; Coverage: 100%)
Gene names: At1g70760, CRR23, F15H11.1, F5A18.6, NDH-L, ndhL
Sequence domains: NADH dehydrogenase transmembrane subunit
NAD(P)H-quinone oxidoreductase subunit M, chloroplastic Chain: M
Molecule details ›
Chain: M
Length: 217 amino acids
Theoretical weight: 24.82 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q2V2S7 (Residues: 1-217; Coverage: 100%)
Gene names: At4g37925, F20D10.40, NDH-M, ndhM
Sequence domains: Cyanobacterial and plastid NDH-1 subunit M
NAD(P)H-quinone oxidoreductase subunit N, chloroplastic Chain: N
Molecule details ›
Chain: N
Length: 209 amino acids
Theoretical weight: 23.43 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9LVM2 (Residues: 1-209; Coverage: 100%)
Gene names: At5g58260, MCK7.13, NDH-N, ndhN
Sequence domains: NADH-quinone oxidoreductase cyanobacterial subunit N
NdhO Chain: O
Molecule details ›
Chain: O
Length: 158 amino acids
Theoretical weight: 17.68 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: A0A178WB24 (Residues: 1-158; Coverage: 100%)
Gene names: AXX17_At1g69270, C24_LOCUS6416
Sequence domains: Cyanobacterial and plant NDH-1 subunit O
NdhT Chain: T
Molecule details ›
Chain: T
Length: 122 amino acids
Theoretical weight: 10.4 KDa
Source organism: Arabidopsis thaliana

Ligands and Environments

13 bound ligands:
Ligand CLA 284 x CLA
Ligand PQN 4 x PQN
Ligand LHG 19 x LHG
Ligand BCR 51 x BCR
Ligand SF4 9 x SF4
Ligand LMU 8 x LMU
Ligand DGD 2 x DGD
Ligand LUT 9 x LUT
Ligand LMG 4 x LMG
Ligand CHL 22 x CHL
Ligand XAT 8 x XAT
Ligand SQD 2 x SQD
Ligand FES 1 x FES
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.89Å
Relevant EMDB volumes: EMD-32477

Quick links

Citations

2 review citations

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