Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-LHCII-ST2)
Chen, S.J.B., Wu, J.H.To be published.
Experimental Data Snapshot
wwPDB Validation   3D Report Full Report
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Chlorophyll a-b binding protein 6, chloroplastic | A [auth 1] | 241 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: LHCA1, CAB6, At3g54890, F28P10.130 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for Q01667 (Arabidopsis thaliana) Explore Q01667  Go to UniProtKB:  Q01667 | |||||
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Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q01667 | ||||
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Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I chlorophyll a/b-binding protein 2, chloroplastic | B [auth 2] | 257 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: LHCA2, At3g61470, F2A19.70 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for Q9SYW8 (Arabidopsis thaliana) Explore Q9SYW8  Go to UniProtKB:  Q9SYW8 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9SYW8 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic | C [auth 3] | 273 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: LHCA3, At1g61520, T25B24.12 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for Q9SY97 (Arabidopsis thaliana) Explore Q9SY97  Go to UniProtKB:  Q9SY97 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9SY97 | ||||
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Entity ID: 4 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Chlorophyll a-b binding protein 4, chloroplastic | D [auth 4] | 251 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: LHCA4, CAB4, At3g47470, F1P2.20 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for P27521 (Arabidopsis thaliana) Explore P27521  Go to UniProtKB:  P27521 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P27521 | ||||
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Entity ID: 5 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I P700 chlorophyll a apoprotein A1 | E [auth A] | 750 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: psaA, AtCg00350 EC: 1.97.1.12 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for P56766 (Arabidopsis thaliana) Explore P56766  Go to UniProtKB:  P56766 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P56766 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 6 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I P700 chlorophyll a apoprotein A2 | F [auth B] | 734 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: psaB, AtCg00340 EC: 1.97.1.12 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for P56767 (Arabidopsis thaliana) Explore P56767  Go to UniProtKB:  P56767 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P56767 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 7 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I iron-sulfur center | G [auth C] | 81 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: psaC, frxA, AtCg01060 EC: 1.97.1.12 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for P62090 (Arabidopsis thaliana) Explore P62090  Go to UniProtKB:  P62090 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P62090 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 8 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I reaction center subunit II-2, chloroplastic | H [auth D] | 204 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: PSAD2, At1g03130, F10O3_4 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for Q9SA56 (Arabidopsis thaliana) Explore Q9SA56  Go to UniProtKB:  Q9SA56 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9SA56 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 9 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I reaction center subunit IV A, chloroplastic | I [auth E] | 143 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: PSAE1, At4g28750, F16A16.140 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for Q9S831 (Arabidopsis thaliana) Explore Q9S831  Go to UniProtKB:  Q9S831 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9S831 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 10 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I reaction center subunit III, chloroplastic | J [auth F] | 221 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: PSAF, At1g31330, T19E23.12 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for Q9SHE8 (Arabidopsis thaliana) Explore Q9SHE8  Go to UniProtKB:  Q9SHE8 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9SHE8 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 11 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I reaction center subunit V, chloroplastic | K [auth G] | 160 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: PSAG, At1g55670, F20N2.21, F20N2.33, F20N2_3 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for Q9S7N7 (Arabidopsis thaliana) Explore Q9S7N7  Go to UniProtKB:  Q9S7N7 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9S7N7 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 12 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I reaction center subunit VI-2, chloroplastic | L [auth H] | 145 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: PSAH2, At1g52230, F9I5.11 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for Q9SUI6 (Arabidopsis thaliana) Explore Q9SUI6  Go to UniProtKB:  Q9SUI6 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9SUI6 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 13 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I reaction center subunit VIII | M [auth I] | 37 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: psaI, AtCg00510 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for P56768 (Arabidopsis thaliana) Explore P56768  Go to UniProtKB:  P56768 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P56768 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 14 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I reaction center subunit IX | N [auth J] | 44 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: psaJ, AtCg00630 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for P56769 (Arabidopsis thaliana) Explore P56769  Go to UniProtKB:  P56769 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P56769 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 15 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I reaction center subunit psaK, chloroplastic | O [auth K] | 130 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: PSAK, At1g30380, T4K22.2 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for Q9SUI5 (Arabidopsis thaliana) Explore Q9SUI5  Go to UniProtKB:  Q9SUI5 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9SUI5 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 16 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I reaction center subunit XI, chloroplastic | P [auth L] | 219 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: PSAL, At4g12800, T20K18.150 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for Q9SUI4 (Arabidopsis thaliana) Explore Q9SUI4  Go to UniProtKB:  Q9SUI4 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9SUI4 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 17 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I subunit O | Q [auth O] | 140 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: PSAO, At1g08380, T27G7 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for Q949Q5 (Arabidopsis thaliana) Explore Q949Q5  Go to UniProtKB:  Q949Q5 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q949Q5 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 18 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Chlorophyll a-b binding protein 2, chloroplastic | R [auth x], S [auth y] | 267 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: LHCB1.1, AB165, CAB2, LHCP-B, At1g29920, F1N18.4 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for P0CJ48 (Arabidopsis thaliana) Explore P0CJ48  Go to UniProtKB:  P0CJ48 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P0CJ48 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 19 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Chlorophyll a-b binding protein 2.1, chloroplastic | T [auth z] | 265 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: LHCB2.1, LHCB2.3, At2g05100, F15L11.2 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for Q9SHR7 (Arabidopsis thaliana) Explore Q9SHR7  Go to UniProtKB:  Q9SHR7 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9SHR7 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 12 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
DGD Query on DGD | ZF [auth B] | DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N | |||
CHL (Subject of Investigation/LOI) Query on CHL | BI [auth x] BJ [auth y] CJ [auth y] DI [auth x] IB [auth 3] | CHLOROPHYLL B C55 H70 Mg N4 O6 MWVCRINOIIOUAU-UYSPMESUSA-M | |||
CL0 (Subject of Investigation/LOI) Query on CL0 | LD [auth A] | CHLOROPHYLL A ISOMER C55 H72 Mg N4 O5 VIQFHHZSLDFWDU-DVXFRRMCSA-M | |||
CLA (Subject of Investigation/LOI) Query on CLA | AA [auth 1] AB [auth 2] AD [auth A] AE [auth A] AF [auth B] | CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M | |||
LMG Query on LMG | CC [auth 4], HC [auth 4] | 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N | |||
LHG Query on LHG | AJ [auth y] BB [auth 2] BG [auth B] CG [auth B] EE [auth A] | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N | |||
NEX Query on NEX | II [auth x], VJ [auth z], ZI [auth y] | (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL C40 H56 O4 PGYAYSRVSAJXTE-OQASCVKESA-N | |||
XAT Query on XAT | HA [auth 1] HI [auth x] NJ [auth z] UB [auth 4] YA [auth 2] | (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL C40 H56 O4 SZCBXWMUOPQSOX-WVJDLNGLSA-N | |||
LUT Query on LUT | JA [auth 1] KB [auth 3] KJ [auth z] RI [auth y] SB [auth 4] | (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL C40 H56 O2 KBPHJBAIARWVSC-NSIPBSJQSA-N | |||
BCR Query on BCR | AC [auth 4] BH [auth K] CF [auth B] EH [auth K] KG [auth B] | BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N | |||
PQN Query on PQN | BF [auth B], HE [auth A] | PHYLLOQUINONE C31 H46 O2 MBWXNTAXLNYFJB-NKFFZRIASA-N | |||
SF4 Query on SF4 | GE [auth A], NG [auth C], OG [auth C] | IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
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ID | Chains | Type | Formula | 2D Diagram | Parent |
TPO Query on TPO | T [auth z] | L-PEPTIDE LINKING | C4 H10 N O6 P | THR |
Task | Software Package | Version |
---|---|---|
MODEL REFINEMENT | PHENIX | 1.20.1_4487: |
Funding Organization | Location | Grant Number |
---|---|---|
National Natural Science Foundation of China (NSFC) | China | -- |