Structure of spinach photosystem II-LHCII supercomplex at 3.2 A resolution
Wei, X.P., Su, X.D., Cao, P., Liu, X.Y., Chang, W.R., Li, M., Zhang, X.Z., Liu, Z.F.(2016) Nature 534: 69-74
Experimental Data Snapshot
wwPDB Validation 3D Report Full Report
(2016) Nature 534: 69-74
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem II protein D1 | A, Z [auth a] | 344 | Spinacia oleracea | Mutation(s): 0 EC: 1.10.3.9 Membrane Entity: Yes | ![]() |
UniProt | |||||
Find proteins for P69560 (Spinacia oleracea) Explore P69560 Go to UniProtKB: P69560 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P69560 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem II CP47 reaction center protein | AA [auth b], B | 508 | Spinacia oleracea | Mutation(s): 0 Membrane Entity: Yes | ![]() |
UniProt | |||||
Find proteins for P04160 (Spinacia oleracea) Explore P04160 Go to UniProtKB: P04160 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P04160 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem II CP43 reaction center protein | BA [auth c], C | 473 | Spinacia oleracea | Mutation(s): 0 Membrane Entity: Yes | ![]() |
UniProt | |||||
Find proteins for P06003 (Spinacia oleracea) Explore P06003 Go to UniProtKB: P06003 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P06003 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 4 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem II D2 protein | CA [auth d], D | 353 | Spinacia oleracea | Mutation(s): 0 EC: 1.10.3.9 Membrane Entity: Yes | ![]() |
UniProt | |||||
Find proteins for P06005 (Spinacia oleracea) Explore P06005 Go to UniProtKB: P06005 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P06005 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 5 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Cytochrome b559 subunit alpha | DA [auth e], E | 83 | Spinacia oleracea | Mutation(s): 0 Membrane Entity: Yes | ![]() |
UniProt | |||||
Find proteins for P69383 (Spinacia oleracea) Explore P69383 Go to UniProtKB: P69383 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P69383 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 6 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Cytochrome b559 subunit beta | EA [auth f], F | 39 | Spinacia oleracea | Mutation(s): 0 Membrane Entity: Yes | ![]() |
UniProt | |||||
Find proteins for P60128 (Spinacia oleracea) Explore P60128 Go to UniProtKB: P60128 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P60128 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 7 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Chlorophyll a-b binding protein, chloroplastic | 267 | Spinacia oleracea | Mutation(s): 0 Membrane Entity: Yes | ![]() | |
UniProt | |||||
Find proteins for P12333 (Spinacia oleracea) Explore P12333 Go to UniProtKB: P12333 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P12333 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 8 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem II reaction center protein H | GA [auth h], H | 73 | Spinacia oleracea | Mutation(s): 0 Membrane Entity: Yes | ![]() |
UniProt | |||||
Find proteins for P05146 (Spinacia oleracea) Explore P05146 Go to UniProtKB: P05146 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P05146 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 9 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Protein Photosystem II reaction center protein I | HA [auth i], I | 36 | Spinacia oleracea | Mutation(s): 0 Membrane Entity: Yes | ![]() |
UniProt | |||||
Find proteins for P62103 (Spinacia oleracea) Explore P62103 Go to UniProtKB: P62103 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P62103 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 10 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem II reaction center protein J | IA [auth j], J | 40 | Spinacia oleracea | Mutation(s): 0 Membrane Entity: Yes | ![]() |
UniProt | |||||
Find proteins for Q9M3L2 (Spinacia oleracea) Explore Q9M3L2 Go to UniProtKB: Q9M3L2 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9M3L2 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 11 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem II reaction center protein K | JA [auth k], K | 59 | Spinacia oleracea | Mutation(s): 0 Membrane Entity: Yes | ![]() |
UniProt | |||||
Find proteins for P12163 (Spinacia oleracea) Explore P12163 Go to UniProtKB: P12163 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P12163 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 12 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Protein Photosystem II reaction center protein L | KA [auth l], L | 38 | Spinacia oleracea | Mutation(s): 0 Membrane Entity: Yes | ![]() |
UniProt | |||||
Find proteins for P60150 (Spinacia oleracea) Explore P60150 Go to UniProtKB: P60150 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P60150 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 13 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem II reaction center protein M | LA [auth m], M | 34 | Spinacia oleracea | Mutation(s): 0 Membrane Entity: Yes | ![]() |
UniProt | |||||
Find proteins for P62112 (Spinacia oleracea) Explore P62112 Go to UniProtKB: P62112 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P62112 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 14 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Oxygen-evolving enhancer protein 1, chloroplastic | NA [auth o], O | 332 | Spinacia oleracea | Mutation(s): 0 Membrane Entity: Yes | ![]() |
UniProt | |||||
Find proteins for P12359 (Spinacia oleracea) Explore P12359 Go to UniProtKB: P12359 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P12359 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 15 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Oxygen-evolving enhancer protein 2, chloroplastic | OA [auth p], P | 267 | Spinacia oleracea | Mutation(s): 0 Membrane Entity: Yes | ![]() |
UniProt | |||||
Find proteins for P12302 (Spinacia oleracea) Explore P12302 Go to UniProtKB: P12302 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P12302 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 16 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Oxygen-evolving enhancer protein 3, chloroplastic | PA [auth q], Q | 232 | Spinacia oleracea | Mutation(s): 0 Membrane Entity: Yes | ![]() |
UniProt | |||||
Find proteins for P12301 (Spinacia oleracea) Explore P12301 Go to UniProtKB: P12301 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P12301 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 17 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Chlorophyll A-B Binding protein 29 kD (CP29) | QA [auth r], R | 243 | Spinacia oleracea | Mutation(s): 0 | ![]() |
UniProt | |||||
Find proteins for F2Z293 (Spinacia oleracea) Explore F2Z293 Go to UniProtKB: F2Z293 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | F2Z293 | ||||
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 26 kD (CP26) | RA [auth s], S | 295 | Spinacia oleracea | Mutation(s): 0 | ![]() |
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 19 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem II Reaction Center protein Tc | SA [auth t], T | 33 | Spinacia oleracea | Mutation(s): 0 Membrane Entity: Yes | ![]() |
UniProt | |||||
Find proteins for P61840 (Spinacia oleracea) Explore P61840 Go to UniProtKB: P61840 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P61840 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 20 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem II Reaction Center Tn protein | TA [auth u], U | 99 | Spinacia oleracea | Mutation(s): 0 | ![]() |
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 21 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem II reaction center W protein, chloroplastic | UA [auth w], V [auth W] | 137 | Spinacia oleracea | Mutation(s): 0 Membrane Entity: Yes | ![]() |
UniProt | |||||
Find proteins for Q41387 (Spinacia oleracea) Explore Q41387 Go to UniProtKB: Q41387 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q41387 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 22 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem II Reaction Center X protein | VA [auth x], W [auth X] | 117 | Spinacia oleracea | Mutation(s): 0 | ![]() |
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 23 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem II reaction center protein Z | XA [auth z], Y [auth Z] | 62 | Spinacia oleracea | Mutation(s): 0 Membrane Entity: Yes | ![]() |
UniProt | |||||
Find proteins for Q9M3M6 (Spinacia oleracea) Explore Q9M3M6 Go to UniProtKB: Q9M3M6 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9M3M6 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 17 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
DGD Query on DGD | BD [auth C] CJ [auth c] EJ [auth c] FJ [auth c] GE [auth H] | DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N | |||
CHL Query on CHL | BM [auth s] CM [auth s] DM [auth s] FF [auth R] GF [auth R] | CHLOROPHYLL B C55 H70 Mg N4 O6 MWVCRINOIIOUAU-UYSPMESUSA-M | |||
CLA Query on CLA | AC [auth B] AG [auth S] AI [auth b] AK [auth g] AL [auth n] | CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M | |||
PHO Query on PHO | FB [auth A], GB [auth A], KH [auth a], LH [auth a] | PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N | |||
SQD Query on SQD | FC [auth B] JB [auth A] KI [auth b] LB [auth A] OH [auth a] | 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C41 H78 O12 S RVUUQPKXGDTQPG-JUDHQOGESA-N | |||
LMG Query on LMG | AD [auth C] CH [auth Z] GC [auth B] GJ [auth c] HN [auth z] | 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N | |||
PL9 Query on PL9 | GD [auth D], MJ [auth d] | 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE C53 H80 O2 FKUYMLZIRPABFK-UHFFFAOYSA-N | |||
LHG Query on LHG | AF [auth N] BH [auth Y] EE [auth G] FL [auth n] GN [auth y] | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N | |||
HEM Query on HEM | LD [auth F], QJ [auth f] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L | |||
NEX Query on NEX | AH [auth Y] DE [auth G] EL [auth n] FN [auth y] HG [auth S] | (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 | CE [auth G] DL [auth n] EN [auth y] HK [auth g] PF [auth R] | (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 | AE [auth G] BE [auth G] BL [auth n] CL [auth n] CN [auth y] | (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 | AJ [auth c] BC [auth B] BJ [auth c] DC [auth B] DJ [auth c] | BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N | |||
OEX Query on OEX | DH [auth a], YA [auth A] | CA-MN4-O5 CLUSTER Ca Mn4 O5 SEXWDHMBWJEXOJ-UHFFFAOYSA-N | |||
BCT Query on BCT | CD [auth D], HJ [auth d] | BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M | |||
FE2 Query on FE2 | EH [auth a], ZA [auth A] | FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N | |||
CL Query on CL | AB [auth A], BB [auth A], FH [auth a], GH [auth a] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Task | Software Package | Version |
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RECONSTRUCTION | EMAN | |
RECONSTRUCTION | RELION |