6wj6

Cryo-EM structure of apo-Photosystem II from Synechocystis sp. PCC 6803

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Photosystem II protein D1 2

OrganismNot specified

UniProt P16033

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 13 Photosystem II CP47 reaction center protein × 1 (P05429) Photosystem II CP43 reaction center protein × 1 (P09193) Photosystem II D2 protein × 1 (P09192) Cytochrome b559 subunit alpha × 1 (P09190) Cytochrome b559 subunit beta × 1 (P09191) Photosystem II reaction center protein H × 1 (P14835) Photosystem II reaction center protein I × 1 (Q54697) Photosystem II reaction center protein K × 1 (P15819) Photosystem II reaction center protein L × 1 (Q55354) Photosystem II reaction center protein M × 1 (P72701) Photosystem II reaction center protein T × 1 (P74787) Photosystem II reaction center X protein × 1 (P72575) FE (II) ION × 1 CHLOROPHYLL A × 35 PHEOPHYTIN A × 2 BETA-CAROTENE × 9 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 7 ;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 ; × 2 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 3 DODECYL-BETA-D-MALTOSIDE × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 2 CHLORIDE ION × 1 BICARBONATE ION × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 4 PROTOPORPHYRIN IX CONTAINING FE × 1 N-FORMYLMETHIONINE × 3 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PSBA2_SYNY3
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–360; UniProt 1–360

Photosystem II CP47 reaction center protein

OrganismNot specified

UniProt P05429

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 13 Photosystem II protein D1 2 × 1 (P16033) Photosystem II CP43 reaction center protein × 1 (P09193) Photosystem II D2 protein × 1 (P09192) Cytochrome b559 subunit alpha × 1 (P09190) Cytochrome b559 subunit beta × 1 (P09191) Photosystem II reaction center protein H × 1 (P14835) Photosystem II reaction center protein I × 1 (Q54697) Photosystem II reaction center protein K × 1 (P15819) Photosystem II reaction center protein L × 1 (Q55354) Photosystem II reaction center protein M × 1 (P72701) Photosystem II reaction center protein T × 1 (P74787) Photosystem II reaction center X protein × 1 (P72575) FE (II) ION × 1 CHLOROPHYLL A × 35 PHEOPHYTIN A × 2 BETA-CAROTENE × 9 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 7 ;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 ; × 2 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 3 DODECYL-BETA-D-MALTOSIDE × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 2 CHLORIDE ION × 1 BICARBONATE ION × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 4 PROTOPORPHYRIN IX CONTAINING FE × 1 N-FORMYLMETHIONINE × 3 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PSBB_SYNY3
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–507; UniProt 1–507

Photosystem II CP43 reaction center protein

OrganismNot specified

UniProt P09193

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 13 Photosystem II protein D1 2 × 1 (P16033) Photosystem II CP47 reaction center protein × 1 (P05429) Photosystem II D2 protein × 1 (P09192) Cytochrome b559 subunit alpha × 1 (P09190) Cytochrome b559 subunit beta × 1 (P09191) Photosystem II reaction center protein H × 1 (P14835) Photosystem II reaction center protein I × 1 (Q54697) Photosystem II reaction center protein K × 1 (P15819) Photosystem II reaction center protein L × 1 (Q55354) Photosystem II reaction center protein M × 1 (P72701) Photosystem II reaction center protein T × 1 (P74787) Photosystem II reaction center X protein × 1 (P72575) FE (II) ION × 1 CHLOROPHYLL A × 35 PHEOPHYTIN A × 2 BETA-CAROTENE × 9 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 7 ;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 ; × 2 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 3 DODECYL-BETA-D-MALTOSIDE × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 2 CHLORIDE ION × 1 BICARBONATE ION × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 4 PROTOPORPHYRIN IX CONTAINING FE × 1 N-FORMYLMETHIONINE × 3 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PSBC_SYNY3
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–460; UniProt 1–460

Photosystem II D2 protein

OrganismNot specified

UniProt P09192

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 13 Photosystem II protein D1 2 × 1 (P16033) Photosystem II CP47 reaction center protein × 1 (P05429) Photosystem II CP43 reaction center protein × 1 (P09193) Cytochrome b559 subunit alpha × 1 (P09190) Cytochrome b559 subunit beta × 1 (P09191) Photosystem II reaction center protein H × 1 (P14835) Photosystem II reaction center protein I × 1 (Q54697) Photosystem II reaction center protein K × 1 (P15819) Photosystem II reaction center protein L × 1 (Q55354) Photosystem II reaction center protein M × 1 (P72701) Photosystem II reaction center protein T × 1 (P74787) Photosystem II reaction center X protein × 1 (P72575) FE (II) ION × 1 CHLOROPHYLL A × 35 PHEOPHYTIN A × 2 BETA-CAROTENE × 9 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 7 ;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 ; × 2 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 3 DODECYL-BETA-D-MALTOSIDE × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 2 CHLORIDE ION × 1 BICARBONATE ION × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 4 PROTOPORPHYRIN IX CONTAINING FE × 1 N-FORMYLMETHIONINE × 3 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PSBD_SYNY3
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–352; UniProt 1–352

Cytochrome b559 subunit alpha

OrganismNot specified

UniProt P09190

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 13 Photosystem II protein D1 2 × 1 (P16033) Photosystem II CP47 reaction center protein × 1 (P05429) Photosystem II CP43 reaction center protein × 1 (P09193) Photosystem II D2 protein × 1 (P09192) Cytochrome b559 subunit beta × 1 (P09191) Photosystem II reaction center protein H × 1 (P14835) Photosystem II reaction center protein I × 1 (Q54697) Photosystem II reaction center protein K × 1 (P15819) Photosystem II reaction center protein L × 1 (Q55354) Photosystem II reaction center protein M × 1 (P72701) Photosystem II reaction center protein T × 1 (P74787) Photosystem II reaction center X protein × 1 (P72575) FE (II) ION × 1 CHLOROPHYLL A × 35 PHEOPHYTIN A × 2 BETA-CAROTENE × 9 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 7 ;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 ; × 2 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 3 DODECYL-BETA-D-MALTOSIDE × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 2 CHLORIDE ION × 1 BICARBONATE ION × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 4 PROTOPORPHYRIN IX CONTAINING FE × 1 N-FORMYLMETHIONINE × 3 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PSBE_SYNY3
Isoform —
PDB entities 5
Chains and sequence ranges Author chain E; PDBConstruct 1–81; UniProt 1–81

Cytochrome b559 subunit beta

OrganismNot specified

UniProt P09191

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 13 Photosystem II protein D1 2 × 1 (P16033) Photosystem II CP47 reaction center protein × 1 (P05429) Photosystem II CP43 reaction center protein × 1 (P09193) Photosystem II D2 protein × 1 (P09192) Cytochrome b559 subunit alpha × 1 (P09190) Photosystem II reaction center protein H × 1 (P14835) Photosystem II reaction center protein I × 1 (Q54697) Photosystem II reaction center protein K × 1 (P15819) Photosystem II reaction center protein L × 1 (Q55354) Photosystem II reaction center protein M × 1 (P72701) Photosystem II reaction center protein T × 1 (P74787) Photosystem II reaction center X protein × 1 (P72575) FE (II) ION × 1 CHLOROPHYLL A × 35 PHEOPHYTIN A × 2 BETA-CAROTENE × 9 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 7 ;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 ; × 2 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 3 DODECYL-BETA-D-MALTOSIDE × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 2 CHLORIDE ION × 1 BICARBONATE ION × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 4 PROTOPORPHYRIN IX CONTAINING FE × 1 N-FORMYLMETHIONINE × 3 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PSBF_SYNY3
Isoform —
PDB entities 6
Chains and sequence ranges Author chain F; PDBConstruct 1–44; UniProt 1–44

Photosystem II reaction center protein H

OrganismNot specified

UniProt P14835

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 13 Photosystem II protein D1 2 × 1 (P16033) Photosystem II CP47 reaction center protein × 1 (P05429) Photosystem II CP43 reaction center protein × 1 (P09193) Photosystem II D2 protein × 1 (P09192) Cytochrome b559 subunit alpha × 1 (P09190) Cytochrome b559 subunit beta × 1 (P09191) Photosystem II reaction center protein I × 1 (Q54697) Photosystem II reaction center protein K × 1 (P15819) Photosystem II reaction center protein L × 1 (Q55354) Photosystem II reaction center protein M × 1 (P72701) Photosystem II reaction center protein T × 1 (P74787) Photosystem II reaction center X protein × 1 (P72575) FE (II) ION × 1 CHLOROPHYLL A × 35 PHEOPHYTIN A × 2 BETA-CAROTENE × 9 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 7 ;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 ; × 2 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 3 DODECYL-BETA-D-MALTOSIDE × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 2 CHLORIDE ION × 1 BICARBONATE ION × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 4 PROTOPORPHYRIN IX CONTAINING FE × 1 N-FORMYLMETHIONINE × 3 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PSBH_SYNY3
Isoform —
PDB entities 7
Chains and sequence ranges Author chain H; PDBConstruct 1–64; UniProt 1–64

Photosystem II reaction center protein I

OrganismNot specified

UniProt Q54697

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 13 Photosystem II protein D1 2 × 1 (P16033) Photosystem II CP47 reaction center protein × 1 (P05429) Photosystem II CP43 reaction center protein × 1 (P09193) Photosystem II D2 protein × 1 (P09192) Cytochrome b559 subunit alpha × 1 (P09190) Cytochrome b559 subunit beta × 1 (P09191) Photosystem II reaction center protein H × 1 (P14835) Photosystem II reaction center protein K × 1 (P15819) Photosystem II reaction center protein L × 1 (Q55354) Photosystem II reaction center protein M × 1 (P72701) Photosystem II reaction center protein T × 1 (P74787) Photosystem II reaction center X protein × 1 (P72575) FE (II) ION × 1 CHLOROPHYLL A × 35 PHEOPHYTIN A × 2 BETA-CAROTENE × 9 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 7 ;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 ; × 2 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 3 DODECYL-BETA-D-MALTOSIDE × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 2 CHLORIDE ION × 1 BICARBONATE ION × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 4 PROTOPORPHYRIN IX CONTAINING FE × 1 N-FORMYLMETHIONINE × 3 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PSBI_SYNY3
Isoform —
PDB entities 8
Chains and sequence ranges Author chain I; PDBConstruct 1–38; UniProt 1–38

Photosystem II reaction center protein K

OrganismNot specified

UniProt P15819

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 13 Photosystem II protein D1 2 × 1 (P16033) Photosystem II CP47 reaction center protein × 1 (P05429) Photosystem II CP43 reaction center protein × 1 (P09193) Photosystem II D2 protein × 1 (P09192) Cytochrome b559 subunit alpha × 1 (P09190) Cytochrome b559 subunit beta × 1 (P09191) Photosystem II reaction center protein H × 1 (P14835) Photosystem II reaction center protein I × 1 (Q54697) Photosystem II reaction center protein L × 1 (Q55354) Photosystem II reaction center protein M × 1 (P72701) Photosystem II reaction center protein T × 1 (P74787) Photosystem II reaction center X protein × 1 (P72575) FE (II) ION × 1 CHLOROPHYLL A × 35 PHEOPHYTIN A × 2 BETA-CAROTENE × 9 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 7 ;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 ; × 2 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 3 DODECYL-BETA-D-MALTOSIDE × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 2 CHLORIDE ION × 1 BICARBONATE ION × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 4 PROTOPORPHYRIN IX CONTAINING FE × 1 N-FORMYLMETHIONINE × 3 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PSBK_SYNY3
Isoform —
PDB entities 9
Chains and sequence ranges Author chain K; PDBConstruct 1–45; UniProt 1–45

Photosystem II reaction center protein L

OrganismNot specified

UniProt Q55354

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 13 Photosystem II protein D1 2 × 1 (P16033) Photosystem II CP47 reaction center protein × 1 (P05429) Photosystem II CP43 reaction center protein × 1 (P09193) Photosystem II D2 protein × 1 (P09192) Cytochrome b559 subunit alpha × 1 (P09190) Cytochrome b559 subunit beta × 1 (P09191) Photosystem II reaction center protein H × 1 (P14835) Photosystem II reaction center protein I × 1 (Q54697) Photosystem II reaction center protein K × 1 (P15819) Photosystem II reaction center protein M × 1 (P72701) Photosystem II reaction center protein T × 1 (P74787) Photosystem II reaction center X protein × 1 (P72575) FE (II) ION × 1 CHLOROPHYLL A × 35 PHEOPHYTIN A × 2 BETA-CAROTENE × 9 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 7 ;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 ; × 2 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 3 DODECYL-BETA-D-MALTOSIDE × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 2 CHLORIDE ION × 1 BICARBONATE ION × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 4 PROTOPORPHYRIN IX CONTAINING FE × 1 N-FORMYLMETHIONINE × 3 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PSBL_SYNY3
Isoform —
PDB entities 10
Chains and sequence ranges Author chain L; PDBConstruct 1–39; UniProt 1–39

Photosystem II reaction center protein M

OrganismNot specified

UniProt P72701

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 13 Photosystem II protein D1 2 × 1 (P16033) Photosystem II CP47 reaction center protein × 1 (P05429) Photosystem II CP43 reaction center protein × 1 (P09193) Photosystem II D2 protein × 1 (P09192) Cytochrome b559 subunit alpha × 1 (P09190) Cytochrome b559 subunit beta × 1 (P09191) Photosystem II reaction center protein H × 1 (P14835) Photosystem II reaction center protein I × 1 (Q54697) Photosystem II reaction center protein K × 1 (P15819) Photosystem II reaction center protein L × 1 (Q55354) Photosystem II reaction center protein T × 1 (P74787) Photosystem II reaction center X protein × 1 (P72575) FE (II) ION × 1 CHLOROPHYLL A × 35 PHEOPHYTIN A × 2 BETA-CAROTENE × 9 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 7 ;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 ; × 2 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 3 DODECYL-BETA-D-MALTOSIDE × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 2 CHLORIDE ION × 1 BICARBONATE ION × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 4 PROTOPORPHYRIN IX CONTAINING FE × 1 N-FORMYLMETHIONINE × 3 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PSBM_SYNY3
Isoform —
PDB entities 11
Chains and sequence ranges Author chain M; PDBConstruct 1–35; UniProt 1–35

Photosystem II reaction center protein T

OrganismNot specified

UniProt P74787

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 13 Photosystem II protein D1 2 × 1 (P16033) Photosystem II CP47 reaction center protein × 1 (P05429) Photosystem II CP43 reaction center protein × 1 (P09193) Photosystem II D2 protein × 1 (P09192) Cytochrome b559 subunit alpha × 1 (P09190) Cytochrome b559 subunit beta × 1 (P09191) Photosystem II reaction center protein H × 1 (P14835) Photosystem II reaction center protein I × 1 (Q54697) Photosystem II reaction center protein K × 1 (P15819) Photosystem II reaction center protein L × 1 (Q55354) Photosystem II reaction center protein M × 1 (P72701) Photosystem II reaction center X protein × 1 (P72575) FE (II) ION × 1 CHLOROPHYLL A × 35 PHEOPHYTIN A × 2 BETA-CAROTENE × 9 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 7 ;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 ; × 2 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 3 DODECYL-BETA-D-MALTOSIDE × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 2 CHLORIDE ION × 1 BICARBONATE ION × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 4 PROTOPORPHYRIN IX CONTAINING FE × 1 N-FORMYLMETHIONINE × 3 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PSBT_SYNY3
Isoform —
PDB entities 12
Chains and sequence ranges Author chain T; PDBConstruct 1–31; UniProt 1–31

Photosystem II reaction center X protein

OrganismNot specified

UniProt P72575

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 13 Photosystem II protein D1 2 × 1 (P16033) Photosystem II CP47 reaction center protein × 1 (P05429) Photosystem II CP43 reaction center protein × 1 (P09193) Photosystem II D2 protein × 1 (P09192) Cytochrome b559 subunit alpha × 1 (P09190) Cytochrome b559 subunit beta × 1 (P09191) Photosystem II reaction center protein H × 1 (P14835) Photosystem II reaction center protein I × 1 (Q54697) Photosystem II reaction center protein K × 1 (P15819) Photosystem II reaction center protein L × 1 (Q55354) Photosystem II reaction center protein M × 1 (P72701) Photosystem II reaction center protein T × 1 (P74787) FE (II) ION × 1 CHLOROPHYLL A × 35 PHEOPHYTIN A × 2 BETA-CAROTENE × 9 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 7 ;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 ; × 2 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 3 DODECYL-BETA-D-MALTOSIDE × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 2 CHLORIDE ION × 1 BICARBONATE ION × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 4 PROTOPORPHYRIN IX CONTAINING FE × 1 N-FORMYLMETHIONINE × 3 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PSBX_SYNY3
Isoform —
PDB entities 13
Chains and sequence ranges Author chain X; PDBConstruct 1–39; UniProt 1–39

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id6wj6
Deposition date deposition_date2020-04-12
Structure title titleCryo-EM structure of apo-Photosystem II from Synechocystis sp. PCC 6803
Keywords keywordsPhotosystem, oxidoreductase, water-splitting, photoactivation, PHOTOSYNTHESIS; PHOTOSYNTHESIS
Experimental Method methodELECTRON MICROSCOPY
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6wj6__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6wj6__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6wj6__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg(Guinier)40.05 Å
Rg (electron density)39.09 Å
Total Rg39.64 Å
Atom count18686
Residues1898
Excluded volume348240 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6wj6__assembly_1__model_1 tridecameric (13) Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (28)

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (9 domains)

Domain ID domain_idd6wj6a_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.26 — Bacterial photosystem II reaction centre, L and M subunits
Superfamily Superfamily superfamilyf.26.1 — Bacterial photosystem II reaction centre, L and M subunits
Family Family familyf.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits
Domain ID domain_idd6wj6b_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.55 — Photosystem II antenna protein-like
Superfamily Superfamily superfamilyf.55.1 — Photosystem II antenna protein-like
Family Family familyf.55.1.1 — Photosystem II antenna protein-like
Domain ID domain_idd6wj6c_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.55 — Photosystem II antenna protein-like
Superfamily Superfamily superfamilyf.55.1 — Photosystem II antenna protein-like
Family Family familyf.55.1.1 — Photosystem II antenna protein-like
Domain ID domain_idd6wj6d_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.26 — Bacterial photosystem II reaction centre, L and M subunits
Superfamily Superfamily superfamilyf.26.1 — Bacterial photosystem II reaction centre, L and M subunits
Family Family familyf.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits
Domain ID domain_idd6wj6e_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.23 — Single transmembrane helix
Superfamily Superfamily superfamilyf.23.38 — Cytochrome b559 subunits
Family Family familyf.23.38.1 — Cytochrome b559 subunits
Domain ID domain_idd6wj6f_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.23 — Single transmembrane helix
Superfamily Superfamily superfamilyf.23.38 — Cytochrome b559 subunits
Family Family familyf.23.38.1 — Cytochrome b559 subunits
Domain ID domain_idd6wj6h_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.23 — Single transmembrane helix
Superfamily Superfamily superfamilyf.23.33 — Photosystem II 10 kDa phosphoprotein PsbH
Family Family familyf.23.33.1 — PsbH-like
Domain ID domain_idd6wj6k_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.23 — Single transmembrane helix
Superfamily Superfamily superfamilyf.23.36 — Photosystem II reaction center protein K, PsbK
Family Family familyf.23.36.1 — PsbK-like
Domain ID domain_idd6wj6m_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.23 — Single transmembrane helix
Superfamily Superfamily superfamilyf.23.35 — Photosystem II reaction center protein M, PsbM
Family Family familyf.23.35.1 — PsbM-like

CATH v4.4 (1 domains)

Domain ID domain_id6wj6A01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily10 — Photosystem II protein D1-like
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7. Citations (1)