6wj6

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

Method: ELECTRON MICROSCOPY

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.

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

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

4. Crystallography and Experiment 4. Crystallography & Experiment

5. Entities and Polymers Entities & Polymers (28)

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

7. Citations (1)