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XFEL structure of cyanobacterial photosystem II (dark state, dataset1)

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Photosystem II protein D1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBA_THEVL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–344； UniProt 1–344 Author chain a； PDBConstruct 1–344； UniProt 1–344

Photosystem II CP47 reaction center protein

OrganismNot specified

UniProt D0VWR1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBB_THEVL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–505； UniProt 1–505 Author chain b； PDBConstruct 1–505； UniProt 1–505

Photosystem II CP43 reaction center protein

OrganismNot specified

UniProt D0VWR7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBC_THEVL
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 5–455； UniProt 1–451 Author chain c； PDBConstruct 5–455； UniProt 1–451

Photosystem II D2 protein

OrganismNot specified

UniProt D0VWR8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBD_THEVL
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–342； UniProt 1–342 Author chain d； PDBConstruct 1–342； UniProt 1–342

Cytochrome b559 subunit alpha

OrganismNot specified

UniProt P12238

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBE_THEVL
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–84； UniProt 1–84 Author chain e； PDBConstruct 1–84； UniProt 1–84

Cytochrome b559 subunit beta

OrganismNot specified

UniProt P12239

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBF_THEVL
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–44； UniProt 2–45 Author chain f； PDBConstruct 1–44； UniProt 2–45

Photosystem II reaction center protein H

OrganismNot specified

UniProt P19052

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBH_THEVL
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain H； PDBConstruct 1–65； UniProt 1–65 Author chain h； PDBConstruct 1–65； UniProt 1–65

Photosystem II reaction center protein I

OrganismNot specified

UniProt P12240

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBI_THEVL
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain I； PDBConstruct 1–38； UniProt 1–38 Author chain i； PDBConstruct 1–38； UniProt 1–38

Photosystem II reaction center protein J

OrganismNot specified

UniProt Q7DGD4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBJ_THEVL
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain J； PDBConstruct 1–39； UniProt 2–40 Author chain j； PDBConstruct 1–39； UniProt 2–40

Photosystem II reaction center protein K

OrganismNot specified

UniProt P19054

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBK_THEVL
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain K； PDBConstruct 1–37； UniProt 1–37 Author chain k； PDBConstruct 1–37； UniProt 1–37

Photosystem II reaction center protein L

OrganismNot specified

UniProt P12241

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBL_THEVL
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain L； PDBConstruct 1–37； UniProt 1–37 Author chain l； PDBConstruct 1–37； UniProt 1–37

Photosystem II reaction center protein M

OrganismNot specified

UniProt P12312

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBM_THEVL
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain M； PDBConstruct 1–36； UniProt 1–36 Author chain m； PDBConstruct 1–36； UniProt 1–36

Photosystem II manganese-stabilizing polypeptide

OrganismNot specified

UniProt D0VWR2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBO_THEVL
Isoform	—
PDB entities	13
Chains and sequence ranges	Author chain O； PDBConstruct 1–244； UniProt 1–244 Author chain o； PDBConstruct 1–244； UniProt 1–244

Photosystem II reaction center protein T

OrganismNot specified

UniProt P12313

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBT_THEVL
Isoform	—
PDB entities	14
Chains and sequence ranges	Author chain T； PDBConstruct 1–32； UniProt 1–32 Author chain t； PDBConstruct 1–32； UniProt 1–32

Photosystem II 12 kDa extrinsic protein

OrganismNot specified

UniProt P56152

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBU_THEVL
Isoform	—
PDB entities	15
Chains and sequence ranges	Author chain U； PDBConstruct 1–104； UniProt 1–104 Author chain u； PDBConstruct 1–104； UniProt 1–104

Cytochrome c-550

OrganismNot specified

UniProt P0A387

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CY550_THEVL
Isoform	—
PDB entities	16
Chains and sequence ranges	Author chain V； PDBConstruct 1–137； UniProt 27–163 Author chain v； PDBConstruct 1–137； UniProt 27–163

Photosystem II reaction center protein Ycf12

OrganismNot specified

UniProt D0VWR3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YCF12_THEVL
Isoform	—
PDB entities	17
Chains and sequence ranges	Author chain Y； PDBConstruct 1–30； UniProt 1–30 Author chain y； PDBConstruct 1–30； UniProt 1–30

Photosystem II reaction center protein X

OrganismNot specified

UniProt D0VWR4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBX_THEVL
Isoform	—
PDB entities	18
Chains and sequence ranges	Author chain X； PDBConstruct 1–40； UniProt 1–40 Author chain x； PDBConstruct 1–40； UniProt 1–40

Photosystem II reaction center protein Z

OrganismNot specified

UniProt D0VWR5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II protein Y × 1 （P0DM37） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBZ_THEVL
Isoform	—
PDB entities	19
Chains and sequence ranges	Author chain Z； PDBConstruct 1–62； UniProt 1–62 Author chain z； PDBConstruct 1–62； UniProt 1–62

Photosystem II protein Y

OrganismNot specified

UniProt P0DM37

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Photosystem II protein D1 × 2 （P51765） Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Z × 2 （D0VWR5） FE (II) ION × 2 CHLORIDE ION × 6 BICARBONATE ION × 2 CHLOROPHYLL A × 70 PHEOPHYTIN A × 4 BETA-CAROTENE × 22 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GLYCEROL × 35 DODECYL-BETA-D-MALTOSIDE × 14 CA-MN4-O5 CLUSTER × 2 ;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 ; × 4 UNKNOWN LIGAND × 18 CALCIUM ION × 9 heptyl 1-thio-beta-D-glucopyranoside × 17 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 PROTOPORPHYRIN IX CONTAINING FE × 2 MAGNESIUM ION × 2 HEME C × 2 water × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBY_THEVL
Isoform	—
PDB entities	20
Chains and sequence ranges	Author chain R； PDBConstruct 1–34； UniProt 1–34

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_id	6jlj
Deposition date deposition_date	2019-03-06
Structure title title	XFEL structure of cyanobacterial photosystem II (dark state, dataset1)
Keywords keywords	photosystem II, photosynthesis, PSII, membrane protein; PHOTOSYNTHESIS
Experimental Method method	X-RAY DIFFRACTION

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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.

6jlj__assembly_1__model_1

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

Download this curve (.dat)

6jlj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6jlj__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	57.29 Å
Rg (electron density)	56.71 Å
Total Rg	57.03 Å
Atom count	51163
Residues	5287
Excluded volume	951270 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6jlj__assembly_1__model_1`	39-meric （39）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (41)

Entity 1 Entity 1 polymer

Description description	Photosystem II protein D1
Molecular weight formula_weight	38235.6 kDa
EC 编号 ec_number	1.10.3.9
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,a
Atom count atom_count	54101

MTTTLQRRESANLWERFCNWVTSTDNRLYVGWFGVIMIPTLLAATICFVIAFIAAPPVDIDGIREPVSGSLLYGNNIITGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIIFHFLLGASCYMGRQWELSYRLGMRPWICVAYSAPLASAFAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHQLGVAGVFGGALFCAMHGSLVTSSLIRETTETESANYGYKFGQEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGVWFAALGISTMAFNLNGFNFNHSVIDAKGNVINTWADIINRANLGMEVMHERNAHNFPLDLA

Entity 2 Entity 2 polymer

Description description	Photosystem II CP47 reaction center protein
Molecular weight formula_weight	56068.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,b

GLPWYRVHTVLINDPGRLIAAHLMHTALVAGWAGSMALYELATFDPSDPVLNPMWRQGMFVLPFMARLGVTGSWSGWSITGETGIDPGFWSFEGVALAHIVLSGLLFLAACWHWVYWDLELFRDPRTGEPALDLPKMFGIHLFLAGLLCFGFGAFHLTGLFGPGMWVSDPYGLTGSVQPVAPEWGPDGFNPYNPGGVVAHHIAAGIVGIIAGLFHILVRPPQRLYKALRMGNIETVLSSSIAAVFFAAFVVAGTMWYGSATTPIELFGPTRYQWDSSYFQQEINRRVQASLASGATLEEAWSAIPEKLAFYDYIGNNPAKGGLFRTGPMNKGDGIAQAWKGHAVFRNKEGEELFVRRMPAFFESFPVILTDKNGVVKADIPFRRAESKYSFEQQGVTVSFYGGELNGQTFTDPPTVKSYARKAIFGEIFEFDTETLNSDGIFRTSPRGWFTFAHAVFALLFFFGHIWHGARTLFRDVFSGIDPELSPEQVEWGFYQKVGDVTTRK

Entity 3 Entity 3 polymer

Description description	Photosystem II CP43 reaction center protein
Molecular weight formula_weight	49668.8 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,c

NSIFATNRDQESSGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMTLFELAHFIPEKPMYEQGLILIPHIATLGWGVGPGGEVVDTFPFFVVGVVHLISSAVLGFGGVYHAIRGPETLEEYSSFFGYDWKDKNKMTTILGFHLIVLGIGALLLVAKAMFFGGLYDTWAPGGGDVRVITNPTLDPRVIFGYLLKSPFGGEGWIVSVNNLEDVVGGHIWIGLICIAGGIWHILTTPFGWARRAFIWSGEAYLSYSLGALSMMGFIATCFVWFNNTVYPSEFYGPTGPEASQAQAMTFLIRDQKLGANVGSAQGPTGLGKYLMRSPTGEIIFGGETMRFWDFRGPWLEPLRGPNGLDLNKIKNDIQPWQERRAAEYMTHAPLGSLNSVGGVATEINSVNFVSPRSWLATSHFVLAFFFLVGHLWHAGRARAAAAGFEKGIDRESEPVLSMPSLD

Entity 4 Entity 4 polymer

Description description	Photosystem II D2 protein
Molecular weight formula_weight	38404.9 kDa
EC 编号 ec_number	1.10.3.9
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,d

ERGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTGTTFVTSWYTHGLASSYLEGCNFLTVAVSTPANSMGHSLLLLWGPEAQGDFTRWCQLGGLWTFIALHGAFGLIGFMLRQFEIARLVGVRPYNAIAFSAPIAVFVSVFLIYPLGQSSWFFAPSFGVAAIFRFLLFFQGFHNWTLNPFHMMGVAGVLGGALLCAIHGATVENTLFQDGEGASTFRAFNPTQAEETYSMVTANRFWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRSYDFISQEIRAAEDPEFETFYTKNLLLNEGIRAWMAPQDQPHENFVFPEEVLPRGNAL

Entity 5 Entity 5 polymer

Description description	Cytochrome b559 subunit alpha
Molecular weight formula_weight	9580.8 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,e

MAGTTGERPFSDIITSVRYWVIHSITIPALFIAGWLFVSTGLAYDVFGTPRPDSYYAQEQRSIPLVTDRFEAKQQVETFLEQLK

Entity 6 Entity 6 polymer

Description description	Cytochrome b559 subunit beta
Molecular weight formula_weight	4936.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,f

TSNTPNQEPVSYPIFTVRWVAVHTLAVPTIFFLGAIAAMQFIQR

Entity 7 Entity 7 polymer

Description description	Photosystem II reaction center protein H
Molecular weight formula_weight	7227.6 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,h

ARRTWLGDILRPLNSEYGKVAPGWGTTPLMAVFMGLFLVFLLIILEIYNSTLILDGVNVSWKALG

Entity 8 Entity 8 polymer

Description description	Photosystem II reaction center protein I
Molecular weight formula_weight	4438.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,i

METLKITVYIVVTFFVLLFVFGFLSGDPARNPKRKDLE

Entity 9 Entity 9 polymer

Description description	Photosystem II reaction center protein J
Molecular weight formula_weight	3974.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,j

MSEGGRIPLWIVATVAGMGVIVIVGLFFYGAYAGLGSSL

Entity 10 Entity 10 polymer

Description description	Photosystem II reaction center protein K
Molecular weight formula_weight	4101.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K,k

KLPEAYAIFDPLVDVLPVIPVLFLALAFVWQAAVGFR

Entity 11 Entity 11 polymer

Description description	Photosystem II reaction center protein L
Molecular weight formula_weight	4299.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,l

MEPNPNRQPVELNRTSLYLGLLLILVLALLFSSYFFN

Entity 12 Entity 12 polymer

Description description	Photosystem II reaction center protein M
Molecular weight formula_weight	4009.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,m

MEVNQLGLIATALFVLVPSVFLIILYVQTESQQKSS

Entity 13 Entity 13 polymer

Description description	Photosystem II manganese-stabilizing polypeptide
Molecular weight formula_weight	26651.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,o

QTLTYDDIVGTGLANKCPTLDDTARGAYPIDSSQTYRIARLCLQPTTFLVKEEPKNKRQEAEFVPTKLVTRETTSLDQIQGELKVNSDGSLTFVEEDGIDFQPVTVQMAGGERIPLLFTVKNLVASTQPNVTSITTSTDFKGEFNVPSYRTANFLDPKGRGLASGYDSAIALPQAKEEELARANVKRFSLTKGQISLNVAKVDGRTGEIAGTFESEQLSDDDMGAHEPHEVKIQGVFYASIEPA

Entity 14 Entity 14 polymer

Description description	Photosystem II reaction center protein T
Molecular weight formula_weight	3906.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	T,t

METITYVFIFACIIALFFFAIFFREPPRITKK

Entity 15 Entity 15 polymer

Description description	Photosystem II 12 kDa extrinsic protein
Molecular weight formula_weight	11656.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U,u

ATASTEEELVNVVDEKLGTAYGEKIDLNNTNIAAFIQYRGLYPTLAKLIVKNAPYESVEDVLNIPGLTERQKQILRENLEHFTVTEVETALVEGGDRYNNGLYK

Entity 16 Entity 16 polymer

Description description	Cytochrome c-550
Molecular weight formula_weight	15148.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V,v

AELTPEVLTVPLNSEGKTITLTEKQYLEGKRLFQYACASCHVGGITKTNPSLDLRTETLALATPPRDNIEGLVDYMKNPTTYDGEQEIAEVHPSLRSADIFPKMRNLTEKDLVAIAGHILVEPKILGDKWGGGKVYY

Entity 17 Entity 17 polymer

Description description	Photosystem II reaction center protein Ycf12
Molecular weight formula_weight	3228.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y,y

EVIAQLTMIAMIGIAGPMIIFLLAVRRGNL

Entity 18 Entity 18 polymer

Description description	Photosystem II reaction center protein X
Molecular weight formula_weight	4191.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,x

TITPSLKGFFIGLLSGAVVLGLTFAVLIAISQIDKVQRSL

Entity 19 Entity 19 polymer

Description description	Photosystem II reaction center protein Z
Molecular weight formula_weight	6766.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Z,z

MTILFQLALAALVILSFVMVIGVPVAYASPQDWDRSKQLIFLGSGLWIALVLVVGVLNFFVV

Entity 20 Entity 20 polymer

Description description	Photosystem II protein Y
Molecular weight formula_weight	3859.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

DWRVLVVLLPVLLAAGWAVRNILPYAVKQVQKLL

Entity 21 Entity 21 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 22 Entity 22 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 23 Entity 23 non-polymer

Description description	BICARBONATE ION
Molecular weight formula_weight	61.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 24 Entity 24 non-polymer

Description description	CHLOROPHYLL A
Molecular weight formula_weight	893.5 kDa
Source method src_method	syn
Copy count entity_count	70

Entity 25 Entity 25 non-polymer

Description description	PHEOPHYTIN A
Molecular weight formula_weight	871.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 26 Entity 26 non-polymer

Description description	BETA-CAROTENE
Molecular weight formula_weight	536.9 kDa
Source method src_method	syn
Copy count entity_count	22

Entity 27 Entity 27 non-polymer

Description description	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
Molecular weight formula_weight	795.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 28 Entity 28 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	35

Entity 29 Entity 29 non-polymer

Description description	DODECYL-BETA-D-MALTOSIDE
Molecular weight formula_weight	510.6 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 30 Entity 30 non-polymer

Description description	CA-MN4-O5 CLUSTER
Molecular weight formula_weight	339.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 31 Entity 31 non-polymer

Description description	;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 ;
Molecular weight formula_weight	749.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 32 Entity 32 non-polymer

Description description	UNKNOWN LIGAND
Source method src_method	syn
Copy count entity_count	18

Entity 33 Entity 33 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 34 Entity 34 non-polymer

Description description	heptyl 1-thio-beta-D-glucopyranoside
Molecular weight formula_weight	294.4 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 35 Entity 35 non-polymer

Description description	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
Molecular weight formula_weight	787.2 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 36 Entity 36 non-polymer

Description description	DIGALACTOSYL DIACYL GLYCEROL (DGDG)
Molecular weight formula_weight	949.3 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 37 Entity 37 non-polymer

Description description	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
Molecular weight formula_weight	723.0 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 38 Entity 38 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 39 Entity 39 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 40 Entity 40 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 41 Entity 41 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2585

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (18 domains)

Domain ID domain_id	d6jlja_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.26 — Bacterial photosystem II reaction centre, L and M subunits
Superfamily Superfamily superfamily	f.26.1 — Bacterial photosystem II reaction centre, L and M subunits
Family Family family	f.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits

Domain ID domain_id	d6jljb_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.55 — Photosystem II antenna protein-like
Superfamily Superfamily superfamily	f.55.1 — Photosystem II antenna protein-like
Family Family family	f.55.1.1 — Photosystem II antenna protein-like

Domain ID domain_id	d6jljc_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.55 — Photosystem II antenna protein-like
Superfamily Superfamily superfamily	f.55.1 — Photosystem II antenna protein-like
Family Family family	f.55.1.1 — Photosystem II antenna protein-like

Domain ID domain_id	d6jljd_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.26 — Bacterial photosystem II reaction centre, L and M subunits
Superfamily Superfamily superfamily	f.26.1 — Bacterial photosystem II reaction centre, L and M subunits
Family Family family	f.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits

Domain ID domain_id	d6jlje_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.38 — Cytochrome b559 subunits
Family Family family	f.23.38.1 — Cytochrome b559 subunits

Domain ID domain_id	d6jljf_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.38 — Cytochrome b559 subunits
Family Family family	f.23.38.1 — Cytochrome b559 subunits

Domain ID domain_id	d6jljh_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.33 — Photosystem II 10 kDa phosphoprotein PsbH
Family Family family	f.23.33.1 — PsbH-like

Domain ID domain_id	d6jlji_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.37 — Photosystem II reaction center protein I, PsbI
Family Family family	f.23.37.1 — PsbI-like

Domain ID domain_id	d6jljj_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.32 — Photosystem II reaction center protein J, PsbJ
Family Family family	f.23.32.1 — PsbJ-like

Domain ID domain_id	d6jljk_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.36 — Photosystem II reaction center protein K, PsbK
Family Family family	f.23.36.1 — PsbK-like

Domain ID domain_id	d6jljl_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.31 — Photosystem II reaction center protein L, PsbL
Family Family family	f.23.31.1 — PsbL-like

Domain ID domain_id	d6jljm_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.35 — Photosystem II reaction center protein M, PsbM
Family Family family	f.23.35.1 — PsbM-like

Domain ID domain_id	d6jljo_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamily	f.4.1 — OMPA-like
Family Family family	f.4.1.4 — PsbO-like

Domain ID domain_id	d6jljt_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.34 — Photosystem II reaction center protein T, PsbT
Family Family family	f.23.34.1 — PsbT-like

Domain ID domain_id	d6jlju_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.12 — PsbU/PolX domain-like
Family Family family	a.60.12.2 — PsbU-like

Domain ID domain_id	d6jljv_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

Domain ID domain_id	d6jljx_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.40 — Photosystem II reaction center protein X, PsbX
Family Family family	f.23.40.1 — PsbX-like

Domain ID domain_id	d6jljz_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.17 — Transmembrane helix hairpin
Superfamily Superfamily superfamily	f.17.5 — PsbZ-like
Family Family family	f.17.5.1 — PsbZ-like

CATH v4.4 (14 domains)

Domain ID domain_id	6jljB02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	680 — Photosystem II CP47 reaction center protein
Homologous superfamily homologous superfamily	10 — Photosystem II CP47 reaction center protein

Domain ID domain_id	6jljC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	670 — photosystem ii from thermosynechococcus elongatus

Domain ID domain_id	6jljE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	860 — Photosystem II cytochrome b559, alpha subunit

Domain ID domain_id	6jljH01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	880 — Photosystem II reaction center protein H

Domain ID domain_id	6jljU01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	320 — Photosystem II 12 kDa extrinsic protein

Domain ID domain_id	6jljV00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	6jljZ00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	740 — Photosystem II PsbZ, reaction centre

Domain ID domain_id	6jljb02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	680 — Photosystem II CP47 reaction center protein
Homologous superfamily homologous superfamily	10 — Photosystem II CP47 reaction center protein

Domain ID domain_id	6jljc02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	670 — photosystem ii from thermosynechococcus elongatus

Domain ID domain_id	6jlje00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	860 — Photosystem II cytochrome b559, alpha subunit

Domain ID domain_id	6jljh01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	880 — Photosystem II reaction center protein H

Domain ID domain_id	6jlju01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	320 — Photosystem II 12 kDa extrinsic protein

Domain ID domain_id	6jljv00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	6jljz00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	740 — Photosystem II PsbZ, reaction centre

▶

Unit-cell length a length_a	121.970 Å
Unit-cell length b length_b	228.720 Å
Unit-cell length c length_c	286.980 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.1540
R_work r_work	0.1520
R_free r_free	0.1980

XFEL structure of cyanobacterial photosystem II (dark state, dataset1)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Photosystem II protein D1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Photosystem II CP47 reaction center protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Photosystem II CP43 reaction center protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Photosystem II D2 protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome b559 subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome b559 subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Photosystem II reaction center protein H

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Photosystem II reaction center protein I

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Photosystem II reaction center protein J

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Photosystem II reaction center protein K

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer