7dxh

Cryo-EM structure of PSII intermediate Psb28-PSII complex

Method: ELECTRON MICROSCOPY

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

Photosystem II reaction center Psb28 protein

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 18	Tsl0063 protein × 1 （Q8DMP8） Photosystem II protein D1 × 1 （P51765） Photosystem II CP47 reaction center protein × 1 （D0VWR1） Photosystem II D2 protein × 1 （D0VWR8） Cytochrome b559 subunit alpha × 1 （P12238） Cytochrome b559 subunit beta × 1 （P12239） Photosystem II reaction center protein H × 1 （P19052） Photosystem II reaction center protein I × 1 （P12240） Photosystem II reaction center protein L × 1 （P12241） Photosystem II reaction center protein M × 1 （P12312） Photosystem II reaction center protein T × 1 （P12313） Photosystem II reaction center protein X × 1 （D0VWR4） Photosystem II CP43 reaction center protein × 1 （D0VWR7） Photosystem II reaction center protein K × 1 （Q9F1K9） Photosystem II reaction center protein Z × 1 （D0VWR5） Photosystem II reaction center protein Ycf12 × 1 （D0VWR3） unidentified transmembrane protein × 1 (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CHLOROPHYLL A × 34 BETA-CAROTENE × 9 CHLORIDE ION × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHEOPHYTIN A × 2 DODECYL-BETA-D-MALTOSIDE × 3 FE (II) ION × 1 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 UNKNOWN LIGAND × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 heptyl 1-thio-beta-D-glucopyranoside × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSB28_THEEB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–116； UniProt 1–116

Tsl0063 protein

OrganismNot specified

UniProt Q8DMP8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 18	Photosystem II reaction center Psb28 protein × 1 （Q8DLJ8） Photosystem II protein D1 × 1 （P51765） Photosystem II CP47 reaction center protein × 1 （D0VWR1） Photosystem II D2 protein × 1 （D0VWR8） Cytochrome b559 subunit alpha × 1 （P12238） Cytochrome b559 subunit beta × 1 （P12239） Photosystem II reaction center protein H × 1 （P19052） Photosystem II reaction center protein I × 1 （P12240） Photosystem II reaction center protein L × 1 （P12241） Photosystem II reaction center protein M × 1 （P12312） Photosystem II reaction center protein T × 1 （P12313） Photosystem II reaction center protein X × 1 （D0VWR4） Photosystem II CP43 reaction center protein × 1 （D0VWR7） Photosystem II reaction center protein K × 1 （Q9F1K9） Photosystem II reaction center protein Z × 1 （D0VWR5） Photosystem II reaction center protein Ycf12 × 1 （D0VWR3） unidentified transmembrane protein × 1 (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CHLOROPHYLL A × 34 BETA-CAROTENE × 9 CHLORIDE ION × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHEOPHYTIN A × 2 DODECYL-BETA-D-MALTOSIDE × 3 FE (II) ION × 1 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 UNKNOWN LIGAND × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 heptyl 1-thio-beta-D-glucopyranoside × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8DMP8_THEEB
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–56； UniProt 1–56

Photosystem II protein D1

OrganismNot specified

UniProt P51765

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 18	Photosystem II reaction center Psb28 protein × 1 （Q8DLJ8） Tsl0063 protein × 1 （Q8DMP8） Photosystem II CP47 reaction center protein × 1 （D0VWR1） Photosystem II D2 protein × 1 （D0VWR8） Cytochrome b559 subunit alpha × 1 （P12238） Cytochrome b559 subunit beta × 1 （P12239） Photosystem II reaction center protein H × 1 （P19052） Photosystem II reaction center protein I × 1 （P12240） Photosystem II reaction center protein L × 1 （P12241） Photosystem II reaction center protein M × 1 （P12312） Photosystem II reaction center protein T × 1 （P12313） Photosystem II reaction center protein X × 1 （D0VWR4） Photosystem II CP43 reaction center protein × 1 （D0VWR7） Photosystem II reaction center protein K × 1 （Q9F1K9） Photosystem II reaction center protein Z × 1 （D0VWR5） Photosystem II reaction center protein Ycf12 × 1 （D0VWR3） unidentified transmembrane protein × 1 (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CHLOROPHYLL A × 34 BETA-CAROTENE × 9 CHLORIDE ION × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHEOPHYTIN A × 2 DODECYL-BETA-D-MALTOSIDE × 3 FE (II) ION × 1 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 UNKNOWN LIGAND × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 heptyl 1-thio-beta-D-glucopyranoside × 1	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	3
Chains and sequence ranges	Author chain a； PDBConstruct 1–360； UniProt 1–360

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 18	Photosystem II reaction center Psb28 protein × 1 （Q8DLJ8） Tsl0063 protein × 1 （Q8DMP8） Photosystem II protein D1 × 1 （P51765） Photosystem II D2 protein × 1 （D0VWR8） Cytochrome b559 subunit alpha × 1 （P12238） Cytochrome b559 subunit beta × 1 （P12239） Photosystem II reaction center protein H × 1 （P19052） Photosystem II reaction center protein I × 1 （P12240） Photosystem II reaction center protein L × 1 （P12241） Photosystem II reaction center protein M × 1 （P12312） Photosystem II reaction center protein T × 1 （P12313） Photosystem II reaction center protein X × 1 （D0VWR4） Photosystem II CP43 reaction center protein × 1 （D0VWR7） Photosystem II reaction center protein K × 1 （Q9F1K9） Photosystem II reaction center protein Z × 1 （D0VWR5） Photosystem II reaction center protein Ycf12 × 1 （D0VWR3） unidentified transmembrane protein × 1 (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CHLOROPHYLL A × 34 BETA-CAROTENE × 9 CHLORIDE ION × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHEOPHYTIN A × 2 DODECYL-BETA-D-MALTOSIDE × 3 FE (II) ION × 1 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 UNKNOWN LIGAND × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 heptyl 1-thio-beta-D-glucopyranoside × 1	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	4
Chains and sequence ranges	Author chain b； PDBConstruct 1–505； UniProt 1–505

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 18	Photosystem II reaction center Psb28 protein × 1 （Q8DLJ8） Tsl0063 protein × 1 （Q8DMP8） Photosystem II protein D1 × 1 （P51765） Photosystem II CP47 reaction center protein × 1 （D0VWR1） Cytochrome b559 subunit alpha × 1 （P12238） Cytochrome b559 subunit beta × 1 （P12239） Photosystem II reaction center protein H × 1 （P19052） Photosystem II reaction center protein I × 1 （P12240） Photosystem II reaction center protein L × 1 （P12241） Photosystem II reaction center protein M × 1 （P12312） Photosystem II reaction center protein T × 1 （P12313） Photosystem II reaction center protein X × 1 （D0VWR4） Photosystem II CP43 reaction center protein × 1 （D0VWR7） Photosystem II reaction center protein K × 1 （Q9F1K9） Photosystem II reaction center protein Z × 1 （D0VWR5） Photosystem II reaction center protein Ycf12 × 1 （D0VWR3） unidentified transmembrane protein × 1 (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CHLOROPHYLL A × 34 BETA-CAROTENE × 9 CHLORIDE ION × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHEOPHYTIN A × 2 DODECYL-BETA-D-MALTOSIDE × 3 FE (II) ION × 1 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 UNKNOWN LIGAND × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 heptyl 1-thio-beta-D-glucopyranoside × 1	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	5
Chains and sequence ranges	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 18	Photosystem II reaction center Psb28 protein × 1 （Q8DLJ8） Tsl0063 protein × 1 （Q8DMP8） Photosystem II protein D1 × 1 （P51765） Photosystem II CP47 reaction center protein × 1 （D0VWR1） Photosystem II D2 protein × 1 （D0VWR8） Cytochrome b559 subunit beta × 1 （P12239） Photosystem II reaction center protein H × 1 （P19052） Photosystem II reaction center protein I × 1 （P12240） Photosystem II reaction center protein L × 1 （P12241） Photosystem II reaction center protein M × 1 （P12312） Photosystem II reaction center protein T × 1 （P12313） Photosystem II reaction center protein X × 1 （D0VWR4） Photosystem II CP43 reaction center protein × 1 （D0VWR7） Photosystem II reaction center protein K × 1 （Q9F1K9） Photosystem II reaction center protein Z × 1 （D0VWR5） Photosystem II reaction center protein Ycf12 × 1 （D0VWR3） unidentified transmembrane protein × 1 (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CHLOROPHYLL A × 34 BETA-CAROTENE × 9 CHLORIDE ION × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHEOPHYTIN A × 2 DODECYL-BETA-D-MALTOSIDE × 3 FE (II) ION × 1 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 UNKNOWN LIGAND × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 heptyl 1-thio-beta-D-glucopyranoside × 1	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	6
Chains and sequence ranges	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 18	Photosystem II reaction center Psb28 protein × 1 （Q8DLJ8） Tsl0063 protein × 1 （Q8DMP8） Photosystem II protein D1 × 1 （P51765） Photosystem II CP47 reaction center protein × 1 （D0VWR1） Photosystem II D2 protein × 1 （D0VWR8） Cytochrome b559 subunit alpha × 1 （P12238） Photosystem II reaction center protein H × 1 （P19052） Photosystem II reaction center protein I × 1 （P12240） Photosystem II reaction center protein L × 1 （P12241） Photosystem II reaction center protein M × 1 （P12312） Photosystem II reaction center protein T × 1 （P12313） Photosystem II reaction center protein X × 1 （D0VWR4） Photosystem II CP43 reaction center protein × 1 （D0VWR7） Photosystem II reaction center protein K × 1 （Q9F1K9） Photosystem II reaction center protein Z × 1 （D0VWR5） Photosystem II reaction center protein Ycf12 × 1 （D0VWR3） unidentified transmembrane protein × 1 (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CHLOROPHYLL A × 34 BETA-CAROTENE × 9 CHLORIDE ION × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHEOPHYTIN A × 2 DODECYL-BETA-D-MALTOSIDE × 3 FE (II) ION × 1 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 UNKNOWN LIGAND × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 heptyl 1-thio-beta-D-glucopyranoside × 1	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	7
Chains and sequence ranges	Author chain f； PDBConstruct 1–45； UniProt 1–45

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 18	Photosystem II reaction center Psb28 protein × 1 （Q8DLJ8） Tsl0063 protein × 1 （Q8DMP8） Photosystem II protein D1 × 1 （P51765） Photosystem II CP47 reaction center protein × 1 （D0VWR1） Photosystem II D2 protein × 1 （D0VWR8） Cytochrome b559 subunit alpha × 1 （P12238） Cytochrome b559 subunit beta × 1 （P12239） Photosystem II reaction center protein I × 1 （P12240） Photosystem II reaction center protein L × 1 （P12241） Photosystem II reaction center protein M × 1 （P12312） Photosystem II reaction center protein T × 1 （P12313） Photosystem II reaction center protein X × 1 （D0VWR4） Photosystem II CP43 reaction center protein × 1 （D0VWR7） Photosystem II reaction center protein K × 1 （Q9F1K9） Photosystem II reaction center protein Z × 1 （D0VWR5） Photosystem II reaction center protein Ycf12 × 1 （D0VWR3） unidentified transmembrane protein × 1 (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CHLOROPHYLL A × 34 BETA-CAROTENE × 9 CHLORIDE ION × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHEOPHYTIN A × 2 DODECYL-BETA-D-MALTOSIDE × 3 FE (II) ION × 1 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 UNKNOWN LIGAND × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 heptyl 1-thio-beta-D-glucopyranoside × 1	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	8
Chains and sequence ranges	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 18	Photosystem II reaction center Psb28 protein × 1 （Q8DLJ8） Tsl0063 protein × 1 （Q8DMP8） Photosystem II protein D1 × 1 （P51765） Photosystem II CP47 reaction center protein × 1 （D0VWR1） Photosystem II D2 protein × 1 （D0VWR8） Cytochrome b559 subunit alpha × 1 （P12238） Cytochrome b559 subunit beta × 1 （P12239） Photosystem II reaction center protein H × 1 （P19052） Photosystem II reaction center protein L × 1 （P12241） Photosystem II reaction center protein M × 1 （P12312） Photosystem II reaction center protein T × 1 （P12313） Photosystem II reaction center protein X × 1 （D0VWR4） Photosystem II CP43 reaction center protein × 1 （D0VWR7） Photosystem II reaction center protein K × 1 （Q9F1K9） Photosystem II reaction center protein Z × 1 （D0VWR5） Photosystem II reaction center protein Ycf12 × 1 （D0VWR3） unidentified transmembrane protein × 1 (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CHLOROPHYLL A × 34 BETA-CAROTENE × 9 CHLORIDE ION × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHEOPHYTIN A × 2 DODECYL-BETA-D-MALTOSIDE × 3 FE (II) ION × 1 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 UNKNOWN LIGAND × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 heptyl 1-thio-beta-D-glucopyranoside × 1	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	9
Chains and sequence ranges	Author chain i； PDBConstruct 1–38； UniProt 1–38

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 18	Photosystem II reaction center Psb28 protein × 1 （Q8DLJ8） Tsl0063 protein × 1 （Q8DMP8） Photosystem II protein D1 × 1 （P51765） Photosystem II CP47 reaction center protein × 1 （D0VWR1） Photosystem II D2 protein × 1 （D0VWR8） Cytochrome b559 subunit alpha × 1 （P12238） Cytochrome b559 subunit beta × 1 （P12239） Photosystem II reaction center protein H × 1 （P19052） Photosystem II reaction center protein I × 1 （P12240） Photosystem II reaction center protein M × 1 （P12312） Photosystem II reaction center protein T × 1 （P12313） Photosystem II reaction center protein X × 1 （D0VWR4） Photosystem II CP43 reaction center protein × 1 （D0VWR7） Photosystem II reaction center protein K × 1 （Q9F1K9） Photosystem II reaction center protein Z × 1 （D0VWR5） Photosystem II reaction center protein Ycf12 × 1 （D0VWR3） unidentified transmembrane protein × 1 (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CHLOROPHYLL A × 34 BETA-CAROTENE × 9 CHLORIDE ION × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHEOPHYTIN A × 2 DODECYL-BETA-D-MALTOSIDE × 3 FE (II) ION × 1 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 UNKNOWN LIGAND × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 heptyl 1-thio-beta-D-glucopyranoside × 1	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	10
Chains and sequence ranges	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 18	Photosystem II reaction center Psb28 protein × 1 （Q8DLJ8） Tsl0063 protein × 1 （Q8DMP8） Photosystem II protein D1 × 1 （P51765） Photosystem II CP47 reaction center protein × 1 （D0VWR1） Photosystem II D2 protein × 1 （D0VWR8） Cytochrome b559 subunit alpha × 1 （P12238） Cytochrome b559 subunit beta × 1 （P12239） Photosystem II reaction center protein H × 1 （P19052） Photosystem II reaction center protein I × 1 （P12240） Photosystem II reaction center protein L × 1 （P12241） Photosystem II reaction center protein T × 1 （P12313） Photosystem II reaction center protein X × 1 （D0VWR4） Photosystem II CP43 reaction center protein × 1 （D0VWR7） Photosystem II reaction center protein K × 1 （Q9F1K9） Photosystem II reaction center protein Z × 1 （D0VWR5） Photosystem II reaction center protein Ycf12 × 1 （D0VWR3） unidentified transmembrane protein × 1 (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CHLOROPHYLL A × 34 BETA-CAROTENE × 9 CHLORIDE ION × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHEOPHYTIN A × 2 DODECYL-BETA-D-MALTOSIDE × 3 FE (II) ION × 1 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 UNKNOWN LIGAND × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 heptyl 1-thio-beta-D-glucopyranoside × 1	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	11
Chains and sequence ranges	Author chain m； PDBConstruct 1–36； UniProt 1–36

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 18	Photosystem II reaction center Psb28 protein × 1 （Q8DLJ8） Tsl0063 protein × 1 （Q8DMP8） Photosystem II protein D1 × 1 （P51765） Photosystem II CP47 reaction center protein × 1 （D0VWR1） Photosystem II D2 protein × 1 （D0VWR8） Cytochrome b559 subunit alpha × 1 （P12238） Cytochrome b559 subunit beta × 1 （P12239） Photosystem II reaction center protein H × 1 （P19052） Photosystem II reaction center protein I × 1 （P12240） Photosystem II reaction center protein L × 1 （P12241） Photosystem II reaction center protein M × 1 （P12312） Photosystem II reaction center protein X × 1 （D0VWR4） Photosystem II CP43 reaction center protein × 1 （D0VWR7） Photosystem II reaction center protein K × 1 （Q9F1K9） Photosystem II reaction center protein Z × 1 （D0VWR5） Photosystem II reaction center protein Ycf12 × 1 （D0VWR3） unidentified transmembrane protein × 1 (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CHLOROPHYLL A × 34 BETA-CAROTENE × 9 CHLORIDE ION × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHEOPHYTIN A × 2 DODECYL-BETA-D-MALTOSIDE × 3 FE (II) ION × 1 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 UNKNOWN LIGAND × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 heptyl 1-thio-beta-D-glucopyranoside × 1	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	12
Chains and sequence ranges	Author chain t； PDBConstruct 1–32； UniProt 1–32

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 18	Photosystem II reaction center Psb28 protein × 1 （Q8DLJ8） Tsl0063 protein × 1 （Q8DMP8） Photosystem II protein D1 × 1 （P51765） Photosystem II CP47 reaction center protein × 1 （D0VWR1） Photosystem II D2 protein × 1 （D0VWR8） Cytochrome b559 subunit alpha × 1 （P12238） Cytochrome b559 subunit beta × 1 （P12239） Photosystem II reaction center protein H × 1 （P19052） Photosystem II reaction center protein I × 1 （P12240） Photosystem II reaction center protein L × 1 （P12241） Photosystem II reaction center protein M × 1 （P12312） Photosystem II reaction center protein T × 1 （P12313） Photosystem II CP43 reaction center protein × 1 （D0VWR7） Photosystem II reaction center protein K × 1 （Q9F1K9） Photosystem II reaction center protein Z × 1 （D0VWR5） Photosystem II reaction center protein Ycf12 × 1 （D0VWR3） unidentified transmembrane protein × 1 (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CHLOROPHYLL A × 34 BETA-CAROTENE × 9 CHLORIDE ION × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHEOPHYTIN A × 2 DODECYL-BETA-D-MALTOSIDE × 3 FE (II) ION × 1 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 UNKNOWN LIGAND × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 heptyl 1-thio-beta-D-glucopyranoside × 1	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	13
Chains and sequence ranges	Author chain x； PDBConstruct 1–40； UniProt 1–40

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 18	Photosystem II reaction center Psb28 protein × 1 （Q8DLJ8） Tsl0063 protein × 1 （Q8DMP8） Photosystem II protein D1 × 1 （P51765） Photosystem II CP47 reaction center protein × 1 （D0VWR1） Photosystem II D2 protein × 1 （D0VWR8） Cytochrome b559 subunit alpha × 1 （P12238） Cytochrome b559 subunit beta × 1 （P12239） Photosystem II reaction center protein H × 1 （P19052） Photosystem II reaction center protein I × 1 （P12240） Photosystem II reaction center protein L × 1 （P12241） Photosystem II reaction center protein M × 1 （P12312） Photosystem II reaction center protein T × 1 （P12313） Photosystem II reaction center protein X × 1 （D0VWR4） Photosystem II reaction center protein K × 1 （Q9F1K9） Photosystem II reaction center protein Z × 1 （D0VWR5） Photosystem II reaction center protein Ycf12 × 1 （D0VWR3） unidentified transmembrane protein × 1 (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CHLOROPHYLL A × 34 BETA-CAROTENE × 9 CHLORIDE ION × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHEOPHYTIN A × 2 DODECYL-BETA-D-MALTOSIDE × 3 FE (II) ION × 1 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 UNKNOWN LIGAND × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 heptyl 1-thio-beta-D-glucopyranoside × 1	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	14
Chains and sequence ranges	Author chain c； PDBConstruct 1–451； UniProt 1–451

Photosystem II reaction center protein K

OrganismNot specified

UniProt Q9F1K9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 18	Photosystem II reaction center Psb28 protein × 1 （Q8DLJ8） Tsl0063 protein × 1 （Q8DMP8） Photosystem II protein D1 × 1 （P51765） Photosystem II CP47 reaction center protein × 1 （D0VWR1） Photosystem II D2 protein × 1 （D0VWR8） Cytochrome b559 subunit alpha × 1 （P12238） Cytochrome b559 subunit beta × 1 （P12239） Photosystem II reaction center protein H × 1 （P19052） Photosystem II reaction center protein I × 1 （P12240） Photosystem II reaction center protein L × 1 （P12241） Photosystem II reaction center protein M × 1 （P12312） Photosystem II reaction center protein T × 1 （P12313） Photosystem II reaction center protein X × 1 （D0VWR4） Photosystem II CP43 reaction center protein × 1 （D0VWR7） Photosystem II reaction center protein Z × 1 （D0VWR5） Photosystem II reaction center protein Ycf12 × 1 （D0VWR3） unidentified transmembrane protein × 1 (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CHLOROPHYLL A × 34 BETA-CAROTENE × 9 CHLORIDE ION × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHEOPHYTIN A × 2 DODECYL-BETA-D-MALTOSIDE × 3 FE (II) ION × 1 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 UNKNOWN LIGAND × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 heptyl 1-thio-beta-D-glucopyranoside × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBK_THEEB
Isoform	—
PDB entities	15
Chains and sequence ranges	Author chain k； PDBConstruct 1–46； UniProt 1–46

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 18	Photosystem II reaction center Psb28 protein × 1 （Q8DLJ8） Tsl0063 protein × 1 （Q8DMP8） Photosystem II protein D1 × 1 （P51765） Photosystem II CP47 reaction center protein × 1 （D0VWR1） Photosystem II D2 protein × 1 （D0VWR8） Cytochrome b559 subunit alpha × 1 （P12238） Cytochrome b559 subunit beta × 1 （P12239） Photosystem II reaction center protein H × 1 （P19052） Photosystem II reaction center protein I × 1 （P12240） Photosystem II reaction center protein L × 1 （P12241） Photosystem II reaction center protein M × 1 （P12312） Photosystem II reaction center protein T × 1 （P12313） Photosystem II reaction center protein X × 1 （D0VWR4） Photosystem II CP43 reaction center protein × 1 （D0VWR7） Photosystem II reaction center protein K × 1 （Q9F1K9） Photosystem II reaction center protein Ycf12 × 1 （D0VWR3） unidentified transmembrane protein × 1 (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CHLOROPHYLL A × 34 BETA-CAROTENE × 9 CHLORIDE ION × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHEOPHYTIN A × 2 DODECYL-BETA-D-MALTOSIDE × 3 FE (II) ION × 1 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 UNKNOWN LIGAND × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 heptyl 1-thio-beta-D-glucopyranoside × 1	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	16
Chains and sequence ranges	Author chain z； PDBConstruct 1–62； UniProt 1–62

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 18	Photosystem II reaction center Psb28 protein × 1 （Q8DLJ8） Tsl0063 protein × 1 （Q8DMP8） Photosystem II protein D1 × 1 （P51765） Photosystem II CP47 reaction center protein × 1 （D0VWR1） Photosystem II D2 protein × 1 （D0VWR8） Cytochrome b559 subunit alpha × 1 （P12238） Cytochrome b559 subunit beta × 1 （P12239） Photosystem II reaction center protein H × 1 （P19052） Photosystem II reaction center protein I × 1 （P12240） Photosystem II reaction center protein L × 1 （P12241） Photosystem II reaction center protein M × 1 （P12312） Photosystem II reaction center protein T × 1 （P12313） Photosystem II reaction center protein X × 1 （D0VWR4） Photosystem II CP43 reaction center protein × 1 （D0VWR7） Photosystem II reaction center protein K × 1 （Q9F1K9） Photosystem II reaction center protein Z × 1 （D0VWR5） unidentified transmembrane protein × 1 (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CHLOROPHYLL A × 34 BETA-CAROTENE × 9 CHLORIDE ION × 2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHEOPHYTIN A × 2 DODECYL-BETA-D-MALTOSIDE × 3 FE (II) ION × 1 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 UNKNOWN LIGAND × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 heptyl 1-thio-beta-D-glucopyranoside × 1	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

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	7dxh
Deposition date deposition_date	2021-01-18
Structure title title	Cryo-EM structure of PSII intermediate Psb28-PSII complex
Keywords keywords	Photosystem II; Cryo-EM; assembly; repair; Psb28; Tsl0063, PLANT PROTEIN; PLANT PROTEIN
Experimental Method method	ELECTRON 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.

7dxh__assembly_1__model_1

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

Download this curve (.dat)

7dxh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7dxh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.19 Å
Rg (electron density)	41.05 Å
Total Rg	41.56 Å
Atom count	20054
Residues	2150
Excluded volume	370580 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7dxh__assembly_1__model_1`	octadecameric （18）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (31)

Entity 1 Entity 1 polymer

Description description	Photosystem II reaction center Psb28 protein
Molecular weight formula_weight	13188.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	20054

MGAMAEIQFIRGINEEVVPDVRLTRARDGSSGQAMFYFDNPKIVQEGNLEVTGMYMVDEEGEIVTRDVNAKFINGQPVAIEATYTMRSPQEWDRFIRFMDRYAASHGLGFQKSENS

Entity 2 Entity 2 polymer

Description description	Tsl0063 protein
Molecular weight formula_weight	5943.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MRYTTDEGGRLNNFAIEPKVYQAQPWTPQQKVRAALLVGGGLLLVAGLVAIAVGVS

Entity 3 Entity 3 polymer

Description description	Photosystem II protein D1
Molecular weight formula_weight	39792.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a

MTTTLQRRESANLWERFCNWVTSTDNRLYVGWFGVIMIPTLLAATICFVIAFIAAPPVDIDGIREPVSGSLLYGNNIITGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIIFHFLLGASCYMGRQWELSYRLGMRPWICVAYSAPLASAFAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHQLGVAGVFGGALFCAMHGSLVTSSLIRETTETESANYGYKFGQEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWRVVGVWFAALGISTMAFNLNGFNFNHSVIDAKGNVINTWADIINRANLGMEVMHERNAHNFPLDLASAESAPVAMIAPSING

Entity 4 Entity 4 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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	b

GLPWYRVHTVLINDPGRLIAAHLMHTALVAGWAGSMALYELATFDPSDPVLNPMWRQGMFVLPFMARLGVTGSWSGWSITGETGIDPGFWSFEGVALAHIVLSGLLFLAACWHWVYWDLELFRDPRTGEPALDLPKMFGIHLFLAGLLCFGFGAFHLTGLFGPGMWVSDPYGLTGSVQPVAPEWGPDGFNPYNPGGVVAHHIAAGIVGIIAGLFHILVRPPQRLYKALRMGNIETVLSSSIAAVFFAAFVVAGTMWYGSATTPIELFGPTRYQWDSSYFQQEINRRVQASLASGATLEEAWSAIPEKLAFYDYIGNNPAKGGLFRTGPMNKGDGIAQAWKGHAVFRNKEGEELFVRRMPAFFESFPVILTDKNGVVKADIPFRRAESKYSFEQQGVTVSFYGGELNGQTFTDPPTVKSYARKAIFGEIFEFDTETLNSDGIFRTSPRGWFTFAHAVFALLFFFGHIWHGARTLFRDVFSGIDPELSPEQVEWGFYQKVGDVTTRK

Entity 5 Entity 5 polymer

Description description	Photosystem II D2 protein
Molecular weight formula_weight	38404.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	d

ERGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTGTTFVTSWYTHGLASSYLEGCNFLTVAVSTPANSMGHSLLLLWGPEAQGDFTRWCQLGGLWTFIALHGAFGLIGFMLRQFEIARLVGVRPYNAIAFSAPIAVFVSVFLIYPLGQSSWFFAPSFGVAAIFRFLLFFQGFHNWTLNPFHMMGVAGVLGGALLCAIHGATVENTLFQDGEGASTFRAFNPTQAEETYSMVTANRFWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRSYDFISQEIRAAEDPEFETFYTKNLLLNEGIRAWMAPQDQPHENFVFPEEVLPRGNAL

Entity 6 Entity 6 polymer

Description description	Cytochrome b559 subunit alpha
Molecular weight formula_weight	9580.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	e

MAGTTGERPFSDIITSVRYWVIHSITIPALFIAGWLFVSTGLAYDVFGTPRPDSYYAQEQRSIPLVTDRFEAKQQVETFLEQLK

Entity 7 Entity 7 polymer

Description description	Cytochrome b559 subunit beta
Molecular weight formula_weight	5067.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	f

MTSNTPNQEPVSYPIFTVRWVAVHTLAVPTIFFLGAIAAMQFIQR

Entity 8 Entity 8 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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	h

ARRTWLGDILRPLNSEYGKVAPGWGTTPLMAVFMGLFLVFLLIILEIYNSTLILDGVNVSWKALG

Entity 9 Entity 9 polymer

Description description	Photosystem II reaction center protein I
Molecular weight formula_weight	4410.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	i

METLKITVYIVVTFFVLLFVFGFLSGDPARNPKRKDLE

Entity 10 Entity 10 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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	l

MEPNPNRQPVELNRTSLYLGLLLILVLALLFSSYFFN

Entity 11 Entity 11 polymer

Description description	Photosystem II reaction center protein M
Molecular weight formula_weight	4015.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	m

MEVNQLGFIATALFVLVPSVFLIILYVQTESQQKSS

Entity 12 Entity 12 polymer

Description description	Photosystem II reaction center protein T
Molecular weight formula_weight	3878.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	t

METITYVFIFACIIALFFFAIFFREPPRITKK

Entity 13 Entity 13 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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	x

TITPSLKGFFIGLLSGAVVLGLTFAVLIAISQIDKVQRSL

Entity 14 Entity 14 polymer

Description description	Photosystem II CP43 reaction center protein
Molecular weight formula_weight	49207.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	c

ATNRDQESSGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMTLFELAHFIPEKPMYEQGLILIPHIATLGWGVGPGGEVVDTFPFFVVGVVHLISSAVLGFGGVYHAIRGPETLEEYSSFFGYDWKDKNKMTTILGFHLIVLGIGALLLVAKAMFFGGLYDTWAPGGGDVRVITNPTLDPRVIFGYLLKSPFGGEGWIVSVNNLEDVVGGHIWIGLICIAGGIWHILTTPFGWARRAFIWSGEAYLSYSLGALSMMGFIATCFVWFNNTVYPSEFYGPTGPEASQAQAMTFLIRDQKLGANVGSAQGPTGLGKYLMRSPTGEIIFGGETMRFWDFRGPWLEPLRGPNGLDLNKIKNDIQPWQERRAAEYMTHAPLGSLNSVGGVATEINSVNFVSPRSWLATSHFVLAFFFLVGHLWHAGRARAAAAGFEKGIDRESEPVLSMPSLD

Entity 15 Entity 15 polymer

Description description	Photosystem II reaction center protein K
Molecular weight formula_weight	5028.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	k

MIDALVLVAKLPEAYAIFDPLVDVLPVIPVLFLALAFVWQAAVGFR

Entity 16 Entity 16 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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	z

MTILFQLALAALVILSFVMVIGVPVAYASPQDWDRSKQLIFLGSGLWIALVLVVGVLNFFVV

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	y

EVIAQLTMIAMIGIAGPMIIFLLAVRRGNL

Entity 18 Entity 18 polymer

Description description	unidentified transmembrane protein
Molecular weight formula_weight	1652.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

AAAAAAAAAAAAAAAAAAAAAAA

Entity 19 Entity 19 non-polymer

Description description	(1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
Molecular weight formula_weight	689.0 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 20 Entity 20 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	2

Entity 21 Entity 21 non-polymer

Description description	CHLOROPHYLL A
Molecular weight formula_weight	893.5 kDa
Source method src_method	syn
Copy count entity_count	34

Entity 22 Entity 22 non-polymer

Description description	BETA-CAROTENE
Molecular weight formula_weight	536.9 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 23 Entity 23 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 24 Entity 24 non-polymer

Description description	DIGALACTOSYL DIACYL GLYCEROL (DGDG)
Molecular weight formula_weight	949.3 kDa
Source method src_method	syn
Copy count entity_count	4

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	2

Entity 26 Entity 26 non-polymer

Description description	DODECYL-BETA-D-MALTOSIDE
Molecular weight formula_weight	510.6 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 27 Entity 27 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 28 Entity 28 non-polymer

Description description	5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE
Molecular weight formula_weight	613.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 29 Entity 29 non-polymer

Description description	UNKNOWN LIGAND
Molecular weight formula_weight	294.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 30 Entity 30 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 31 Entity 31 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	1

▼

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d7dxha_
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	d7dxhb_
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	d7dxhc_
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	d7dxhd_
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	d7dxhe_
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	d7dxhf_
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	d7dxhh_
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	d7dxhi_
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	d7dxhk_
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	d7dxhl_
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	d7dxhm_
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	d7dxht_
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	d7dxhx_
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	d7dxhz_
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

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.14 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	194738

Cryo-EM structure of PSII intermediate Psb28-PSII complex

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

Photosystem II reaction center Psb28 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

Tsl0063 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 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 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 L

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer