8kde

Cryo-EM structure of an intermediate-state complex during the process of photosystem II repair

Method: ELECTRON MICROSCOPY

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

Photosystem II CP47 reaction center 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	Photosystem II D2 protein × 1 （P06007） Cytochrome b559 subunit alpha × 1 （P48268） Cytochrome b559 subunit beta × 1 （Q08363） Photosystem II reaction center protein H × 1 （P22666） Photosystem II reaction center protein I × 1 （P59763） Photosystem II reaction center protein K × 1 （P18263） Photosystem II reaction center protein L × 1 （P32974） Photosystem II reaction center protein M × 1 （P92277） Photosystem II reaction center protein T × 1 （P37256） Photosystem II reaction center protein Ycf12 × 1 （P50370） Uncharacterized protein × 1 （A8I846） Photosystem II reaction center protein Z × 1 （P92276） Thylakoid enriched factor 14 (TEF14) × 1 （A8HY43） Photosystem II repair factor 1 (PRF1) × 1 （A0A2K3DWM2） Photosystem II CP43 reaction center protein × 1 （P10898） Photosystem II protein D1 × 1 （P07753） Photosystem II repair factor 2 (PRF2) × 1 （A8HNG8） CHLOROPHYLL A × 35 BETA-CAROTENE × 10 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 ;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 ; × 1 PHEOPHYTIN A × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 RRR-ALPHA-TOCOPHERYLQUINONE × 1 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 1 BICARBONATE ION × 1 FE (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A218N8S0_CHLRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–508； UniProt 1–508

Photosystem II D2 protein

OrganismNot specified

UniProt P06007

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 CP47 reaction center protein × 1 （A0A218N8S0） Cytochrome b559 subunit alpha × 1 （P48268） Cytochrome b559 subunit beta × 1 （Q08363） Photosystem II reaction center protein H × 1 （P22666） Photosystem II reaction center protein I × 1 （P59763） Photosystem II reaction center protein K × 1 （P18263） Photosystem II reaction center protein L × 1 （P32974） Photosystem II reaction center protein M × 1 （P92277） Photosystem II reaction center protein T × 1 （P37256） Photosystem II reaction center protein Ycf12 × 1 （P50370） Uncharacterized protein × 1 （A8I846） Photosystem II reaction center protein Z × 1 （P92276） Thylakoid enriched factor 14 (TEF14) × 1 （A8HY43） Photosystem II repair factor 1 (PRF1) × 1 （A0A2K3DWM2） Photosystem II CP43 reaction center protein × 1 （P10898） Photosystem II protein D1 × 1 （P07753） Photosystem II repair factor 2 (PRF2) × 1 （A8HNG8） CHLOROPHYLL A × 35 BETA-CAROTENE × 10 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 ;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 ; × 1 PHEOPHYTIN A × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 RRR-ALPHA-TOCOPHERYLQUINONE × 1 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 1 BICARBONATE ION × 1 FE (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBD_CHLRE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–352； UniProt 1–352

Cytochrome b559 subunit alpha

OrganismNot specified

UniProt P48268

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 CP47 reaction center protein × 1 （A0A218N8S0） Photosystem II D2 protein × 1 （P06007） Cytochrome b559 subunit beta × 1 （Q08363） Photosystem II reaction center protein H × 1 （P22666） Photosystem II reaction center protein I × 1 （P59763） Photosystem II reaction center protein K × 1 （P18263） Photosystem II reaction center protein L × 1 （P32974） Photosystem II reaction center protein M × 1 （P92277） Photosystem II reaction center protein T × 1 （P37256） Photosystem II reaction center protein Ycf12 × 1 （P50370） Uncharacterized protein × 1 （A8I846） Photosystem II reaction center protein Z × 1 （P92276） Thylakoid enriched factor 14 (TEF14) × 1 （A8HY43） Photosystem II repair factor 1 (PRF1) × 1 （A0A2K3DWM2） Photosystem II CP43 reaction center protein × 1 （P10898） Photosystem II protein D1 × 1 （P07753） Photosystem II repair factor 2 (PRF2) × 1 （A8HNG8） CHLOROPHYLL A × 35 BETA-CAROTENE × 10 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 ;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 ; × 1 PHEOPHYTIN A × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 RRR-ALPHA-TOCOPHERYLQUINONE × 1 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 1 BICARBONATE ION × 1 FE (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBE_CHLRE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–82； UniProt 1–82

Cytochrome b559 subunit beta

OrganismNot specified

UniProt Q08363

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 CP47 reaction center protein × 1 （A0A218N8S0） Photosystem II D2 protein × 1 （P06007） Cytochrome b559 subunit alpha × 1 （P48268） Photosystem II reaction center protein H × 1 （P22666） Photosystem II reaction center protein I × 1 （P59763） Photosystem II reaction center protein K × 1 （P18263） Photosystem II reaction center protein L × 1 （P32974） Photosystem II reaction center protein M × 1 （P92277） Photosystem II reaction center protein T × 1 （P37256） Photosystem II reaction center protein Ycf12 × 1 （P50370） Uncharacterized protein × 1 （A8I846） Photosystem II reaction center protein Z × 1 （P92276） Thylakoid enriched factor 14 (TEF14) × 1 （A8HY43） Photosystem II repair factor 1 (PRF1) × 1 （A0A2K3DWM2） Photosystem II CP43 reaction center protein × 1 （P10898） Photosystem II protein D1 × 1 （P07753） Photosystem II repair factor 2 (PRF2) × 1 （A8HNG8） CHLOROPHYLL A × 35 BETA-CAROTENE × 10 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 ;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 ; × 1 PHEOPHYTIN A × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 RRR-ALPHA-TOCOPHERYLQUINONE × 1 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 1 BICARBONATE ION × 1 FE (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBF_CHLRE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 1–44； UniProt 1–44

Photosystem II reaction center protein H

OrganismNot specified

UniProt P22666

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 CP47 reaction center protein × 1 （A0A218N8S0） Photosystem II D2 protein × 1 （P06007） Cytochrome b559 subunit alpha × 1 （P48268） Cytochrome b559 subunit beta × 1 （Q08363） Photosystem II reaction center protein I × 1 （P59763） Photosystem II reaction center protein K × 1 （P18263） Photosystem II reaction center protein L × 1 （P32974） Photosystem II reaction center protein M × 1 （P92277） Photosystem II reaction center protein T × 1 （P37256） Photosystem II reaction center protein Ycf12 × 1 （P50370） Uncharacterized protein × 1 （A8I846） Photosystem II reaction center protein Z × 1 （P92276） Thylakoid enriched factor 14 (TEF14) × 1 （A8HY43） Photosystem II repair factor 1 (PRF1) × 1 （A0A2K3DWM2） Photosystem II CP43 reaction center protein × 1 （P10898） Photosystem II protein D1 × 1 （P07753） Photosystem II repair factor 2 (PRF2) × 1 （A8HNG8） CHLOROPHYLL A × 35 BETA-CAROTENE × 10 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 ;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 ; × 1 PHEOPHYTIN A × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 RRR-ALPHA-TOCOPHERYLQUINONE × 1 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 1 BICARBONATE ION × 1 FE (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBH_CHLRE
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain H； PDBConstruct 1–88； UniProt 1–88

Photosystem II reaction center protein I

OrganismNot specified

UniProt P59763

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 CP47 reaction center protein × 1 （A0A218N8S0） Photosystem II D2 protein × 1 （P06007） Cytochrome b559 subunit alpha × 1 （P48268） Cytochrome b559 subunit beta × 1 （Q08363） Photosystem II reaction center protein H × 1 （P22666） Photosystem II reaction center protein K × 1 （P18263） Photosystem II reaction center protein L × 1 （P32974） Photosystem II reaction center protein M × 1 （P92277） Photosystem II reaction center protein T × 1 （P37256） Photosystem II reaction center protein Ycf12 × 1 （P50370） Uncharacterized protein × 1 （A8I846） Photosystem II reaction center protein Z × 1 （P92276） Thylakoid enriched factor 14 (TEF14) × 1 （A8HY43） Photosystem II repair factor 1 (PRF1) × 1 （A0A2K3DWM2） Photosystem II CP43 reaction center protein × 1 （P10898） Photosystem II protein D1 × 1 （P07753） Photosystem II repair factor 2 (PRF2) × 1 （A8HNG8） CHLOROPHYLL A × 35 BETA-CAROTENE × 10 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 ;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 ; × 1 PHEOPHYTIN A × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 RRR-ALPHA-TOCOPHERYLQUINONE × 1 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 1 BICARBONATE ION × 1 FE (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBI_CHLRE
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain I； PDBConstruct 1–37； UniProt 1–37

Photosystem II reaction center protein K

OrganismNot specified

UniProt P18263

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 CP47 reaction center protein × 1 （A0A218N8S0） Photosystem II D2 protein × 1 （P06007） Cytochrome b559 subunit alpha × 1 （P48268） Cytochrome b559 subunit beta × 1 （Q08363） Photosystem II reaction center protein H × 1 （P22666） Photosystem II reaction center protein I × 1 （P59763） Photosystem II reaction center protein L × 1 （P32974） Photosystem II reaction center protein M × 1 （P92277） Photosystem II reaction center protein T × 1 （P37256） Photosystem II reaction center protein Ycf12 × 1 （P50370） Uncharacterized protein × 1 （A8I846） Photosystem II reaction center protein Z × 1 （P92276） Thylakoid enriched factor 14 (TEF14) × 1 （A8HY43） Photosystem II repair factor 1 (PRF1) × 1 （A0A2K3DWM2） Photosystem II CP43 reaction center protein × 1 （P10898） Photosystem II protein D1 × 1 （P07753） Photosystem II repair factor 2 (PRF2) × 1 （A8HNG8） CHLOROPHYLL A × 35 BETA-CAROTENE × 10 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 ;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 ; × 1 PHEOPHYTIN A × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 RRR-ALPHA-TOCOPHERYLQUINONE × 1 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 1 BICARBONATE ION × 1 FE (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBK_CHLRE
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain K； PDBConstruct 1–46； UniProt 1–46

Photosystem II reaction center protein L

OrganismNot specified

UniProt P32974

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 CP47 reaction center protein × 1 （A0A218N8S0） Photosystem II D2 protein × 1 （P06007） Cytochrome b559 subunit alpha × 1 （P48268） Cytochrome b559 subunit beta × 1 （Q08363） Photosystem II reaction center protein H × 1 （P22666） Photosystem II reaction center protein I × 1 （P59763） Photosystem II reaction center protein K × 1 （P18263） Photosystem II reaction center protein M × 1 （P92277） Photosystem II reaction center protein T × 1 （P37256） Photosystem II reaction center protein Ycf12 × 1 （P50370） Uncharacterized protein × 1 （A8I846） Photosystem II reaction center protein Z × 1 （P92276） Thylakoid enriched factor 14 (TEF14) × 1 （A8HY43） Photosystem II repair factor 1 (PRF1) × 1 （A0A2K3DWM2） Photosystem II CP43 reaction center protein × 1 （P10898） Photosystem II protein D1 × 1 （P07753） Photosystem II repair factor 2 (PRF2) × 1 （A8HNG8） CHLOROPHYLL A × 35 BETA-CAROTENE × 10 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 ;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 ; × 1 PHEOPHYTIN A × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 RRR-ALPHA-TOCOPHERYLQUINONE × 1 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 1 BICARBONATE ION × 1 FE (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBL_CHLRE
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain L； PDBConstruct 1–38； UniProt 1–38

Photosystem II reaction center protein M

OrganismNot specified

UniProt P92277

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 CP47 reaction center protein × 1 （A0A218N8S0） Photosystem II D2 protein × 1 （P06007） Cytochrome b559 subunit alpha × 1 （P48268） Cytochrome b559 subunit beta × 1 （Q08363） Photosystem II reaction center protein H × 1 （P22666） Photosystem II reaction center protein I × 1 （P59763） Photosystem II reaction center protein K × 1 （P18263） Photosystem II reaction center protein L × 1 （P32974） Photosystem II reaction center protein T × 1 （P37256） Photosystem II reaction center protein Ycf12 × 1 （P50370） Uncharacterized protein × 1 （A8I846） Photosystem II reaction center protein Z × 1 （P92276） Thylakoid enriched factor 14 (TEF14) × 1 （A8HY43） Photosystem II repair factor 1 (PRF1) × 1 （A0A2K3DWM2） Photosystem II CP43 reaction center protein × 1 （P10898） Photosystem II protein D1 × 1 （P07753） Photosystem II repair factor 2 (PRF2) × 1 （A8HNG8） CHLOROPHYLL A × 35 BETA-CAROTENE × 10 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 ;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 ; × 1 PHEOPHYTIN A × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 RRR-ALPHA-TOCOPHERYLQUINONE × 1 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 1 BICARBONATE ION × 1 FE (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBM_CHLRE
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain M； PDBConstruct 1–34； UniProt 1–34

Photosystem II reaction center protein T

OrganismNot specified

UniProt P37256

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 CP47 reaction center protein × 1 （A0A218N8S0） Photosystem II D2 protein × 1 （P06007） Cytochrome b559 subunit alpha × 1 （P48268） Cytochrome b559 subunit beta × 1 （Q08363） Photosystem II reaction center protein H × 1 （P22666） Photosystem II reaction center protein I × 1 （P59763） Photosystem II reaction center protein K × 1 （P18263） Photosystem II reaction center protein L × 1 （P32974） Photosystem II reaction center protein M × 1 （P92277） Photosystem II reaction center protein Ycf12 × 1 （P50370） Uncharacterized protein × 1 （A8I846） Photosystem II reaction center protein Z × 1 （P92276） Thylakoid enriched factor 14 (TEF14) × 1 （A8HY43） Photosystem II repair factor 1 (PRF1) × 1 （A0A2K3DWM2） Photosystem II CP43 reaction center protein × 1 （P10898） Photosystem II protein D1 × 1 （P07753） Photosystem II repair factor 2 (PRF2) × 1 （A8HNG8） CHLOROPHYLL A × 35 BETA-CAROTENE × 10 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 ;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 ; × 1 PHEOPHYTIN A × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 RRR-ALPHA-TOCOPHERYLQUINONE × 1 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 1 BICARBONATE ION × 1 FE (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBT_CHLRE
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain T； PDBConstruct 1–31； UniProt 1–31

Photosystem II reaction center protein Ycf12

OrganismNot specified

UniProt P50370

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 CP47 reaction center protein × 1 （A0A218N8S0） Photosystem II D2 protein × 1 （P06007） Cytochrome b559 subunit alpha × 1 （P48268） Cytochrome b559 subunit beta × 1 （Q08363） Photosystem II reaction center protein H × 1 （P22666） Photosystem II reaction center protein I × 1 （P59763） Photosystem II reaction center protein K × 1 （P18263） Photosystem II reaction center protein L × 1 （P32974） Photosystem II reaction center protein M × 1 （P92277） Photosystem II reaction center protein T × 1 （P37256） Uncharacterized protein × 1 （A8I846） Photosystem II reaction center protein Z × 1 （P92276） Thylakoid enriched factor 14 (TEF14) × 1 （A8HY43） Photosystem II repair factor 1 (PRF1) × 1 （A0A2K3DWM2） Photosystem II CP43 reaction center protein × 1 （P10898） Photosystem II protein D1 × 1 （P07753） Photosystem II repair factor 2 (PRF2) × 1 （A8HNG8） CHLOROPHYLL A × 35 BETA-CAROTENE × 10 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 ;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 ; × 1 PHEOPHYTIN A × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 RRR-ALPHA-TOCOPHERYLQUINONE × 1 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 1 BICARBONATE ION × 1 FE (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YCF12_CHLRE
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain V； PDBConstruct 1–33； UniProt 1–33

Uncharacterized protein

OrganismNot specified

UniProt A8I846

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 CP47 reaction center protein × 1 （A0A218N8S0） Photosystem II D2 protein × 1 （P06007） Cytochrome b559 subunit alpha × 1 （P48268） Cytochrome b559 subunit beta × 1 （Q08363） Photosystem II reaction center protein H × 1 （P22666） Photosystem II reaction center protein I × 1 （P59763） Photosystem II reaction center protein K × 1 （P18263） Photosystem II reaction center protein L × 1 （P32974） Photosystem II reaction center protein M × 1 （P92277） Photosystem II reaction center protein T × 1 （P37256） Photosystem II reaction center protein Ycf12 × 1 （P50370） Photosystem II reaction center protein Z × 1 （P92276） Thylakoid enriched factor 14 (TEF14) × 1 （A8HY43） Photosystem II repair factor 1 (PRF1) × 1 （A0A2K3DWM2） Photosystem II CP43 reaction center protein × 1 （P10898） Photosystem II protein D1 × 1 （P07753） Photosystem II repair factor 2 (PRF2) × 1 （A8HNG8） CHLOROPHYLL A × 35 BETA-CAROTENE × 10 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 ;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 ; × 1 PHEOPHYTIN A × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 RRR-ALPHA-TOCOPHERYLQUINONE × 1 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 1 BICARBONATE ION × 1 FE (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8I846_CHLRE
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain X； PDBConstruct 1–101； UniProt 1–101

Photosystem II reaction center protein Z

OrganismNot specified

UniProt P92276

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 CP47 reaction center protein × 1 （A0A218N8S0） Photosystem II D2 protein × 1 （P06007） Cytochrome b559 subunit alpha × 1 （P48268） Cytochrome b559 subunit beta × 1 （Q08363） Photosystem II reaction center protein H × 1 （P22666） Photosystem II reaction center protein I × 1 （P59763） Photosystem II reaction center protein K × 1 （P18263） Photosystem II reaction center protein L × 1 （P32974） Photosystem II reaction center protein M × 1 （P92277） Photosystem II reaction center protein T × 1 （P37256） Photosystem II reaction center protein Ycf12 × 1 （P50370） Uncharacterized protein × 1 （A8I846） Thylakoid enriched factor 14 (TEF14) × 1 （A8HY43） Photosystem II repair factor 1 (PRF1) × 1 （A0A2K3DWM2） Photosystem II CP43 reaction center protein × 1 （P10898） Photosystem II protein D1 × 1 （P07753） Photosystem II repair factor 2 (PRF2) × 1 （A8HNG8） CHLOROPHYLL A × 35 BETA-CAROTENE × 10 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 ;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 ; × 1 PHEOPHYTIN A × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 RRR-ALPHA-TOCOPHERYLQUINONE × 1 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 1 BICARBONATE ION × 1 FE (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBZ_CHLRE
Isoform	—
PDB entities	13
Chains and sequence ranges	Author chain Z； PDBConstruct 1–62； UniProt 1–62

Thylakoid enriched factor 14 (TEF14)

OrganismNot specified

UniProt A8HY43

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 CP47 reaction center protein × 1 （A0A218N8S0） Photosystem II D2 protein × 1 （P06007） Cytochrome b559 subunit alpha × 1 （P48268） Cytochrome b559 subunit beta × 1 （Q08363） Photosystem II reaction center protein H × 1 （P22666） Photosystem II reaction center protein I × 1 （P59763） Photosystem II reaction center protein K × 1 （P18263） Photosystem II reaction center protein L × 1 （P32974） Photosystem II reaction center protein M × 1 （P92277） Photosystem II reaction center protein T × 1 （P37256） Photosystem II reaction center protein Ycf12 × 1 （P50370） Uncharacterized protein × 1 （A8I846） Photosystem II reaction center protein Z × 1 （P92276） Photosystem II repair factor 1 (PRF1) × 1 （A0A2K3DWM2） Photosystem II CP43 reaction center protein × 1 （P10898） Photosystem II protein D1 × 1 （P07753） Photosystem II repair factor 2 (PRF2) × 1 （A8HNG8） CHLOROPHYLL A × 35 BETA-CAROTENE × 10 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 ;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 ; × 1 PHEOPHYTIN A × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 RRR-ALPHA-TOCOPHERYLQUINONE × 1 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 1 BICARBONATE ION × 1 FE (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8HY43_CHLRE
Isoform	—
PDB entities	14
Chains and sequence ranges	Author chain G； PDBConstruct 1–196； UniProt 1–196

Photosystem II repair factor 1 (PRF1)

OrganismNot specified

UniProt A0A2K3DWM2

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 CP47 reaction center protein × 1 （A0A218N8S0） Photosystem II D2 protein × 1 （P06007） Cytochrome b559 subunit alpha × 1 （P48268） Cytochrome b559 subunit beta × 1 （Q08363） Photosystem II reaction center protein H × 1 （P22666） Photosystem II reaction center protein I × 1 （P59763） Photosystem II reaction center protein K × 1 （P18263） Photosystem II reaction center protein L × 1 （P32974） Photosystem II reaction center protein M × 1 （P92277） Photosystem II reaction center protein T × 1 （P37256） Photosystem II reaction center protein Ycf12 × 1 （P50370） Uncharacterized protein × 1 （A8I846） Photosystem II reaction center protein Z × 1 （P92276） Thylakoid enriched factor 14 (TEF14) × 1 （A8HY43） Photosystem II CP43 reaction center protein × 1 （P10898） Photosystem II protein D1 × 1 （P07753） Photosystem II repair factor 2 (PRF2) × 1 （A8HNG8） CHLOROPHYLL A × 35 BETA-CAROTENE × 10 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 ;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 ; × 1 PHEOPHYTIN A × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 RRR-ALPHA-TOCOPHERYLQUINONE × 1 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 1 BICARBONATE ION × 1 FE (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2K3DWM2_CHLRE
Isoform	—
PDB entities	15
Chains and sequence ranges	Author chain 3； PDBConstruct 1–131； UniProt 1–131

Photosystem II CP43 reaction center protein

OrganismNot specified

UniProt P10898

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 CP47 reaction center protein × 1 （A0A218N8S0） Photosystem II D2 protein × 1 （P06007） Cytochrome b559 subunit alpha × 1 （P48268） Cytochrome b559 subunit beta × 1 （Q08363） Photosystem II reaction center protein H × 1 （P22666） Photosystem II reaction center protein I × 1 （P59763） Photosystem II reaction center protein K × 1 （P18263） Photosystem II reaction center protein L × 1 （P32974） Photosystem II reaction center protein M × 1 （P92277） Photosystem II reaction center protein T × 1 （P37256） Photosystem II reaction center protein Ycf12 × 1 （P50370） Uncharacterized protein × 1 （A8I846） Photosystem II reaction center protein Z × 1 （P92276） Thylakoid enriched factor 14 (TEF14) × 1 （A8HY43） Photosystem II repair factor 1 (PRF1) × 1 （A0A2K3DWM2） Photosystem II protein D1 × 1 （P07753） Photosystem II repair factor 2 (PRF2) × 1 （A8HNG8） CHLOROPHYLL A × 35 BETA-CAROTENE × 10 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 ;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 ; × 1 PHEOPHYTIN A × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 RRR-ALPHA-TOCOPHERYLQUINONE × 1 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 1 BICARBONATE ION × 1 FE (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBC_CHLRE
Isoform	—
PDB entities	16
Chains and sequence ranges	Author chain C； PDBConstruct 1–461； UniProt 1–461

Photosystem II protein D1

OrganismNot specified

UniProt P07753

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 CP47 reaction center protein × 1 （A0A218N8S0） Photosystem II D2 protein × 1 （P06007） Cytochrome b559 subunit alpha × 1 （P48268） Cytochrome b559 subunit beta × 1 （Q08363） Photosystem II reaction center protein H × 1 （P22666） Photosystem II reaction center protein I × 1 （P59763） Photosystem II reaction center protein K × 1 （P18263） Photosystem II reaction center protein L × 1 （P32974） Photosystem II reaction center protein M × 1 （P92277） Photosystem II reaction center protein T × 1 （P37256） Photosystem II reaction center protein Ycf12 × 1 （P50370） Uncharacterized protein × 1 （A8I846） Photosystem II reaction center protein Z × 1 （P92276） Thylakoid enriched factor 14 (TEF14) × 1 （A8HY43） Photosystem II repair factor 1 (PRF1) × 1 （A0A2K3DWM2） Photosystem II CP43 reaction center protein × 1 （P10898） Photosystem II repair factor 2 (PRF2) × 1 （A8HNG8） CHLOROPHYLL A × 35 BETA-CAROTENE × 10 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 ;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 ; × 1 PHEOPHYTIN A × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 RRR-ALPHA-TOCOPHERYLQUINONE × 1 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 1 BICARBONATE ION × 1 FE (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSBA_CHLRE
Isoform	—
PDB entities	17
Chains and sequence ranges	Author chain A； PDBConstruct 1–352； UniProt 1–352

Photosystem II repair factor 2 (PRF2)

OrganismNot specified

UniProt A8HNG8

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 CP47 reaction center protein × 1 （A0A218N8S0） Photosystem II D2 protein × 1 （P06007） Cytochrome b559 subunit alpha × 1 （P48268） Cytochrome b559 subunit beta × 1 （Q08363） Photosystem II reaction center protein H × 1 （P22666） Photosystem II reaction center protein I × 1 （P59763） Photosystem II reaction center protein K × 1 （P18263） Photosystem II reaction center protein L × 1 （P32974） Photosystem II reaction center protein M × 1 （P92277） Photosystem II reaction center protein T × 1 （P37256） Photosystem II reaction center protein Ycf12 × 1 （P50370） Uncharacterized protein × 1 （A8I846） Photosystem II reaction center protein Z × 1 （P92276） Thylakoid enriched factor 14 (TEF14) × 1 （A8HY43） Photosystem II repair factor 1 (PRF1) × 1 （A0A2K3DWM2） Photosystem II CP43 reaction center protein × 1 （P10898） Photosystem II protein D1 × 1 （P07753） CHLOROPHYLL A × 35 BETA-CAROTENE × 10 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 ;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 ; × 1 PHEOPHYTIN A × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 RRR-ALPHA-TOCOPHERYLQUINONE × 1 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 1 BICARBONATE ION × 1 FE (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8HNG8_CHLRE
Isoform	—
PDB entities	18
Chains and sequence ranges	Author chain 1； PDBConstruct 1–117； UniProt 1–117

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8kde
Deposition date deposition_date	2023-08-09
Structure title title	Cryo-EM structure of an intermediate-state complex during the process of photosystem II repair
Keywords keywords	monomeric Photosystem II, PSII repair, PHOTOSYNTHESIS; PHOTOSYNTHESIS
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

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

8kde__assembly_1__model_1

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

Download this curve (.dat)

8kde__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8kde__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.00 Å
Rg (electron density)	42.83 Å
Total Rg	43.32 Å
Atom count	22087
Residues	2344
Excluded volume	410540 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8kde__assembly_1__model_1`	octadecameric （18）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (30)

Entity 1 Entity 1 polymer

Description description	Photosystem II CP47 reaction center protein
Molecular weight formula_weight	56089.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	22087

MGLPWYRVHTVVINDPGRLISVHLMHTALVSGWAGSMALFEISVFDPSDPVLNPMWRQGMFVLPFMTRLGITQSWGGWTISGETATNPGIWSYEGVAAAHIILSGALFLASVWHWTYWDLELFRDPRTGKTALDLPKIFGIHLFLSGLLCFGFGAFHVTGVFGPGIWVSDPYGLTGSVQPVAPSWGADGFDPYNPGGIASHHIAAGILGVLAGLFHLCVRPSIRLYFGLSMGSIETVLSSSIAAVFWAAFVVAGTMWYGSAATPIELFGPTRYQWDQGFFQQEIQKRVQASLAEGASLSDAWSRIPEKLAFYDYIGNNPAKGGLFRTGAMNSGDGIAVGWLGHASFKDQEGRELFVRRMPTFFETFPVLLLDKDGIVRADVPFRKAESKYSIEQVGVSVTFYGGELDGLTFTDPATVKKYARKAQLGEIFEFDRSTLQSDGVFRSSPRGWFTFGHVCFALLFFFGHIWHGARTIFRDVFAGIDDDINDQVEFGKYKKLGDTSSLREAF

Entity 2 Entity 2 polymer

Description description	Photosystem II D2 protein
Molecular weight formula_weight	39474.0 kDa
EC 编号 ec_number	1.10.3.9
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MTIAIGTYQEKRTWFDDADDWLRQDRFVFVGWSGLLLFPCAYFALGGWLTGTTFVTSWYTHGLATSYLEGCNFLTAAVSTPANSMAHSLLFVWGPEAQGDFTRWCQLGGLWAFVALHGAFGLIGFMLRQFEIARSVNLRPYNAIAFSAPIAVFVSVFLIYPLGQSGWFFAPSFGVAAIFRFILFFQGFHNWTLNPFHMMGVAGVLGAALLCAIHGATVENTLFEDGDGANTFRAFNPTQAEETYSMVTANRFWSQIFGVAFSNKRWLHFFMLLVPVTGLWMSAIGVVGLALNLRAYDFVSQEIRAAEDPEFETFYTKNILLNEGIRAWMAAQDQPHERLVFPEEVLPRGNAL

Entity 3 Entity 3 polymer

Description description	Cytochrome b559 subunit alpha
Molecular weight formula_weight	9312.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MAGKPVERPFSDILTSIRYWVIHSITVPALFIAGWLFVSTGLAYDVFGTPRPNEYFTEDRQEAPLITDRFNALEQVKKLSGN

Entity 4 Entity 4 polymer

Description description	Cytochrome b559 subunit beta
Molecular weight formula_weight	4986.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MTTKKSAEVLVYPIFTVRWLAIHGIAVPTIFFLGAITAMQFIQR

Entity 5 Entity 5 polymer

Description description	Photosystem II reaction center protein H
Molecular weight formula_weight	9445.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MATGTSKAKPSKVNSDFQEPGLVTPLGTLLRPLNSEAGKVLPGWGTTVLMAVFILLFAAFLLIILEIYNSSLILDDVSMSWETLAKVS

Entity 6 Entity 6 polymer

Description description	Photosystem II reaction center protein I
Molecular weight formula_weight	4245.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MLTLKIFVYTVVTFFVCLFIFGFLSNDPARNPGKNLD

Entity 7 Entity 7 polymer

Description description	Photosystem II reaction center protein K
Molecular weight formula_weight	5062.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MTTLALVLAKLPEAYAPFAPIVDVLPVIPVFFILLAFVWQAAVSFR

Entity 8 Entity 8 polymer

Description description	Photosystem II reaction center protein L
Molecular weight formula_weight	4431.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MARPNPNKQVVELNRTSLYWGLLLIFVLAVLFSSYIFN

Entity 9 Entity 9 polymer

Description description	Photosystem II reaction center protein M
Molecular weight formula_weight	3762.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MEVNIYGLTATALFIIIPTSFLLILYVKTASTQD

Entity 10 Entity 10 polymer

Description description	Photosystem II reaction center protein T
Molecular weight formula_weight	3639.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	T

MEALVYTFLLVGTLGIIFFSIFFRDPPRMIK

Entity 11 Entity 11 polymer

Description description	Photosystem II reaction center protein Ycf12
Molecular weight formula_weight	3333.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V

MNIELALTLVSLVLVVSAGPLVVVLLSARGGNL

Entity 12 Entity 12 polymer

Description description	Uncharacterized protein
Molecular weight formula_weight	9894.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

MAAVCVSSKAVAVRPATRVASRPAARMVVRASAKPAQISEKAIAAGVSAAAAASLALAPIAEAAVTPSLKNFLGSLIAGATVLGGIALAITAVSKFDKTIR

Entity 13 Entity 13 polymer

Description description	Photosystem II reaction center protein Z
Molecular weight formula_weight	6565.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Z

MTSILQVALLALIFVSFALVVGVPVVFATPNGWTDNKGAVFSGLSLWLLLVFVVGILNSFVV

Entity 14 Entity 14 polymer

Description description	Thylakoid enriched factor 14 (TEF14)
Molecular weight formula_weight	20601.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MALMMQKVAAPVSRRGMKVVAQATPNTASRRAILGVALLPALMYAPKALALIPDEEDEDLVEKAKANRRARLAQQRGVTRDFMASENLTDRRLEQELVPVQKAVYKLAKSGSQLESGDLKGAASTLSESWVGDFSTVASTVSGSTTAGKLVEAIKSVQAAAAKGDAAGSKRAYVSLVSDLQSWADASGLATSLKGL

Entity 15 Entity 15 polymer

Description description	Photosystem II repair factor 1 (PRF1)
Molecular weight formula_weight	13341.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	3

MLSNARAAVSKVHTSSAAVAPARPARVSHIVRASDKKLDERGVIAKDNSGRQNIFPTSSKAYYSSPTSSAVASSGLGGQQGLGVLAAAFAIVALATAGVVLKQGDETLAQVNNAYQGDSLTVISSRIAESL

Entity 16 Entity 16 polymer

Description description	Photosystem II CP43 reaction center protein
Molecular weight formula_weight	50680.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

METLFNGTLTVGGRDQETTGFAWWSGNARLINLSGKLLGAHVAHAGLIVFWAGAMNLFEVSHFVPEKPMYEQGLILLPHIATLGYGVGPGGEIIDTFPYFVSGVLHLISSAVLGFGGVYHSLIGPETLEESYPFFGYVWKDKNKMTNILGYHLIMLGLGAWLLVWKAMYFGGVYDTWAPGGGDVRVITNPTTNAAVIFGYLVKSPFGGDGWICSVDNMEDIIGGHIWIGTLEILGGIWHIYTTPWPWARRAFVWSGEAYLSYSLGAIGVMGFIACCMSWFNNTAYPSEFYGPTGPEASQSQAFTFLVRDQRLGANVASAQGPTGLGKYLMRSPTGEIIFGGETMRFWDFRGPWLEPLRGPNGLDLNKLKNDIQPWQERRAAEYMTHAPLGSLNSVGGVATEINAVNFVSPRSWLACSHFCLGFFFFIGHLWHAGRARAAAAGFEKGIDRFDEPVLSMRPLD

Entity 17 Entity 17 polymer

Description description	Photosystem II protein D1
Molecular weight formula_weight	39066.3 kDa
EC 编号 ec_number	1.10.3.9
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MTAILERRENSSLWARFCEWITSTENRLYIGWFGVIMIPCLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIITGAVIPTSNAIGLHFYPIWEAASLDEWLYNGGPYQLIVCHFLLGVYCYMGREWELSFRLGMRPWIAVAYSAPVAAASAVFLVYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANEGYRFGQEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVIGIWFTALGLSTMAFNLNGFNFNQSVVDSQGRVLNTWADIINRANLGMEVMHERNAHNFPLDLASTNSSSNN

Entity 18 Entity 18 polymer

Description description	Photosystem II repair factor 2 (PRF2)
Molecular weight formula_weight	12002.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1

MAALRCSVATRAAVPARRSSVVVRASTEQTTKRAMLGLLAGAVAGALLVAPAEAIRIPSHEFTGGMVKGGGSSPKSPTAASMESYTLEGTKKQGVSLKTKKKLLAKVRENAQKSASS

Entity 19 Entity 19 non-polymer

Description description	CHLOROPHYLL A
Molecular weight formula_weight	893.5 kDa
Source method src_method	syn
Copy count entity_count	35

Entity 20 Entity 20 non-polymer

Description description	BETA-CAROTENE
Molecular weight formula_weight	536.9 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 21 Entity 21 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	6

Entity 22 Entity 22 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 23 Entity 23 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	1

Entity 24 Entity 24 non-polymer

Description description	PHEOPHYTIN A
Molecular weight formula_weight	871.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 25 Entity 25 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 26 Entity 26 non-polymer

Description description	RRR-ALPHA-TOCOPHERYLQUINONE
Molecular weight formula_weight	446.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 27 Entity 27 non-polymer

Description description	DIGALACTOSYL DIACYL GLYCEROL (DGDG)
Molecular weight formula_weight	949.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 28 Entity 28 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	1

Entity 29 Entity 29 non-polymer

Description description	BICARBONATE ION
Molecular weight formula_weight	61.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 30 Entity 30 non-polymer

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

▶

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	2.60 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	510932

Cryo-EM structure of an intermediate-state complex during the process of photosystem II repair

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

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 K

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

Other homooligomers

Heteromeric or nucleic-acid complex

Photosystem II reaction center protein M

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 T

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer