9au4

Cryo-EM structure of a photosystem I variant containing an unusual plastoquinone derivative in its electron transfer chain

Method: ELECTRON MICROSCOPY

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

Photosystem I P700 chlorophyll a apoprotein A1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 33	Photosystem I P700 chlorophyll a apoprotein A2 × 3 Photosystem I iron-sulfur center × 3 （P32422） Photosystem I reaction center subunit II × 3 （P19569） Photosystem I reaction center subunit IV × 3 （P12975） Photosystem I reaction center subunit III × 3 （P29256） Photosystem I reaction center subunit VIII × 3 （Q55330） Photosystem I reaction center subunit IX × 3 （Q55329） Photosystem I reaction center subunit PsaK 2 × 3 （P74564） Photosystem I reaction center subunit XI × 3 （P37277） Photosystem I reaction center subunit XII × 3 （P72986） CHLOROPHYLL A × 282 2,3-dimethyl-5-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione × 6 IRON/SULFUR CLUSTER × 9 BETA-CAROTENE × 45 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 12 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 9 beta,beta-carotene-4,4'-dione × 3 CHLORIDE ION × 3 beta,beta-caroten-4-one × 6 CALCIUM ION × 6 (3'R)-3'-hydroxy-beta,beta-caroten-4-one × 3 ;(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol ; × 6 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 6 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 DODECYL-BETA-D-MALTOSIDE × 3 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSAA_SYNY3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–751； UniProt 1–751 Author chain G； PDBConstruct 1–751； UniProt 1–751 Author chain a； PDBConstruct 1–751； UniProt 1–751

Photosystem I iron-sulfur center

OrganismNot specified

UniProt P32422

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 33	Photosystem I P700 chlorophyll a apoprotein A1 × 3 （P29254） Photosystem I P700 chlorophyll a apoprotein A2 × 3 Photosystem I reaction center subunit II × 3 （P19569） Photosystem I reaction center subunit IV × 3 （P12975） Photosystem I reaction center subunit III × 3 （P29256） Photosystem I reaction center subunit VIII × 3 （Q55330） Photosystem I reaction center subunit IX × 3 （Q55329） Photosystem I reaction center subunit PsaK 2 × 3 （P74564） Photosystem I reaction center subunit XI × 3 （P37277） Photosystem I reaction center subunit XII × 3 （P72986） CHLOROPHYLL A × 282 2,3-dimethyl-5-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione × 6 IRON/SULFUR CLUSTER × 9 BETA-CAROTENE × 45 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 12 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 9 beta,beta-carotene-4,4'-dione × 3 CHLORIDE ION × 3 beta,beta-caroten-4-one × 6 CALCIUM ION × 6 (3'R)-3'-hydroxy-beta,beta-caroten-4-one × 3 ;(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol ; × 6 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 6 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 DODECYL-BETA-D-MALTOSIDE × 3 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSAC_SYNY3
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–81； UniProt 1–81 Author chain N； PDBConstruct 1–81； UniProt 1–81 Author chain c； PDBConstruct 1–81； UniProt 1–81

Photosystem I reaction center subunit II

OrganismNot specified

UniProt P19569

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 33	Photosystem I P700 chlorophyll a apoprotein A1 × 3 （P29254） Photosystem I P700 chlorophyll a apoprotein A2 × 3 Photosystem I iron-sulfur center × 3 （P32422） Photosystem I reaction center subunit IV × 3 （P12975） Photosystem I reaction center subunit III × 3 （P29256） Photosystem I reaction center subunit VIII × 3 （Q55330） Photosystem I reaction center subunit IX × 3 （Q55329） Photosystem I reaction center subunit PsaK 2 × 3 （P74564） Photosystem I reaction center subunit XI × 3 （P37277） Photosystem I reaction center subunit XII × 3 （P72986） CHLOROPHYLL A × 282 2,3-dimethyl-5-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione × 6 IRON/SULFUR CLUSTER × 9 BETA-CAROTENE × 45 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 12 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 9 beta,beta-carotene-4,4'-dione × 3 CHLORIDE ION × 3 beta,beta-caroten-4-one × 6 CALCIUM ION × 6 (3'R)-3'-hydroxy-beta,beta-caroten-4-one × 3 ;(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol ; × 6 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 6 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 DODECYL-BETA-D-MALTOSIDE × 3 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSAD_SYNY3
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–141； UniProt 1–141 Author chain O； PDBConstruct 1–141； UniProt 1–141 Author chain d； PDBConstruct 1–141； UniProt 1–141

Photosystem I reaction center subunit IV

OrganismNot specified

UniProt P12975

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 33	Photosystem I P700 chlorophyll a apoprotein A1 × 3 （P29254） Photosystem I P700 chlorophyll a apoprotein A2 × 3 Photosystem I iron-sulfur center × 3 （P32422） Photosystem I reaction center subunit II × 3 （P19569） Photosystem I reaction center subunit III × 3 （P29256） Photosystem I reaction center subunit VIII × 3 （Q55330） Photosystem I reaction center subunit IX × 3 （Q55329） Photosystem I reaction center subunit PsaK 2 × 3 （P74564） Photosystem I reaction center subunit XI × 3 （P37277） Photosystem I reaction center subunit XII × 3 （P72986） CHLOROPHYLL A × 282 2,3-dimethyl-5-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione × 6 IRON/SULFUR CLUSTER × 9 BETA-CAROTENE × 45 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 12 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 9 beta,beta-carotene-4,4'-dione × 3 CHLORIDE ION × 3 beta,beta-caroten-4-one × 6 CALCIUM ION × 6 (3'R)-3'-hydroxy-beta,beta-caroten-4-one × 3 ;(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol ; × 6 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 6 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 DODECYL-BETA-D-MALTOSIDE × 3 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSAE_SYNY3
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–74； UniProt 1–74 Author chain P； PDBConstruct 1–74； UniProt 1–74 Author chain e； PDBConstruct 1–74； UniProt 1–74

Photosystem I reaction center subunit III

OrganismNot specified

UniProt P29256

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 33	Photosystem I P700 chlorophyll a apoprotein A1 × 3 （P29254） Photosystem I P700 chlorophyll a apoprotein A2 × 3 Photosystem I iron-sulfur center × 3 （P32422） Photosystem I reaction center subunit II × 3 （P19569） Photosystem I reaction center subunit IV × 3 （P12975） Photosystem I reaction center subunit VIII × 3 （Q55330） Photosystem I reaction center subunit IX × 3 （Q55329） Photosystem I reaction center subunit PsaK 2 × 3 （P74564） Photosystem I reaction center subunit XI × 3 （P37277） Photosystem I reaction center subunit XII × 3 （P72986） CHLOROPHYLL A × 282 2,3-dimethyl-5-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione × 6 IRON/SULFUR CLUSTER × 9 BETA-CAROTENE × 45 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 12 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 9 beta,beta-carotene-4,4'-dione × 3 CHLORIDE ION × 3 beta,beta-caroten-4-one × 6 CALCIUM ION × 6 (3'R)-3'-hydroxy-beta,beta-caroten-4-one × 3 ;(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol ; × 6 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 6 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 DODECYL-BETA-D-MALTOSIDE × 3 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSAF_SYNY3
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–165； UniProt 1–165 Author chain Q； PDBConstruct 1–165； UniProt 1–165 Author chain f； PDBConstruct 1–165； UniProt 1–165

Photosystem I reaction center subunit VIII

OrganismNot specified

UniProt Q55330

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 33	Photosystem I P700 chlorophyll a apoprotein A1 × 3 （P29254） Photosystem I P700 chlorophyll a apoprotein A2 × 3 Photosystem I iron-sulfur center × 3 （P32422） Photosystem I reaction center subunit II × 3 （P19569） Photosystem I reaction center subunit IV × 3 （P12975） Photosystem I reaction center subunit III × 3 （P29256） Photosystem I reaction center subunit IX × 3 （Q55329） Photosystem I reaction center subunit PsaK 2 × 3 （P74564） Photosystem I reaction center subunit XI × 3 （P37277） Photosystem I reaction center subunit XII × 3 （P72986） CHLOROPHYLL A × 282 2,3-dimethyl-5-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione × 6 IRON/SULFUR CLUSTER × 9 BETA-CAROTENE × 45 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 12 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 9 beta,beta-carotene-4,4'-dione × 3 CHLORIDE ION × 3 beta,beta-caroten-4-one × 6 CALCIUM ION × 6 (3'R)-3'-hydroxy-beta,beta-caroten-4-one × 3 ;(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol ; × 6 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 6 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 DODECYL-BETA-D-MALTOSIDE × 3 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSAI_SYNY3
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain I； PDBConstruct 1–40； UniProt 1–40 Author chain R； PDBConstruct 1–40； UniProt 1–40 Author chain i； PDBConstruct 1–40； UniProt 1–40

Photosystem I reaction center subunit IX

OrganismNot specified

UniProt Q55329

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 33	Photosystem I P700 chlorophyll a apoprotein A1 × 3 （P29254） Photosystem I P700 chlorophyll a apoprotein A2 × 3 Photosystem I iron-sulfur center × 3 （P32422） Photosystem I reaction center subunit II × 3 （P19569） Photosystem I reaction center subunit IV × 3 （P12975） Photosystem I reaction center subunit III × 3 （P29256） Photosystem I reaction center subunit VIII × 3 （Q55330） Photosystem I reaction center subunit PsaK 2 × 3 （P74564） Photosystem I reaction center subunit XI × 3 （P37277） Photosystem I reaction center subunit XII × 3 （P72986） CHLOROPHYLL A × 282 2,3-dimethyl-5-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione × 6 IRON/SULFUR CLUSTER × 9 BETA-CAROTENE × 45 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 12 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 9 beta,beta-carotene-4,4'-dione × 3 CHLORIDE ION × 3 beta,beta-caroten-4-one × 6 CALCIUM ION × 6 (3'R)-3'-hydroxy-beta,beta-caroten-4-one × 3 ;(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol ; × 6 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 6 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 DODECYL-BETA-D-MALTOSIDE × 3 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSAJ_SYNY3
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain J； PDBConstruct 1–40； UniProt 1–40 Author chain S； PDBConstruct 1–40； UniProt 1–40 Author chain j； PDBConstruct 1–40； UniProt 1–40

Photosystem I reaction center subunit PsaK 2

OrganismNot specified

UniProt P74564

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 33	Photosystem I P700 chlorophyll a apoprotein A1 × 3 （P29254） Photosystem I P700 chlorophyll a apoprotein A2 × 3 Photosystem I iron-sulfur center × 3 （P32422） Photosystem I reaction center subunit II × 3 （P19569） Photosystem I reaction center subunit IV × 3 （P12975） Photosystem I reaction center subunit III × 3 （P29256） Photosystem I reaction center subunit VIII × 3 （Q55330） Photosystem I reaction center subunit IX × 3 （Q55329） Photosystem I reaction center subunit XI × 3 （P37277） Photosystem I reaction center subunit XII × 3 （P72986） CHLOROPHYLL A × 282 2,3-dimethyl-5-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione × 6 IRON/SULFUR CLUSTER × 9 BETA-CAROTENE × 45 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 12 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 9 beta,beta-carotene-4,4'-dione × 3 CHLORIDE ION × 3 beta,beta-caroten-4-one × 6 CALCIUM ION × 6 (3'R)-3'-hydroxy-beta,beta-caroten-4-one × 3 ;(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol ; × 6 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 6 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 DODECYL-BETA-D-MALTOSIDE × 3 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSAK2_SYNY3
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain K； PDBConstruct 1–90； UniProt 1–90 Author chain T； PDBConstruct 1–90； UniProt 1–90 Author chain k； PDBConstruct 1–90； UniProt 1–90

Photosystem I reaction center subunit XI

OrganismNot specified

UniProt P37277

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 33	Photosystem I P700 chlorophyll a apoprotein A1 × 3 （P29254） Photosystem I P700 chlorophyll a apoprotein A2 × 3 Photosystem I iron-sulfur center × 3 （P32422） Photosystem I reaction center subunit II × 3 （P19569） Photosystem I reaction center subunit IV × 3 （P12975） Photosystem I reaction center subunit III × 3 （P29256） Photosystem I reaction center subunit VIII × 3 （Q55330） Photosystem I reaction center subunit IX × 3 （Q55329） Photosystem I reaction center subunit PsaK 2 × 3 （P74564） Photosystem I reaction center subunit XII × 3 （P72986） CHLOROPHYLL A × 282 2,3-dimethyl-5-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione × 6 IRON/SULFUR CLUSTER × 9 BETA-CAROTENE × 45 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 12 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 9 beta,beta-carotene-4,4'-dione × 3 CHLORIDE ION × 3 beta,beta-caroten-4-one × 6 CALCIUM ION × 6 (3'R)-3'-hydroxy-beta,beta-caroten-4-one × 3 ;(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol ; × 6 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 6 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 DODECYL-BETA-D-MALTOSIDE × 3 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSAL_SYNY3
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain L； PDBConstruct 1–157； UniProt 1–157 Author chain U； PDBConstruct 1–157； UniProt 1–157 Author chain l； PDBConstruct 1–157； UniProt 1–157

Photosystem I reaction center subunit XII

OrganismNot specified

UniProt P72986

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 33	Photosystem I P700 chlorophyll a apoprotein A1 × 3 （P29254） Photosystem I P700 chlorophyll a apoprotein A2 × 3 Photosystem I iron-sulfur center × 3 （P32422） Photosystem I reaction center subunit II × 3 （P19569） Photosystem I reaction center subunit IV × 3 （P12975） Photosystem I reaction center subunit III × 3 （P29256） Photosystem I reaction center subunit VIII × 3 （Q55330） Photosystem I reaction center subunit IX × 3 （Q55329） Photosystem I reaction center subunit PsaK 2 × 3 （P74564） Photosystem I reaction center subunit XI × 3 （P37277） CHLOROPHYLL A × 282 2,3-dimethyl-5-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione × 6 IRON/SULFUR CLUSTER × 9 BETA-CAROTENE × 45 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 12 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 9 beta,beta-carotene-4,4'-dione × 3 CHLORIDE ION × 3 beta,beta-caroten-4-one × 6 CALCIUM ION × 6 (3'R)-3'-hydroxy-beta,beta-caroten-4-one × 3 ;(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol ; × 6 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 6 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 3 DODECYL-BETA-D-MALTOSIDE × 3 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSAM_SYNY3
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain M； PDBConstruct 1–31； UniProt 1–31 Author chain V； PDBConstruct 1–31； UniProt 1–31 Author chain m； PDBConstruct 1–31； UniProt 1–31

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	9au4
Deposition date deposition_date	2024-02-28
Last revision last_revision	2024-12-25
Structure title title	Cryo-EM structure of a photosystem I variant containing an unusual plastoquinone derivative in its electron transfer chain
Keywords keywords	cyanobacteria, photosystem I, MenB, phylloquinone, plastoquinone, benzoquinone, naphthoquinone, redox potential, 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.

9au4__assembly_1__model_1

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

Download this curve (.dat)

9au4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9au4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	68.05 Å
Rg (electron density)	67.20 Å
Total Rg	67.15 Å
Atom count	72957
Residues	6678
Excluded volume	1364800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9au4__assembly_1__model_1`	33-meric （33）	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 (27)

Entity 1 Entity 1 polymer

Description description	Photosystem I P700 chlorophyll a apoprotein A1
Molecular weight formula_weight	83036.4 kDa
EC 编号 ec_number	1.97.1.12
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,a,A
Atom count atom_count	73866

MTISPPEREAKAKVSVDNNPVPTSFEKWGKPGHFDRTLARGPKTTTWIWNLHANAHDFDSQTSDLEDVSRKIFSAHFGHLAVVFVWLSGMYFHGAKFSNYEGWLADPTHIKPSAQVVWPIVGQGILNGDVGGGFHGIQITSGLFYLWRASGFTDSYQLYCTAIGGLVMAALMLFAGWFHYHVKAPKLEWFQNVESMMNHHLAGLLGLGSLGWAGHQIHVSMPINKLLDAGVAPKDIPLPHEFILEPSKMAELYPSFAQGLTPFFTLNWGVYSDFLTFKGGLNPVTGGLWLSDTAHHHLAIAVLFIIAGHMYRTNWGIGHSMKEILEAHKGPFTGEGHKGLYEILTTSWHAQLAINLALLGSLTIIVAQHMYAMPPYPYQAIDYATQLSLFTHHMWIGGFLIVGAGAHGAIFMVRDYDPAKNVNNLLDRMLRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMRALGRPQDMFSDTAIQLQPIFAQWVQHLHTLAPGATAPNALATASYAFGGETIAVAGKVAMMPITLGTADFMVHHIHAFTIHVTALILLKGVLYARSSRLVPDKANLGFRFPCDGPGRGGTCQVSGWDHVFLGLFWMYNSLSIVIFHFSWKMQSDVWGTVSPDGSVTHVTLGNFAQSAITINGWLRDFLWAQAANVINSYGSALSAYGIMFLAGHFVFAFSLMFLFSGRGYWQELIESIVWAHNKLNVAPAIQPRALSIIQGRAVGVAHYLLGGIVTTWAFFLARSLSIG

Entity 2 Entity 2 polymer

Description description	Photosystem I P700 chlorophyll a apoprotein A2
Molecular weight formula_weight	81298.5 kDa
EC 编号 ec_number	1.97.1.12
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

MTKFPKFSQDLAQDPTTRRIWYGIATAHDFETHDGMTEENLYQKIFASHFGHIAIIFLWTSGTLFHVAWQGNFEQWIKDPLNIRPIAHAIWDPHFGEGAVNAFTQAGASNPVNIAYSGVYHWFYTIGMTTNQELYSGAVFLLVLASLFLFAGWLHLQPKFRPSLAWFKNAESRLNHHLAGLFGVSSLAWAGHLVHVAIPEARGQHVGWDNFLSTPPHPAGLMPFFTGNWGVYAADPDTAGHIFGTSEGAGTAILTFLGGFHPQTESLWLTDIAHHHLAIAVIFIIAGHMYRTNWGIGHSIKEILNAHKGPLTGAGHTNLYDTINNSLHFQLGLALASLGVITSLVAQHMYSLPSYAFIAQDHTTQAALYTHHQYIAGFLMVGAFAHGAIFFVRDYDPVANKDNVLARMLEHKEALISHLSWVSLFLGFHTLGLYVHNDVVVAFGTPEKQILIEPVFAQWIQATSGKALYGFDVLLSNPDSIASTTGAAWLPGWLDAINSGTNSLFLTIGPGDFLVHHAIALGLHTTALILIKGALDARGSKLMPDKKDFGYSFPCDGPGRGGTCDISAWDAFYLAMFWMLNTLGWLTFYWHWKHLGVWSGNVAQFNENSTYLMGWFRDYLWANSAQLINGYNPYGVNNLSVWAWMFLFGHLVWATGFMFLISWRGYWQELIETIVWAHERTPLANLVRWKDKPVALSIVQARLVGLAHFTVGYVLTYAAFLIASTAGKFG

Entity 3 Entity 3 polymer

Description description	Photosystem I iron-sulfur center
Molecular weight formula_weight	8837.3 kDa
EC 编号 ec_number	1.97.1.12
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

MSHSVKIYDTCIGCTQCVRACPLDVLEMVPWDGCKAAQIASSPRTEDCVGCKRCETACPTDFLSIRVYLGAETTRSMGLAY

Entity 4 Entity 4 polymer

Description description	Photosystem I reaction center subunit II
Molecular weight formula_weight	15663.7 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

MTELSGQPPKFGGSTGGLLSKANREEKYAITWTSASEQVFEMPTGGAAIMNEGENLLYLARKEQCLALGTQLRTKFKPKIQDYKIYRVYPSGEVQYLHPADGVFPEKVNEGREAQGTKTRRIGQNPEPVTIKFSGKAPYEV

Entity 5 Entity 5 polymer

Description description	Photosystem I reaction center subunit IV
Molecular weight formula_weight	8154.1 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

MALNRGDKVRIKRTESYWYGDVGTVASVEKSGILYPVIVRFDRVNYNGFSGSASGVNTNNFAENELELVQAAAK

Entity 6 Entity 6 polymer

Description description	Photosystem I reaction center subunit III
Molecular weight formula_weight	18267.1 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

MKHLLALLLAFTLWFNFAPSASADDFANLTPCSENPAYLAKSKNFLNTTNDPNSGKIRAERYASALCGPEGYPHLIVDGRFTHAGDFLIPSILFLYIAGWIGWVGRSYLIEIRESKNPEMQEVVINVPLAIKKMLGGFLWPLAAVGEYTSGKLVMKDSEIPTSPR

Entity 7 Entity 7 polymer

Description description	Photosystem I reaction center subunit VIII
Molecular weight formula_weight	4414.1 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

MDGSYAASYLPWILIPMVGWLFPAVTMGLLFIHIESEGEG

Entity 8 Entity 8 polymer

Description description	Photosystem I reaction center subunit IX
Molecular weight formula_weight	4535.4 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

MDGLKSFLSTAPVMIMALLTFTAGILIEFNRFYPDLLFHP

Entity 9 Entity 9 polymer

Description description	Photosystem I reaction center subunit PsaK 2
Molecular weight formula_weight	9312.1 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

MFNTALLLAQASPTTAGWSLSVGIIMCLCNVFAFVIGYFAIQKTGKGKDLALPQLASKKTFGLPELLATMSFGHILGAGMVLGLASSGIL

Entity 10 Entity 10 polymer

Description description	Photosystem I reaction center subunit XI
Molecular weight formula_weight	16631.8 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

MAESNQVVQAYNGDPFVGHLSTPISDSAFTRTFIGNLPAYRKGLSPILRGLEVGMAHGYFLIGPWTLLGPLRDSEYQYIGGLIGALALILVATAALSSYGLVTFQGEQGSGDTLQTADGWSQFAAGFFVGGMGGAFVAYFLLENLSVVDGIFRGLFN

Entity 11 Entity 11 polymer

Description description	Photosystem I reaction center subunit XII
Molecular weight formula_weight	3382.1 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

MALSDTQILAALVVALLPAFLAFRLSTELYK

Entity 12 Entity 12 non-polymer

Description description	CHLOROPHYLL A
Molecular weight formula_weight	893.5 kDa
Source method src_method	syn
Copy count entity_count	282

Entity 13 Entity 13 non-polymer

Description description	2,3-dimethyl-5-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione
Molecular weight formula_weight	414.7 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 14 Entity 14 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 15 Entity 15 non-polymer

Description description	BETA-CAROTENE
Molecular weight formula_weight	536.9 kDa
Source method src_method	syn
Copy count entity_count	45

Entity 16 Entity 16 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	12

Entity 17 Entity 17 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	9

Entity 18 Entity 18 non-polymer

Description description	beta,beta-carotene-4,4'-dione
Molecular weight formula_weight	564.8 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 19 Entity 19 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 20 Entity 20 non-polymer

Description description	beta,beta-caroten-4-one
Molecular weight formula_weight	550.9 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 21 Entity 21 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 22 Entity 22 non-polymer

Description description	(3'R)-3'-hydroxy-beta,beta-caroten-4-one
Molecular weight formula_weight	566.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 23 Entity 23 non-polymer

Description description	;(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol ;
Molecular weight formula_weight	568.9 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 24 Entity 24 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	6

Entity 25 Entity 25 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 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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	909

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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	2.03 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	375816

Cryo-EM structure of a photosystem I variant containing an unusual plastoquinone derivative in its electron transfer chain

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

Photosystem I P700 chlorophyll a apoprotein A1

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 I iron-sulfur center

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 I reaction center subunit II

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 I reaction center subunit IV

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 I reaction center subunit III

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 I reaction center subunit VIII

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 I reaction center subunit IX

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 I reaction center subunit PsaK 2

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 I reaction center subunit XI

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 I reaction center subunit XII

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer