Photosystem II protein D1
Thermostichus vulcanus
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein heterocomplex Heteromer Protein × 39 PDB declaration: 39-meric（39） Consistent with protein copy count | Chain A； UniProt 1–344 Chain a； UniProt 1–344 | Not recorded | Photosystem II CP47 reaction center protein × 2 （D0VWR1） Photosystem II CP43 reaction center protein × 2 （D0VWR7） Photosystem II D2 protein × 2 （D0VWR8） Cytochrome b559 subunit alpha × 2 （P12238） Cytochrome b559 subunit beta × 2 （P12239） Photosystem II reaction center protein H × 2 （P19052） Photosystem II reaction center protein I × 2 （P12240） Photosystem II reaction center protein J × 2 （Q7DGD4） Photosystem II reaction center protein K × 2 （P19054） Photosystem II reaction center protein L × 2 （P12241） Photosystem II reaction center protein M × 2 （P12312） Photosystem II manganese-stabilizing polypeptide × 2 （D0VWR2） Photosystem II reaction center protein T × 2 （P12313） Photosystem II 12 kDa extrinsic protein × 2 （P56152） Cytochrome c-550 × 2 （P0A387） Photosystem II reaction center protein X × 2 （D0VWR4） Photosystem II reaction center protein Ycf12 × 2 （D0VWR3） Photosystem II reaction center protein Z × 2 （D0VWR5） Photosystem II protein Y × 1 （P0DM37） OEY CA-MN4-O6 CLUSTER × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 21 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 LMT DODECYL-BETA-D-MALTOSIDE × 14 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 HTG heptyl 1-thio-beta-D-glucopyranoside × 11 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 CA CALCIUM ION × 7 FE2 FE (II) ION × 2 BCT BICARBONATE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 | X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 6；293 K；5.5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM Mes BUFFER | Resolution 2.25 Å R-free 0.181 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 8IRI | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1IZL Crystal Structure of Photosystem II Deposited 2002-10-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric |
Chain A
1–360（360 aa）
Chain J
1–360（360 aa）
|
Not recorded | MN MANGANESE (II) ION × 8 CLA CHLOROPHYLL A × 72 PHO PHEOPHYTIN A × 4 FE FE (III) ION × 2 PLA 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID × 2 BCR BETA-CAROTENE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICRODIALYSIS；pH 6.5；293 K；PEG 1450, MES, calcium chloride, magnesium sulfate, dodecyl maltoside, pH 6.5, MICRODIALYSIS, temperature 293.0K
|
Resolution 3.70 Å |
| 3A0B Crystal structure of Br-substituted Photosystem II complex Deposited 2009-03-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 40 PDB declaration: 40-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | OEC OXYGEN EVOLVING SYSTEM × 2 FE2 FE (II) ION × 2 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 PQ9 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 × 4 BCR BETA-CAROTENE × 22 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 2 BR BROMIDE ION × 4 MGE (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 8 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20% PEG 1450, 40mM MgSO4, 10mM MgCl2, 25% glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.70 Å R-free 0.358 |
| 3A0H Crystal structure of I-substituted Photosystem II complex Deposited 2009-03-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 40 PDB declaration: 40-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | OEC OXYGEN EVOLVING SYSTEM × 2 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 PQ9 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 × 4 BCR BETA-CAROTENE × 22 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 2 IOD IODIDE ION × 10 MGE (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 8 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 FE2 FE (II) ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；4% PEG 1450, 40mM MgSO4, 10mM MgCl2, 13% glycerol, 0.01% DM, 20mM MES (pH6.0), 10mM NaI, 5mM CaI, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 4.00 Å R-free 0.326 |
| 3WU2 Crystal structure analysis of Photosystem II complex Deposited 2014-04-21 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 38 PDB declaration: 38-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | OEX CA-MN4-O5 CLUSTER × 2 FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 20 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 10 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 43 LMT DODECYL-BETA-D-MALTOSIDE × 16 GOL GLYCEROL × 36 CA CALCIUM ION × 7 HTG heptyl 1-thio-beta-D-glucopyranoside × 19 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 BCT BICARBONATE ION × 2 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 RRX (3R)-beta,beta-caroten-3-ol × 2 MG MAGNESIUM ION × 2 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICRO-BATCH METHOD UNDER OIL；pH 6.1；285 K；5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM MES buffer, pH 6.1, MICRO-BATCH METHOD UNDER OIL, temperature 285K
|
Resolution 1.90 Å R-free 0.194 |
| 4IL6 Structure of Sr-substituted photosystem II Deposited 2012-12-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
11–344（334 aa）
Fragment：UNP residues 11-344
Chain a
11–344（334 aa）
Fragment：UNP residues 11-344
|
Not recorded | OER SR-MN4-O5 CLUSTER × 2 FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DMS DIMETHYL SULFOXIDE × 35 UNL UNKNOWN LIGAND × 24 LMT DODECYL-BETA-D-MALTOSIDE × 15 GOL GLYCEROL × 12 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 HTG heptyl 1-thio-beta-D-glucopyranoside × 17 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 BCT BICARBONATE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
Oil-Microbatch Method；pH 6.1；285 K；Sr-PSII protein was crystallised in 4.5-5.5%PEG1450, 20mM Mes-NaOH, pH 6.1, 20mM NaCl, 3-4mM SrCl2, Oil-Microbatch Method, temperature 285K
|
Resolution 2.10 Å R-free 0.205 |
| 5B5E Crystal structure analysis of Photosystem II complex Deposited 2016-05-02 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 38 PDB declaration: 38-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | OEX CA-MN4-O5 CLUSTER × 2 FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 20 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 14 UNL UNKNOWN LIGAND × 53 LMT DODECYL-BETA-D-MALTOSIDE × 16 DMS DIMETHYL SULFOXIDE × 112 BCT BICARBONATE ION × 2 CA CALCIUM ION × 5 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 HTG heptyl 1-thio-beta-D-glucopyranoside × 20 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 RRX (3R)-beta,beta-caroten-3-ol × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.1；285 K；Mes,NaCl,CaCl2,MgSO4
|
Resolution 1.87 Å R-free 0.212 |
| 5B66 Crystal structure analysis of Photosystem II complex Deposited 2016-05-25 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 38 PDB declaration: 38-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 20 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 10 CL CHLORIDE ION × 4 UNL UNKNOWN LIGAND × 55 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 DMS DIMETHYL SULFOXIDE × 95 FE2 FE (II) ION × 2 OEX CA-MN4-O5 CLUSTER × 2 BCT BICARBONATE ION × 2 HTG heptyl 1-thio-beta-D-glucopyranoside × 21 CA CALCIUM ION × 6 LMT DODECYL-BETA-D-MALTOSIDE × 17 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 9 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 RRX (3R)-beta,beta-caroten-3-ol × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.1；285 K；Mes, NaCl, CaCl2, MgSO4, PEG 1450
|
Resolution 1.85 Å R-free 0.201 |
| 5V2C RE-REFINEMENT OF CRYSTAL STRUCTURE OF PHOTOSYSTEM II COMPLEX Deposited 2017-03-03 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 38 PDB declaration: 38-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | OEX CA-MN4-O5 CLUSTER × 2 FE2 FE (II) ION × 2 CL CHLORIDE ION × 6 BCT BICARBONATE ION × 3 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 11 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 14 GOL GLYCEROL × 60 LMT DODECYL-BETA-D-MALTOSIDE × 18 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 12 PG4 TETRAETHYLENE GLYCOL × 57 PGE TRIETHYLENE GLYCOL × 65 P6G HEXAETHYLENE GLYCOL × 17 EDO 1,2-ETHANEDIOL × 22 CA CALCIUM ION × 6 HTG heptyl 1-thio-beta-D-glucopyranoside × 24 1PE PENTAETHYLENE GLYCOL × 7 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 4 HEC HEME C × 2 2PE NONAETHYLENE GLYCOL × 1 PE8 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION, RECRYSTALLIZATION；pH 6.1；285 K；5% PEG1450, 20MM NACL, 10MM CACL2,
40MM MGSO4, 20MM MES BUFFER, PH 6.1, MICRO-BATCH METHOD UNDER
OIL, TEMPERATURE 285K
|
Resolution 1.90 Å R-free 0.163 |
| 6JLJ XFEL structure of cyanobacterial photosystem II (dark state, dataset1) Deposited 2019-03-06 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 6 BCT BICARBONATE ION × 2 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 35 LMT DODECYL-BETA-D-MALTOSIDE × 14 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 CA CALCIUM ION × 9 HTG heptyl 1-thio-beta-D-glucopyranoside × 17 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；293 K；PEG, magnesium sulfate
|
Resolution 2.15 Å R-free 0.198 |
| 6JLK XFEL structure of cyanobacterial photosystem II (1F state, dataset1) Deposited 2019-03-06 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 6 BCT BICARBONATE ION × 2 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 35 LMT DODECYL-BETA-D-MALTOSIDE × 14 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 CA CALCIUM ION × 9 HTG heptyl 1-thio-beta-D-glucopyranoside × 17 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；293 K；PEG, magnesium sulfate
|
Resolution 2.15 Å R-free 0.193 |
| 6JLL XFEL structure of cyanobacterial photosystem II (2F state, dataset1) Deposited 2019-03-06 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 6 BCT BICARBONATE ION × 2 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 35 LMT DODECYL-BETA-D-MALTOSIDE × 14 OEX CA-MN4-O5 CLUSTER × 2 OEY CA-MN4-O6 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 CA CALCIUM ION × 9 HTG heptyl 1-thio-beta-D-glucopyranoside × 17 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；298 K；PEG, magnesium sulfate
|
Resolution 2.15 Å R-free 0.203 |
| 6JLM XFEL structure of cyanobacterial photosystem II (dark state, dataset2) Deposited 2019-03-06 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 6 BCT BICARBONATE ION × 2 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 35 LMT DODECYL-BETA-D-MALTOSIDE × 14 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 CA CALCIUM ION × 9 HTG heptyl 1-thio-beta-D-glucopyranoside × 17 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；293 K；PEG, magnesium sulfate
|
Resolution 2.35 Å R-free 0.209 |
| 6JLN XFEL structure of cyanobacterial photosystem II (1F state, dataset2) Deposited 2019-03-06 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 6 BCT BICARBONATE ION × 2 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 35 LMT DODECYL-BETA-D-MALTOSIDE × 14 OEX CA-MN4-O5 CLUSTER × 4 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 CA CALCIUM ION × 9 HTG heptyl 1-thio-beta-D-glucopyranoside × 17 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；293 K；PEG, magnesium sulfate
|
Resolution 2.40 Å R-free 0.212 |
| 6JLO XFEL structure of cyanobacterial photosystem II (2F state, dataset2) Deposited 2019-03-06 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | CL CHLORIDE ION × 6 BCT BICARBONATE ION × 2 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 35 LMT DODECYL-BETA-D-MALTOSIDE × 14 OEX CA-MN4-O5 CLUSTER × 2 OEY CA-MN4-O6 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 CA CALCIUM ION × 9 HTG heptyl 1-thio-beta-D-glucopyranoside × 17 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 FE2 FE (II) ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；293 K；PEG, magnesium sulfate
|
Resolution 2.40 Å R-free 0.207 |
| 6JLP XFEL structure of cyanobacterial photosystem II (3F state, dataset2) Deposited 2019-03-06 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 6 CLA CHLOROPHYLL A × 70 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 35 LMT DODECYL-BETA-D-MALTOSIDE × 14 OEX CA-MN4-O5 CLUSTER × 2 OEY CA-MN4-O6 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 CA CALCIUM ION × 9 HTG heptyl 1-thio-beta-D-glucopyranoside × 17 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 BCT BICARBONATE ION × 2 PHO PHEOPHYTIN A × 4 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；293 K；PEG, magnesium sulfate
|
Resolution 2.50 Å R-free 0.211 |
| 7CJI Photosystem II structure in the S1 state Deposited 2020-07-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 GOL GLYCEROL × 12 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 HTG heptyl 1-thio-beta-D-glucopyranoside × 11 LMT DODECYL-BETA-D-MALTOSIDE × 14 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 CA CALCIUM ION × 7 BCT BICARBONATE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；293 K；PEG, magnesium sulfate
|
Resolution 2.35 Å R-free 0.208 |
| 7CJJ Photosystem II structure in the S2 state Deposited 2020-07-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 12 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 HTG heptyl 1-thio-beta-D-glucopyranoside × 11 LMT DODECYL-BETA-D-MALTOSIDE × 14 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 CA CALCIUM ION × 7 BCT BICARBONATE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；293 K；PEG, magnesium sulfate
|
Resolution 2.40 Å R-free 0.218 |
| 7COU Structure of cyanobacterial photosystem II in the dark S1 state Deposited 2020-08-05 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 GOL GLYCEROL × 12 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 HTG heptyl 1-thio-beta-D-glucopyranoside × 11 LMT DODECYL-BETA-D-MALTOSIDE × 14 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 CA CALCIUM ION × 7 BCT BICARBONATE ION × 2 HEC HEME C × 4 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；293 K；PEG, magnesium sulfate
|
Resolution 2.25 Å R-free 0.211 |
| 7CZL Structural insights into a dimeric Psb27-photosystem II complex from a cyanobacterium Thermosynechococcus vulcanus Deposited 2020-09-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric |
Chain A
10–333（324 aa）
Chain a
10–333（324 aa）
|
Not recorded | CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 PQ9 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 × 4 BCR BETA-CAROTENE × 22 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 2 LMT DODECYL-BETA-D-MALTOSIDE × 6 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 6 BCT BICARBONATE ION × 2 MGE (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 14 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 CA CALCIUM ION × 2 FE2 FE (II) ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 CL CHLORIDE ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.78 Å |
| 7D1T Cryo-EM Structure of PSII at 1.95 angstrom resolution Deposited 2020-09-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 40 PDB declaration: 40-meric |
Chain A
11–344（334 aa）
Chain a
11–344（334 aa）
|
Not recorded | OEX CA-MN4-O5 CLUSTER × 2 FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 20 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 36 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 10 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 LMT DODECYL-BETA-D-MALTOSIDE × 8 BCT BICARBONATE ION × 2 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 RRX (3R)-beta,beta-caroten-3-ol × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 1.95 Å |
| 7D1U Cryo-EM Structure of PSII at 2.08 angstrom resolution Deposited 2020-09-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 40 PDB declaration: 40-meric |
Chain A
11–344（334 aa）
Chain a
11–344（334 aa）
|
Not recorded | OEX CA-MN4-O5 CLUSTER × 2 FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 20 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 36 BCT BICARBONATE ION × 2 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 10 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 RRX (3R)-beta,beta-caroten-3-ol × 2 LMT DODECYL-BETA-D-MALTOSIDE × 8 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.08 Å |
| 7DXA PSII intermediate Psb28-RC47 Deposited 2021-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric |
Chain a
1–360（360 aa）
|
Not recorded | SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CLA CHLOROPHYLL A × 22 PHO PHEOPHYTIN A × 2 BCR BETA-CAROTENE × 6 CL CHLORIDE ION × 1 MGE (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 UNL UNKNOWN LIGAND × 2 LMT DODECYL-BETA-D-MALTOSIDE × 3 FE2 FE (II) ION × 1 PQ9 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 HTG heptyl 1-thio-beta-D-glucopyranoside × 1 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.14 Å |
| 7DXH Cryo-EM structure of PSII intermediate Psb28-PSII complex Deposited 2021-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain a
1–360（360 aa）
|
Not recorded | MGE (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CLA CHLOROPHYLL A × 34 BCR BETA-CAROTENE × 9 CL CHLORIDE ION × 2 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHO PHEOPHYTIN A × 2 LMT DODECYL-BETA-D-MALTOSIDE × 3 FE2 FE (II) ION × 1 PQ9 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 UNL UNKNOWN LIGAND × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HTG heptyl 1-thio-beta-D-glucopyranoside × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.14 Å |
| 7EDA Structure of monomeric photosystem II Deposited 2021-03-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric |
Chain A
11–344（334 aa）
|
Not recorded | OEX CA-MN4-O5 CLUSTER × 1 FE2 FE (II) ION × 1 CLA CHLOROPHYLL A × 35 PHO PHEOPHYTIN A × 2 BCR BETA-CAROTENE × 8 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 3 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 2 UNL UNKNOWN LIGAND × 1 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 BCT BICARBONATE ION × 1 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 4 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 RRX (3R)-beta,beta-caroten-3-ol × 1 HEC HEME C × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.78 Å |
| 8GN0 Crystal structure of DCBQ-bound photosystem II complex Deposited 2022-08-22 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 38 PDB declaration: 38-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | OEX CA-MN4-O5 CLUSTER × 2 FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 20 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 9 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 10 LMT DODECYL-BETA-D-MALTOSIDE × 18 GOL GLYCEROL × 30 UNL UNKNOWN LIGAND × 37 JOX 2,6-bis(chloranyl)cyclohexa-2,5-diene-1,4-dione × 4 BCT BICARBONATE ION × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 DMS DIMETHYL SULFOXIDE × 134 CA CALCIUM ION × 5 HTG heptyl 1-thio-beta-D-glucopyranoside × 22 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 9 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 RRX (3R)-beta,beta-caroten-3-ol × 2 MG MAGNESIUM ION × 4 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.1；285 K；5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM MES buffer, pH 6.1, MICRO-BATCH METHOD UNDER OIL, temperature 285K
|
Resolution 2.15 Å R-free 0.185 |
| 8GN1 Crystal structure of DBBQ-bound photosystem II complex Deposited 2022-08-22 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | OEX CA-MN4-O5 CLUSTER × 2 FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 20 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 10 LMT DODECYL-BETA-D-MALTOSIDE × 20 UNL UNKNOWN LIGAND × 44 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 K2I 2,5-bis(bromanyl)cyclohexa-2,5-diene-1,4-dione × 4 BCT BICARBONATE ION × 2 DMS DIMETHYL SULFOXIDE × 128 CA CALCIUM ION × 5 HTG heptyl 1-thio-beta-D-glucopyranoside × 21 GOL GLYCEROL × 21 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 9 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 RRX (3R)-beta,beta-caroten-3-ol × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.1；285 K；5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM MES buffer, pH 6.1, MICRO-BATCH METHOD UNDER OIL, temperature 285K
|
Resolution 2.10 Å R-free 0.191 |
| 8GN2 Crystal structure of PPBQ-bound photosystem II complex Deposited 2022-08-22 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | OEX CA-MN4-O5 CLUSTER × 2 FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 20 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 10 LMT DODECYL-BETA-D-MALTOSIDE × 17 GOL GLYCEROL × 48 UNL UNKNOWN LIGAND × 57 K3C 2-phenylcyclohexa-2,5-diene-1,4-dione × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 BCT BICARBONATE ION × 2 CA CALCIUM ION × 7 HTG heptyl 1-thio-beta-D-glucopyranoside × 21 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 DMS DIMETHYL SULFOXIDE × 31 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 9 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 RRX (3R)-beta,beta-caroten-3-ol × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.1；285 K；5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM MES buffer, pH 6.1, MICRO-BATCH METHOD UNDER OIL, temperature 285K
|
Resolution 1.95 Å R-free 0.181 |
| 8IR5 XFEL structure of cyanobacterial photosystem II under dark conditions Deposited 2023-03-17 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 21 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 LMT DODECYL-BETA-D-MALTOSIDE × 14 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 HTG heptyl 1-thio-beta-D-glucopyranoside × 11 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 CA CALCIUM ION × 7 BCT BICARBONATE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6；293 K；5.5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM Mes BUFFER
|
Resolution 2.15 Å R-free 0.175 |
| 8IR6 XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 20-nanosecond delay Deposited 2023-03-17 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 21 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 LMT DODECYL-BETA-D-MALTOSIDE × 14 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 HTG heptyl 1-thio-beta-D-glucopyranoside × 11 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 CA CALCIUM ION × 7 BCT BICARBONATE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6；293 K；5.5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM Mes BUFFER
|
Resolution 2.20 Å R-free 0.179 |
| 8IR7 XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 200-nanosecond delay Deposited 2023-03-17 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 21 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 LMT DODECYL-BETA-D-MALTOSIDE × 14 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 HTG heptyl 1-thio-beta-D-glucopyranoside × 11 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 CA CALCIUM ION × 7 BCT BICARBONATE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6；293 K；5.5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM Mes BUFFER
|
Resolution 2.25 Å R-free 0.177 |
| 8IR8 XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 1-microsecond delay Deposited 2023-03-17 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 21 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 LMT DODECYL-BETA-D-MALTOSIDE × 14 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 HTG heptyl 1-thio-beta-D-glucopyranoside × 11 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 CA CALCIUM ION × 7 BCT BICARBONATE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6；293 K；5.5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM Mes BUFFER
|
Resolution 2.25 Å R-free 0.175 |
| 8IR9 XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 30-microsecond delay Deposited 2023-03-17 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 21 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 BCT BICARBONATE ION × 2 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 LMT DODECYL-BETA-D-MALTOSIDE × 14 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 HTG heptyl 1-thio-beta-D-glucopyranoside × 11 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 CA CALCIUM ION × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6；293 K；5.5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM Mes BUFFER
|
Resolution 2.20 Å R-free 0.176 |
| 8IRA XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 200-microsecond delay Deposited 2023-03-17 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 21 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 LMT DODECYL-BETA-D-MALTOSIDE × 14 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 HTG heptyl 1-thio-beta-D-glucopyranoside × 11 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 CA CALCIUM ION × 7 BCT BICARBONATE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6；293 K；5.5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM Mes BUFFER
|
Resolution 2.20 Å R-free 0.178 |
| 8IRB XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 5-millisecond delay Deposited 2023-03-17 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 21 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 BCT BICARBONATE ION × 2 LMT DODECYL-BETA-D-MALTOSIDE × 14 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 HTG heptyl 1-thio-beta-D-glucopyranoside × 11 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 CA CALCIUM ION × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6；293 K；5.5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM Mes BUFFER
|
Resolution 2.30 Å R-free 0.180 |
| 8IRC XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 5-millisecond delay (Single conformation) Deposited 2023-03-17 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 21 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 BCT BICARBONATE ION × 2 LMT DODECYL-BETA-D-MALTOSIDE × 14 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 HTG heptyl 1-thio-beta-D-glucopyranoside × 11 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 CA CALCIUM ION × 7 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6；293 K；5.5% PEG 1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM Mes BUFFER, pH
6.0, micro-batch, RT.
|
Resolution 2.25 Å R-free 0.180 |
| 8IRD XFEL structure of cyanobacterial photosystem II following two flashes (2F) with a 20-nanosecond delay Deposited 2023-03-17 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 21 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 BCT BICARBONATE ION × 2 PHO PHEOPHYTIN A × 4 LMT DODECYL-BETA-D-MALTOSIDE × 14 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 HTG heptyl 1-thio-beta-D-glucopyranoside × 11 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 CA CALCIUM ION × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6；293 K；5.5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM Mes BUFFER
|
Resolution 2.30 Å R-free 0.183 |
| 8IRE XFEL structure of cyanobacterial photosystem II following two flashes (2F) with a 200-nanosecond delay Deposited 2023-03-17 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 21 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 BCT BICARBONATE ION × 2 LMT DODECYL-BETA-D-MALTOSIDE × 14 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 HTG heptyl 1-thio-beta-D-glucopyranoside × 11 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 CA CALCIUM ION × 7 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6；293 K；5.5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM Mes BUFFER
|
Resolution 2.25 Å R-free 0.177 |
| 8IRF XFEL structure of cyanobacterial photosystem II following two flashes (2F) with a 1-microsecond delay Deposited 2023-03-17 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 21 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 LMT DODECYL-BETA-D-MALTOSIDE × 14 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 HTG heptyl 1-thio-beta-D-glucopyranoside × 11 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 CA CALCIUM ION × 7 BCT BICARBONATE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6；293 K；5.5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM Mes BUFFER
|
Resolution 2.25 Å R-free 0.177 |
| 8IRG XFEL structure of cyanobacterial photosystem II following two flashes (2F) with a 30-microsecond delay Deposited 2023-03-17 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 BCR BETA-CAROTENE × 22 GOL GLYCEROL × 21 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 BCT BICARBONATE ION × 2 LMT DODECYL-BETA-D-MALTOSIDE × 14 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 HTG heptyl 1-thio-beta-D-glucopyranoside × 11 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 CA CALCIUM ION × 7 PHO PHEOPHYTIN A × 4 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6；293 K；5.5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM Mes BUFFER
|
Resolution 2.30 Å R-free 0.180 |
| 8IRH XFEL structure of cyanobacterial photosystem II following two flashes (2F) with a 200-microsecond delay Deposited 2023-03-17 | Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric |
Chain A
1–344（344 aa）
Chain a
1–344（344 aa）
|
Not recorded | OEY CA-MN4-O6 CLUSTER × 2 FE2 FE (II) ION × 2 CL CHLORIDE ION × 4 CLA CHLOROPHYLL A × 70 PHO PHEOPHYTIN A × 4 BCR BETA-CAROTENE × 22 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 8 GOL GLYCEROL × 21 OEX CA-MN4-O5 CLUSTER × 2 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 4 UNL UNKNOWN LIGAND × 18 LMT DODECYL-BETA-D-MALTOSIDE × 14 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 10 HTG heptyl 1-thio-beta-D-glucopyranoside × 11 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 12 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8 CA CALCIUM ION × 7 BCT BICARBONATE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 MG MAGNESIUM ION × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6；293 K；5.5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM Mes BUFFER
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Resolution 2.25 Å R-free 0.183 |
40 other PDB entries and 40 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | PSBA_THEVL |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–344； UniProt 1–344 Author chain a； PDBConstruct 1–344； UniProt 1–344 |