|
6KAC
Cryo-EM structure of the C2S2-type PSII-LHCII supercomplex from Chlamydomonas reihardtii
Deposited 2019-06-21
|
Different construct
Different mutation/modification
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein heterocomplex
Heteromer;Protein × 56
PDB declaration: 56-meric
|
Chain N
1–257(257 aa)
Chain n
1–257(257 aa)
|
Not recorded
|
OEX CA-MN4-O5 CLUSTER × 2
FE2 FE (II) ION × 2
CL CHLORIDE ION × 4
CLA CHLOROPHYLL A × 148
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 × 4
LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 10
DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10
LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 18
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 × 2
HEM PROTOPORPHYRIN IX CONTAINING FE × 2
LMU DODECYL-ALPHA-D-MALTOSIDE × 6
CHL CHLOROPHYLL B × 50
LUT (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 16
XAT (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 8
NEX (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL × 10
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å
|
|
6KAD
Cryo-EM structure of the C2S2M2L2-type PSII-LHCII supercomplex from Chlamydomonas reihardtii
Deposited 2019-06-21
|
Different construct
Different mutation/modification
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein heterocomplex
Heteromer;Protein × 58
PDB declaration: 58-meric
|
Chain 2
1–257(257 aa)
Chain 3
1–257(257 aa)
Chain 5
1–257(257 aa)
Chain 8
1–257(257 aa)
Chain 9
1–257(257 aa)
Chain N
1–257(257 aa)
Chain n
1–257(257 aa)
Chain p
1–257(257 aa)
|
Not recorded
|
CHL CHLOROPHYLL B × 122
CLA CHLOROPHYLL A × 254
LUT (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 42
XAT (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 20
NEX (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL × 22
LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 32
OEX CA-MN4-O5 CLUSTER × 2
FE2 FE (II) ION × 2
CL CHLORIDE ION × 2
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 × 14
DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10
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 × 2
HEM PROTOPORPHYRIN IX CONTAINING FE × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å
|
|
6KAF
C2S2M2N2-type PSII-LHCII
Deposited 2019-06-22
|
Different construct
Different mutation/modification
Different oligomeric state
Different ligand/ion
Different structure-quality metrics
|
Assembly 1
Protein heterocomplex
Heteromer;Protein × 58
PDB declaration: 58-meric
|
Chain 1
1–257(257 aa)
Chain 2
1–257(257 aa)
Chain 3
1–257(257 aa)
Chain 4
1–257(257 aa)
Chain 5
1–257(257 aa)
Chain 6
1–257(257 aa)
Chain G
1–257(257 aa)
Chain N
1–257(257 aa)
Chain P
1–257(257 aa)
Chain Q
1–257(257 aa)
Chain U
1–257(257 aa)
Chain V
1–257(257 aa)
Chain g
1–257(257 aa)
Chain n
1–257(257 aa)
Chain p
1–257(257 aa)
Chain q
1–257(257 aa)
Chain u
1–257(257 aa)
Chain v
1–257(257 aa)
|
Not recorded
|
CLA CHLOROPHYLL A × 252
LUT (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 30
XAT (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 20
LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 40
CHL CHLOROPHYLL B × 122
NEX (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL × 16
FE2 FE (II) ION × 2
CL CHLORIDE ION × 4
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
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
LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 14
BCT BICARBONATE ION × 2
DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 10
HEM PROTOPORPHYRIN IX CONTAINING FE × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.73 Å
|
|
7DZ7
State transition supercomplex PSI-LHCI-LHCII from double phosphatase mutant pph1;pbcp of green alga Chlamydomonas reinhardtii
Deposited 2021-01-23
|
Different construct
Different mutation/modification
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein heterocomplex
Heteromer;Protein × 29
PDB declaration: 29-meric
|
Chain U
1–257(257 aa)
Chain Y
1–257(257 aa)
|
Not recorded
|
CLA CHLOROPHYLL A × 298
PQN PHYLLOQUINONE × 2
LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 27
BCR BETA-CAROTENE × 40
SF4 IRON/SULFUR CLUSTER × 3
LMU DODECYL-ALPHA-D-MALTOSIDE × 7
LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 11
DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 1
LUT (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 22
XAT (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 16
NEX (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL × 8
CHL CHLOROPHYLL B × 36
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.84 Å
|
|
7DZ8
State transition supercomplex PSI-LHCI-LHCII from the LhcbM1 lacking mutant of Chlamydomonas reinhardtii
Deposited 2021-01-23
|
Different construct
Different mutation/modification
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein heterocomplex
Heteromer;Protein × 29
PDB declaration: 29-meric
|
Chain U
1–257(257 aa)
Chain Y
1–257(257 aa)
Chain Z
1–257(257 aa)
|
Not recorded
|
CLA CHLOROPHYLL A × 298
PQN PHYLLOQUINONE × 2
LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 27
BCR BETA-CAROTENE × 40
SF4 IRON/SULFUR CLUSTER × 3
LMU DODECYL-ALPHA-D-MALTOSIDE × 7
LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 11
DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 1
LUT (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 22
XAT (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 16
NEX (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL × 8
CHL CHLOROPHYLL B × 36
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å
|
|
7E0H
LHCII-1 in the state transition supercomplex PSI-LHCI-LHCII from the LhcbM1 lacking mutant of Chlamydomonas reinhardtii
Deposited 2021-01-28
|
Different construct
Different mutation/modification
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein heterocomplex
Heteromer;Protein × 3
PDB declaration: trimeric
|
Chain Y
1–257(257 aa)
Chain Z
1–257(257 aa)
|
Not recorded
|
CHL CHLOROPHYLL B × 18
CLA CHLOROPHYLL A × 24
LUT (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 6
XAT (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 3
NEX (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL × 3
LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 3
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.75 Å
|
|
7E0I
LHCII-2 in the state transition supercomplex PSI-LHCI-LHCII from the LhcbM1 lacking mutant of Chlamydomonas reinhardti
Deposited 2021-01-28
|
Different construct
Different mutation/modification
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein heterocomplex
Heteromer;Protein × 3
PDB declaration: trimeric
|
Chain U
1–257(257 aa)
|
Not recorded
|
CHL CHLOROPHYLL B × 18
CLA CHLOROPHYLL A × 24
LUT (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 6
XAT (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 3
NEX (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL × 3
LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 3
LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.53 Å
|
|
7E0J
LHCII-1 in the state transition supercomplex PSI-LHCI-LHCII from the double phosphatase mutant pph1;pbcp of Chlamydomonas reinhardti.
Deposited 2021-01-28
|
Different construct
Different mutation/modification
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein heterocomplex
Heteromer;Protein × 3
PDB declaration: trimeric
|
Chain Y
1–257(257 aa)
|
Not recorded
|
CHL CHLOROPHYLL B × 17
CLA CHLOROPHYLL A × 24
LUT (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 6
XAT (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 3
NEX (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL × 3
LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 3
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.13 Å
|
|
7E0K
LHCII-2 in the state transition supercomplex PSI-LHCI-LHCII from the double phosphatase mutant pph1;pbcp of Chlamydomonas reinhardti.
Deposited 2021-01-28
|
Different construct
Different mutation/modification
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein heterocomplex
Heteromer;Protein × 3
PDB declaration: trimeric
|
Chain U
1–257(257 aa)
|
Not recorded
|
CHL CHLOROPHYLL B × 18
CLA CHLOROPHYLL A × 24
LUT (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 6
XAT (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 3
NEX (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL × 3
LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 3
LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.09 Å
|
|
9IS4
Cryo-EM structure of a TEF30-associated intermediate C2S-type PSII-LHCII supercomplex from Chlamydomonas reinhardtii
Deposited 2024-07-16
|
Different construct
Different mutation/modification
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 N
39–257(219 aa)
|
Not recorded
|
FE2 FE (II) ION × 2
CLA CHLOROPHYLL A × 109
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 × 3
LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 10
LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 15
DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 8
LMU DODECYL-ALPHA-D-MALTOSIDE × 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 × 2
HEM PROTOPORPHYRIN IX CONTAINING FE × 2
CHL CHLOROPHYLL B × 25
LUT (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 8
NEX (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL × 5
XAT (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 4
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å
|