EMD-9777
Structure of C2S2M2-type PSII-FCPII supercomplex from diatom
EMD-9777
Single-particle3.8 Å
Deposition: 07/01/2019
Map released: 07/08/2019
Last modified: 06/11/2019
Name: C2S2M2-type PSII-FCPII supercomplex
Summary:
- Complex
- Protein
- Photosystem II reaction center protein D1
- Photosystem II chlorophyll protein CP47
- Photosystem II chlorophyll protein CP43
- Photosystem II reaction center protein D2
- Cytochrome b559 subunit alpha
- Cytochrome b559 subunit beta
- Photosystem II reaction center protein H
- Photosystem II reaction center protein I
- Photosystem II reaction center protein J
- Photosystem II reaction center protein K
- Photosystem II reaction center protein L
- Photosystem II reaction center protein M
- Extrinsic protein in photosystem II
- Photosystem II reaction center protein T
- Extrinsic protein in photosystem II
- Cytochrome c-550
- Photosystem II reaction center protein Ycf12
- Photosystem II reaction center X protein
- Photosystem II reaction center protein Z
- Extrinsic protein in photosystem II
- Photosystem II reaction center protein W
- Unknown protein 0
- Unknown protein 1
- Unknown protein 2
- Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
- Fucoxanthin chlorophyll a/c-binding protein monomer 1
- Fucoxanthin chlorophyll a/c-binding protein monomer 2
- Fucoxanthin chlorophyll a/c-binding protein monomer 3
- Ligand
- FE (II) ION
- CHLOROPHYLL A
- PHEOPHYTIN A
- BETA-CAROTENE
- 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
- BICARBONATE ION
- 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
- 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
- CA-MN4-O5 CLUSTER
- DIGALACTOSYL DIACYL GLYCEROL (DGDG)
- 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
- PROTOPORPHYRIN IX CONTAINING FE
- (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'-yl acetate
- DODECYL-ALPHA-D-MALTOSIDE
C2S2M2-type PSII-FCPII supercomplex
Name: Natural source [1]
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 1 MDa | - |
Photosystem II reaction center protein D1
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Name: Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 38 kDa | - |
Photosystem II chlorophyll protein CP47
Number of copies: 2
Name: Number of copies: 2
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 56 kDa | - |
Photosystem II chlorophyll protein CP43
Number of copies: 2
Name: Number of copies: 2
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 51 kDa | - |
Photosystem II reaction center protein D2
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Name: Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 39 kDa | - |
Cytochrome b559 subunit alpha
Number of copies: 2
Name: Number of copies: 2
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 9 kDa | - |
Cytochrome b559 subunit beta
Number of copies: 2
Name: Number of copies: 2
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 4 kDa | - |
Photosystem II reaction center protein H
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Name: Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [6]
Biological process:
photosynthesis protein stabilization
Molecular function:
phosphate ion binding
Cellular location:
photosystem II chloroplast thylakoid membrane integral component of membrane
photosynthesis protein stabilization
Molecular function:
phosphate ion binding
Cellular location:
photosystem II chloroplast thylakoid membrane integral component of membrane
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 7 kDa | - |
Photosystem II reaction center protein I
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Name: Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 4 kDa | - |
Photosystem II reaction center protein J
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Name: Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 4 kDa | - |
Photosystem II reaction center protein K
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Name: Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 4 kDa | - |
Photosystem II reaction center protein L
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Name: Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 4 kDa | - |
Photosystem II reaction center protein M
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Name: Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 14 kDa | - |
Extrinsic protein in photosystem II
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Name: Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [3]
Biological process:
photosystem II assembly photosystem II stabilization
Cellular location:
photosystem II oxygen evolving complex
photosystem II assembly photosystem II stabilization
Cellular location:
photosystem II oxygen evolving complex
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 26 kDa | - |
Photosystem II reaction center protein T
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Name: Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 3 kDa | - |
Extrinsic protein in photosystem II
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Name: Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 10 kDa | - |
Cytochrome c-550
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Name: Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
respiratory electron transport chain
Molecular function:
heme binding iron ion binding electron transfer activity
Cellular location:
photosystem II
respiratory electron transport chain
Molecular function:
heme binding iron ion binding electron transfer activity
Cellular location:
photosystem II
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 14 kDa | - |
Photosystem II reaction center protein Ycf12
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Name: Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 3 kDa | - |
Photosystem II reaction center X protein
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Name: Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [4]
Biological process:
photosynthesis
Cellular location:
integral component of membrane photosystem II chloroplast thylakoid membrane
photosynthesis
Cellular location:
integral component of membrane photosystem II chloroplast thylakoid membrane
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 3 kDa | - |
Photosystem II reaction center protein Z
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Name: Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 6 kDa | - |
Extrinsic protein in photosystem II
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Name: Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 17 kDa | - |
Photosystem II reaction center protein W
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Name: Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 7 kDa | - |
Unknown protein 0
Number of copies: 2
Name: Number of copies: 2
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 2 kDa | - |
Unknown protein 1
Number of copies: 2
Name: Number of copies: 2
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 2 kDa | - |
Unknown protein 2
Number of copies: 2
Name: Number of copies: 2
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 869 Da | - |
Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
Number of copies: 16
Name: Number of copies: 16
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 22 kDa | - |
Fucoxanthin chlorophyll a/c-binding protein monomer 1
Number of copies: 2
Name: Number of copies: 2
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 18 kDa | - |
Fucoxanthin chlorophyll a/c-binding protein monomer 2
Number of copies: 2
Name: Number of copies: 2
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 12 kDa | - |
Fucoxanthin chlorophyll a/c-binding protein monomer 3
Number of copies: 2
Name: Number of copies: 2
Natural source
Organism: Chaetoceros gracilis
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 13 kDa | - |
FE (II) ION
HET code: FE2
Number of copies: 2
ChEBI DrugBank
Name: HET code: FE2
Number of copies: 2
ChEBI DrugBank
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 55 Da | - |
CHLOROPHYLL A
HET code: CLA
Number of copies: 290
ChEBI DrugBank
Name: HET code: CLA
Number of copies: 290
ChEBI DrugBank
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 893 Da | - |
PHEOPHYTIN A
HET code: PHO
Number of copies: 4
ChEMBL ChEBI
Name: HET code: PHO
Number of copies: 4
ChEMBL ChEBI
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 871 Da | - |
BETA-CAROTENE
HET code: BCR
Number of copies: 24
ChEMBL ChEBI DrugBank
Name: HET code: BCR
Number of copies: 24
ChEMBL ChEBI DrugBank
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 536 Da | - |
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
HET code: SQD
Number of copies: 6
ChEMBL
Name: HET code: SQD
Number of copies: 6
ChEMBL
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 795 Da | - |
BICARBONATE ION
HET code: BCT
Number of copies: 2
ChEBI
Name: HET code: BCT
Number of copies: 2
ChEBI
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 61 Da | - |
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
HET code: LHG
Number of copies: 8
ChEBI
Name: HET code: LHG
Number of copies: 8
ChEBI
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 722 Da | - |
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
HET code: LMG
Number of copies: 14
Name: HET code: LMG
Number of copies: 14
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 787 Da | - |
CA-MN4-O5 CLUSTER
HET code: OEX
Number of copies: 2
ChEBI
Name: HET code: OEX
Number of copies: 2
ChEBI
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 339 Da | - |
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
HET code: DGD
Number of copies: 8
DrugBank
Name: HET code: DGD
Number of copies: 8
DrugBank
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 949 Da | - |
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
HET code: PL9
Number of copies: 4
Name: HET code: PL9
Number of copies: 4
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 749 Da | - |
PROTOPORPHYRIN IX CONTAINING FE
HET code: HEM
Number of copies: 4
ChEBI
Name: HET code: HEM
Number of copies: 4
ChEBI
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 616 Da | - |
(3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'-yl acetate
HET code: A86
Number of copies: 118
ChEBI DrugBank
Name: HET code: A86
Number of copies: 118
ChEBI DrugBank
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 658 Da | - |
DODECYL-ALPHA-D-MALTOSIDE
HET code: LMU
Number of copies: 2
ChEMBL DrugBank
Name: HET code: LMU
Number of copies: 2
ChEMBL DrugBank
Molecular weight
Experimental | Theoretical | Method |
---|---|---|
- | 510 Da | - |