8C29: Cryo-EM structure of photosystem II C2S2 supercomplex from Norway spruce (Picea abies) at 2.8 Angstrom resolution

PDB ID: 8C29Download
MMDB ID: 233215
PDB Deposition Date: 2022/12/21
Updated in MMDB: 2023/09
Experimental Method:
electron microscopy
Resolution: 2.785  Å
Source Organism:
Similar Structures:
Biological Unit for 8C29: 46-meric; determined by author
Molecular Components in 8C29
Label Count Molecule
Proteins (46 molecules)
2
Photosystem II Protein D1
Molecule annotation
2
Photosystem II Cp47 Reaction Center Protein
Molecule annotation
2
Photosystem II Cp43 Reaction Center Protein
Molecule annotation
2
Photosystem II D2 Protein
Molecule annotation
2
Cytochrome B559 Subunit Alpha
Molecule annotation
2
Cytochrome B559 Subunit Beta
Molecule annotation
6
Chlorophyll A-B Binding Protein, Chloroplastic
Molecule annotation
2
Photosystem II Reaction Center Protein H
Molecule annotation
2
Photosystem II Reaction Center Protein I
Molecule annotation
2
Photosystem II Reaction Center Protein K
Molecule annotation
2
Photosystem II Reaction Center Protein L
Molecule annotation
2
Photosystem II Reaction Center Protein M
Molecule annotation
2
Oxygen-evolving Enhancer Protein 1, Chloroplastic
Molecule annotation
2
Chlorophyll A-B Binding Protein, Chloroplastic
Molecule annotation
2
Chlorophyll A-B Binding Protein, Chloroplastic
Molecule annotation
2
Photosystem II Reaction Center Protein T
Molecule annotation
2
Photosystem II 5 KDA Protein, Chloroplastic
Molecule annotation
2
Photosystem II Reaction Center Protein Ycf12
Molecule annotation
2
Psii 6.1 KDA Protein
Molecule annotation
2
Photosystem II Psbx
Molecule annotation
2
Photosystem II Reaction Center Protein Z
Molecule annotation
Chemicals and Non-standard biopolymers (358 molecules)
1
2
FE (II) IONFE (II) ION
2
154
CHLOROPHYLL ACHLOROPHYLL A
3
4
PHEOPHYTIN APHEOPHYTIN A
4
20
BETA-CAROTENEBETA-CAROTENE
5
4
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
6
12
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
7
12
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
8
4
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-BENZOQUINONE2,3-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
9
18
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
10
26
ALPHA-LINOLENIC ACIDALPHA-LINOLENIC ACID
11
2
PALMITOLEIC ACIDPALMITOLEIC ACID
12
4
DIGALACTOSYL DIACYL GLYCEROL (DGDG)DIGALACTOSYL DIACYL GLYCEROL (DGDG)
13
2
MAGNESIUM IONMAGNESIUM ION
14
2
(2R)-2,5,7,8-TETRAMETHYL-2-[(4R,8R)-4,8,12-TRIMETHYLTRIDECYL]CHROMAN-6-OL(2R)-2,5,7,8-TETRAMETHYL-2-[(4R,8R)-4,8,12-TRIMETHYLTRIDECYL]CHROMAN-6-OL
15
2
BICARBONATE IONBICARBONATE ION
16
2
DIACYL GLYCEROLDIACYL GLYCEROL
17
2
PROTOPORPHYRIN IX CONTAINING FEPROTOPORPHYRIN IX CONTAINING FE
18
50
CHLOROPHYLL BCHLOROPHYLL B
19
18
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
20
10
(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(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
21
8
(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(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
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303