6KAD: Cryo-EM structure of the C2S2M2L2-type PSII-LHCII supercomplex from Chlamydomonas reihardtii

PDB ID: 6KADDownload
MMDB ID: 190953
PDB Deposition Date: 2019/6/21
Updated in MMDB: 2022/11
Experimental Method:
electron microscopy
Resolution: 3.4  Å
Source Organism:
Similar Structures:
Biological Unit for 6KAD: 58-meric; determined by author
Molecular Components in 6KAD
Label Count Molecule
Proteins (58 molecules)
6
Chlorophyll A-B Binding Protein, Chloroplastic
Molecule annotation
8
Chlorophyll A-B Binding Protein, Chloroplastic
Molecule annotation
4
Chlorophyll A-B Binding Protein, Chloroplastic
Molecule annotation
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
2
Photosystem II Reaction Center Protein H
Molecule annotation
2
Photosystem II Reaction Center Protein I
Molecule annotation
2
Photosystem II Reaction Center Protein J
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 Cp29
Molecule annotation
2
Chlorophyll A-B Binding Protein, Chloroplastic
Molecule annotation
2
Photosystem II Reaction Center Protein T
Molecule annotation
2
Photosystem II Reaction Center Protein Ycf12
Molecule annotation
2
Photosystem II Reaction Center W Protein, Chloroplastic
Molecule annotation
2
4.1 KDA Photosystem II Subunit
Molecule annotation
2
Photosystem II Reaction Center Protein Z
Molecule annotation
Chemicals and Non-standard biopolymers (560 molecules)
1
122
CHLOROPHYLL BCHLOROPHYLL B
2
254
CHLOROPHYLL ACHLOROPHYLL A
3
42
(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
4
20
(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
5
22
(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
6
32
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
7
2
CA-MN4-O5 CLUSTERCA-MN4-O5 CLUSTER
8
2
FE (II) IONFE (II) ION
9
2
CHLORIDE IONCHLORIDE ION
10
4
PHEOPHYTIN APHEOPHYTIN A
11
20
BETA-CAROTENEBETA-CAROTENE
12
8
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
13
14
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
14
10
DIGALACTOSYL DIACYL GLYCEROL (DGDG)DIGALACTOSYL DIACYL GLYCEROL (DGDG)
15
2
BICARBONATE IONBICARBONATE ION
16
2
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
17
2
PROTOPORPHYRIN IX CONTAINING FEPROTOPORPHYRIN IX CONTAINING FE
* 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