3JCU: Cryo-EM structure of spinach PSII-LHCII supercomplex at 3.2 Angstrom resolution

PDB ID: 3JCUDownload
MMDB ID: 139444
PDB Deposition Date: 2016/3/10
Updated in MMDB: 2019/12
Experimental Method:
electron microscopy
Resolution: 3.2  Å
Source Organism:
Similar Structures:
Biological Unit for 3JCU: 50-meric; determined by author
Molecular Components in 3JCU
Label Count Molecule
Proteins (50 molecules)
2
Photosystem II Protein D1
(Gene symbol: psbA)
Molecule annotation
2
Photosystem II Cp47 Reaction Center Protein
(Gene symbol: psbB)
Molecule annotation
2
Photosystem II Cp43 Reaction Center Protein
(Gene symbol: psbC)
Molecule annotation
2
Photosystem II D2 Protein
(Gene symbol: psbD)
Molecule annotation
2
Cytochrome B559 Subunit Alpha
(Gene symbol: psbE)
Molecule annotation
2
Cytochrome B559 Subunit Beta
(Gene symbol: psbF)
Molecule annotation
6
Chlorophyll A-B Binding Protein, Chloroplastic
Molecule annotation
2
Photosystem II Reaction Center Protein H
(Gene symbol: psbH)
Molecule annotation
2
Protein Photosystem II Reaction Center Protein I
(Gene symbol: psbI)
Molecule annotation
2
Photosystem II Reaction Center Protein J
(Gene symbol: psbJ)
Molecule annotation
2
Photosystem II Reaction Center Protein K
(Gene symbol: psbK)
Molecule annotation
2
Protein Photosystem II Reaction Center Protein L
(Gene symbol: psbL)
Molecule annotation
2
Photosystem II Reaction Center Protein M
(Gene symbol: psbM)
Molecule annotation
2
Oxygen-evolving Enhancer Protein 1, Chloroplastic
Molecule annotation
2
Oxygen-evolving Enhancer Protein 2, Chloroplastic
Molecule annotation
2
Oxygen-evolving Enhancer Protein 3, Chloroplastic
Molecule annotation
2
Chlorophyll A-B Binding Protein 29 KD (Cp29)
Molecule annotation
2
Chlorophyll A-B Binding Protein 26 KD (Cp26)
Molecule annotation
2
Photosystem II Reaction Center Protein TC
(Gene symbol: psbT)
Molecule annotation
2
Photosystem II Reaction Center TN Protein
Molecule annotation
2
Photosystem II Reaction Center W Protein, Chloroplastic
Molecule annotation
2
Photosystem II Reaction Center X Protein
Molecule annotation
2
Photosystem II Reaction Center Protein Z
(Gene symbol: psbZ)
Molecule annotation
Chemicals and Non-standard biopolymers (322 molecules)
1
2
CA-MN4-O5 CLUSTER (Link to PubChem not yet available)CA-MN4-O5 CLUSTER
2
2
FE (II) ION (Link to PubChem not yet available)FE (II) ION
3
4
CHLORIDE ION (Link to PubChem not yet available)CHLORIDE ION
4
156
CHLOROPHYLL A (Link to PubChem not yet available)CHLOROPHYLL A
5
4
PHEOPHYTIN A (Link to PubChem not yet available)PHEOPHYTIN A
6
20
BETA-CAROTENE (Link to PubChem not yet available)BETA-CAROTENE
7
6
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL (Link to PubChem not yet available)1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
8
10
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE (Link to PubChem not yet available)1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
9
8
DIGALACTOSYL DIACYL GLYCEROL (DGDG) (Link to PubChem not yet available)DIGALACTOSYL DIACYL GLYCEROL (DGDG)
10
2
BICARBONATE ION (Link to PubChem not yet available)BICARBONATE ION
11
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-BENZOQUINONE (Link to PubChem not yet available)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
12
18
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE (Link to PubChem not yet available)1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
13
2
PROTOPORPHYRIN IX CONTAINING FE (Link to PubChem not yet available)PROTOPORPHYRIN IX CONTAINING FE
14
50
CHLOROPHYLL B (Link to PubChem not yet available)CHLOROPHYLL B
15
18
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL (Link to PubChem not yet available)(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
16
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 (Link to PubChem not yet available)(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
17
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 (Link to PubChem not yet available)(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
* 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