5XNM: Structure of unstacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum

PDB ID: 5XNMDownload
MMDB ID: 154689
PDB Deposition Date: 2017/5/23
Updated in MMDB: 2022/11
Experimental Method:
electron microscopy
Resolution: 3.2  Å
Source Organism:
Similar Structures:
Biological Unit for 5XNM: 54-meric; determined by author
Molecular Components in 5XNM
Label Count Molecule
Proteins (54 molecules)
10
Chlorophyll A-B Binding Protein 8, Chloroplastic
Molecule annotation
2
Chlorophyll A-B Binding Protein, Chloroplastic
Molecule annotation
2
Light Harvesting Chlorophyll A/b-binding Protein Lhcb6, Cp24
Molecule annotation
2
Photosystem II Protein D1
(Gene symbol: psbA)
Molecule annotation
2
Photosystem II Cp47 Reaction Center Protein
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, Psbf
Molecule annotation
2
Photosystem II Reaction Center Protein H
Molecule annotation
2
Photosystem II Reaction Center Protein I, Psbi
Molecule annotation
2
Photosystem II Reaction Center Protein J
(Gene symbol: psbJ)
Molecule annotation
2
Photosystem II Reaction Center Protein K
Molecule annotation
2
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
Light Harvesting Chlorophyll A/b-binding Protein Lhcb4, Cp29
Molecule annotation
2
Light Harvesting Chlorophyll A/b-binding Protein Lhcb5, Cp26
Molecule annotation
2
Photosystem II Reaction Center Protein T
(Gene symbol: psbT)
Molecule annotation
2
Photosystem II Luminal Extrinsic Protein TN, Psbtn
Molecule annotation
2
Photosystem II Reaction Center Protein W, Psbw
Molecule annotation
2
Photosystem II Reaction Center Protein X
Molecule annotation
2
Photosystem II Reaction Center Protein Z
(Gene symbol: psbZ)
Molecule annotation
Chemicals and Non-standard biopolymers (486 molecules)
1
98
CHLOROPHYLL B (Link to PubChem not yet available)CHLOROPHYLL B
2
216
CHLOROPHYLL A (Link to PubChem not yet available)CHLOROPHYLL A
3
32
(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
4
16
(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
5
16
(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
6
36
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE (Link to PubChem not yet available)1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
7
24
BETA-CAROTENE (Link to PubChem not yet available)BETA-CAROTENE
8
2
CA-MN4-O5 CLUSTER (Link to PubChem not yet available)CA-MN4-O5 CLUSTER
9
2
FE (II) ION (Link to PubChem not yet available)FE (II) ION
10
4
PHEOPHYTIN A (Link to PubChem not yet available)PHEOPHYTIN A
11
8
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
12
14
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE (Link to PubChem not yet available)1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
13
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-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
14
10
DIGALACTOSYL DIACYL GLYCEROL (DGDG) (Link to PubChem not yet available)DIGALACTOSYL DIACYL GLYCEROL (DGDG)
15
2
BICARBONATE ION (Link to PubChem not yet available)BICARBONATE ION
16
2
PROTOPORPHYRIN IX CONTAINING FE (Link to PubChem not yet available)PROTOPORPHYRIN 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