8XLP: Structure of inactive Photosystem II associated with CAC antenna from Rhodomonas Salina

PDB ID: 8XLPDownload
MMDB ID: 250460
PDB Deposition Date: 2023/12/26
Updated in MMDB: 2024/10
Experimental Method:
electron microscopy
Resolution: 2.57  Å
Source Organism:
Similar Structures:
Biological Unit for 8XLP: 46-meric; determined by author
Molecular Components in 8XLP
Label Count Molecule
Proteins (46 molecules)
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
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
(Gene symbol: psbI)
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 Protein M
Molecule annotation
2
Photosystem II Reaction Center Protein T
Molecule annotation
2
Photosystem II Protein W
Molecule annotation
2
Photosystem II Reaction Center X Protein
Molecule annotation
2
Photosystem II Reaction Center Protein Psb30
(Gene symbol: ycf12)
Molecule annotation
2
Photosystem II Reaction Center Protein Z
Molecule annotation
2
NCP
Molecule annotation
2
Cac2
Molecule annotation
2
Cac3
Molecule annotation
2
Cac4
Molecule annotation
2
Cac5
Molecule annotation
2
Cac6
Molecule annotation
2
Cac1
Molecule annotation
Chemicals and Non-standard biopolymers (370 molecules)
1
2
FE (II) IONFE (II) ION
2
194
CHLOROPHYLL ACHLOROPHYLL A
3
4
PHEOPHYTIN APHEOPHYTIN A
4
24
1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyl-18-[(1R)-2,6,6-trimethylcyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohexene1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyl-18-[(1R)-2,6,6-trimethylcyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohexene
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
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
7
2
BICARBONATE IONBICARBONATE ION
8
20
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
9
4
CHLORIDE IONCHLORIDE ION
10
4
MANGANESE (II) IONMANGANESE (II) ION
11
22
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
12
4
DIGALACTOSYL DIACYL GLYCEROL (DGDG)DIGALACTOSYL DIACYL GLYCEROL (DGDG)
13
2
PROTOPORPHYRIN IX CONTAINING FEPROTOPORPHYRIN IX CONTAINING FE
14
24
Chlorophyll c2Chlorophyll c2
15
48
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol
16
8
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
* 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