8XR6: Cryo-EM structure of cryptophyte photosystem II

PDB ID: 8XR6Download
MMDB ID: 248650
PDB Deposition Date: 2024/1/6
Updated in MMDB: 2024/06
Experimental Method:
electron microscopy
Resolution: 2.53  Å
Source Organism:
Similar Structures:
Biological Unit for 8XR6: 56-meric; determined by author
Molecular Components in 8XR6
Label Count Molecule
Proteins (56 molecules)
2
Photosystem II Protein D1
Molecule annotation
2
Acpii-4
Molecule annotation
2
Acpii-1
Molecule annotation
2
Acpii-2
Molecule annotation
2
Acpii-3
Molecule annotation
2
Acpii-5
Molecule annotation
2
Acpii-6
Molecule annotation
2
Photosystem II Cp47 Reaction Center Protein
Molecule annotation
2
Psbc_cp43
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
Psbm
Molecule annotation
2
Psb-gama_linker
Molecule annotation
2
Psbo
Molecule annotation
2
Psbq
Molecule annotation
2
Photosystem II Reaction Center Protein T
Molecule annotation
2
Psbu
Molecule annotation
2
Photosystem II Cytochrome C550
Molecule annotation
2
Psbw
Molecule annotation
2
Photosystem II Reaction Center Protein X
Molecule annotation
2
Photosystem II Reaction Center Protein Psb30
Molecule annotation
2
Photosystem II Reaction Center Protein Z
Molecule annotation
Chemicals and Non-standard biopolymers (380 molecules)
1
2
CA-MN4-O5 CLUSTERCA-MN4-O5 CLUSTER
2
2
FE (II) IONFE (II) ION
3
2
BICARBONATE IONBICARBONATE ION
4
2
CHLORIDE IONCHLORIDE ION
5
210
CHLOROPHYLL ACHLOROPHYLL A
6
4
PHEOPHYTIN APHEOPHYTIN A
7
24
(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
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
24
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
10
14
Chlorophyll c2Chlorophyll c2
11
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
12
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
13
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
14
16
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
15
8
DIGALACTOSYL DIACYL GLYCEROL (DGDG)DIGALACTOSYL DIACYL GLYCEROL (DGDG)
16
4
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