8J5K: Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana

PDB ID: 8J5KDownload
MMDB ID: 240230
PDB Deposition Date: 2023/4/23
Updated in MMDB: 2023/12
Experimental Method:
electron microscopy
Resolution: 2.93  Å
Source Organism:
Similar Structures:
Biological Unit for 8J5K: 56-meric; determined by author
Molecular Components in 8J5K
Label Count Molecule
Proteins (56 molecules)
2
Psba
Molecule annotation
2
Psbb
Molecule annotation
2
Psbc
Molecule annotation
2
Psbd
Molecule annotation
2
Psbe
Molecule annotation
2
Psbf
Molecule annotation
2
Psbh
Molecule annotation
2
Psbi
Molecule annotation
2
Psbj
Molecule annotation
2
Psbk
Molecule annotation
2
Psbl
Molecule annotation
2
Psbm
Molecule annotation
2
Psb34
Molecule annotation
2
Psbo
Molecule annotation
2
Psbq'
Molecule annotation
2
Psbt
Molecule annotation
2
Psbu
Molecule annotation
2
Psbv
Molecule annotation
2
Psbw
Molecule annotation
2
Psbx
Molecule annotation
2
Psby
Molecule annotation
2
Psbz
Molecule annotation
2
Fcpii-g, Fucoxanthin Chlorophyll A/C Binding Protein
Molecule annotation
2
Fcpii-h2, Fucoxanthin Chlorophyll A/C Binding Protein
Molecule annotation
2
Fcpii-h1, Fucoxanthin Chlorophyll A/C Binding Protein
Molecule annotation
2
Fcpii-i, Fucoxanthin Chlorophyll A/C Binding Protein
Molecule annotation
2
Fcpii-k, Fucoxanthin Chlorophyll A/C Binding Protein
Molecule annotation
2
Fcpii-j, Fucoxanthin Chlorophyll A/C Binding Protein
Molecule annotation
Chemicals and Non-standard biopolymers (336 molecules)
1
2
CA-MN4-O5 CLUSTERCA-MN4-O5 CLUSTER
2
2
FE (II) IONFE (II) ION
3
206
CHLOROPHYLL ACHLOROPHYLL A
4
4
PHEOPHYTIN APHEOPHYTIN A
5
20
BETA-CAROTENEBETA-CAROTENE
6
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
7
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
8
14
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
9
22
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
10
2
CHLORIDE IONCHLORIDE ION
11
8
DIGALACTOSYL DIACYL GLYCEROL (DGDG)DIGALACTOSYL DIACYL GLYCEROL (DGDG)
12
2
BICARBONATE IONBICARBONATE ION
13
4
PROTOPORPHYRIN IX CONTAINING FEPROTOPORPHYRIN IX CONTAINING FE
14
24
(3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate(3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate
15
2
(1~{R})-3,5,5-trimethyl-4-[(1~{E},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-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol(1~{R})-3,5,5-trimethyl-4-[(1~{E},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-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol
16
12
(3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol(3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-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