8IRD: XFEL structure of cyanobacterial photosystem II following two flashes (2F) with a 20-nanosecond delay

PDB ID: 8IRDDownload
MMDB ID: 244455
PDB Deposition Date: 2023/3/17
Updated in MMDB: 2024/03
Experimental Method:
x-ray diffraction
Resolution: 2.3  Å
Source Organism:
Similar Structures:
Biological Unit for 8IRD: 39-meric; determined by author and by software
Molecular Components in 8IRD
Label Count Molecule
Proteins (39 molecules)
2
Photosystem II Protein D1
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
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
Photosystem II Reaction Center Protein M
Molecule annotation
2
Photosystem II Manganese-stabilizing Polypeptide
Molecule annotation
2
Photosystem II Reaction Center Protein T
Molecule annotation
2
Photosystem II 12 KDA Extrinsic Protein
Molecule annotation
2
Cytochrome C-550
Molecule annotation
2
Photosystem II Reaction Center Protein X
Molecule annotation
2
Photosystem II Reaction Center Protein Ycf12
Molecule annotation
2
Photosystem II Reaction Center Protein Z
Molecule annotation
1
Photosystem II Protein Y
Molecule annotation
Chemicals and Non-standard biopolymers (225 molecules)
1
2
FE (II) IONFE (II) ION
2
4
CHLORIDE IONCHLORIDE ION
3
70
CHLOROPHYLL ACHLOROPHYLL A
4
22
BETA-CAROTENEBETA-CAROTENE
5
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
6
21
GLYCEROLGLYCEROL
7
2
CA-MN4-O5 CLUSTERCA-MN4-O5 CLUSTER
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
18
UNKNOWN LIGANDUNKNOWN LIGAND
10
2
BICARBONATE IONBICARBONATE ION
11
4
PHEOPHYTIN APHEOPHYTIN A
12
14
DODECYL-BETA-D-MALTOSIDEDODECYL-BETA-D-MALTOSIDE
13
10
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
14
12
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
15
11
heptyl 1-thio-beta-D-glucopyranosideheptyl 1-thio-beta-D-glucopyranoside
16
8
DIGALACTOSYL DIACYL GLYCEROL (DGDG)DIGALACTOSYL DIACYL GLYCEROL (DGDG)
17
7
CALCIUM IONCALCIUM ION
18
2
PROTOPORPHYRIN IX CONTAINING FEPROTOPORPHYRIN IX CONTAINING FE
19
2
MAGNESIUM IONMAGNESIUM ION
20
2
HEME CHEME C
* 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