5TIS: Room temperature XFEL structure of the native, doubly-illuminated photosystem II complex

PDB ID: 5TISDownload
MMDB ID: 145181
PDB Deposition Date: 2016/10/3
Updated in MMDB: 2016/12
Experimental Method:
x-ray diffraction
Resolution: 2.25  Å
Source Organism:
Similar Structures:
Biological Unit for 5TIS: 40-meric; determined by author
Molecular Components in 5TIS
Label Count Molecule
Proteins (40 molecules)
2
Photosystem II Protein D1 1
(Gene symbol: psbA1)
Molecule annotation
2
Photosystem II Cp47 Reaction Center Protein
(Gene symbol: psbB)
Molecule annotation
2
Photosystem II Cp43 Reaction Center Protein
(Gene symbol: psbC)
Molecule annotation
2
Photosystem II D2 Protein
(Gene symbol: psbD1)
Molecule annotation
2
Cytochrome B559 Subunit Alpha
(Gene symbol: psbE)
Molecule annotation
2
Cytochrome B559 Subunit Beta
(Gene symbol: psbF)
Molecule annotation
2
Photosystem II Reaction Center Protein H
(Gene symbol: psbH)
Molecule annotation
2
Photosystem II Reaction Center Protein I
(Gene symbol: psbI)
Molecule annotation
2
Photosystem II Reaction Center Protein J
(Gene symbol: psbJ)
Molecule annotation
2
Photosystem II Reaction Center Protein K
(Gene symbol: psbK)
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
Photosystem II Manganese-stabilizing Polypeptide
(Gene symbol: psbO)
Molecule annotation
2
Photosystem II Reaction Center Protein T
(Gene symbol: psbT)
Molecule annotation
2
Photosystem II 12 KDA Extrinsic Protein
(Gene symbol: psbU)
Molecule annotation
2
Cytochrome C-550
(Gene symbol: psbV)
Molecule annotation
2
Photosystem II Reaction Center Protein Ycf12
(Gene symbol: ycf12)
Molecule annotation
2
Photosystem II Reaction Center X Protein
(Gene symbol: psbX)
Molecule annotation
2
Photosystem II Reaction Center Protein Z
(Gene symbol: psbZ)
Molecule annotation
2
Photosystem II Protein Y
(Gene symbol: psbY)
Molecule annotation
Chemicals and Non-standard biopolymers (189 molecules)
1
2
CA-MN4-O5 CLUSTERCA-MN4-O5 CLUSTER
2
2
FE (II) IONFE (II) ION
3
4
CHLORIDE IONCHLORIDE ION
4
2
BICARBONATE IONBICARBONATE ION
5
70
CHLOROPHYLL ACHLOROPHYLL A
6
4
PHEOPHYTIN APHEOPHYTIN A
7
22
BETA-CAROTENEBETA-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
10
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
10
10
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
11
33
UNKNOWN LIGANDUNKNOWN LIGAND
12
14
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
13
8
DIGALACTOSYL DIACYL GLYCEROL (DGDG)DIGALACTOSYL DIACYL GLYCEROL (DGDG)
14
2
PROTOPORPHYRIN IX CONTAINING FEPROTOPORPHYRIN IX CONTAINING FE
15
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