8GN2
Crystal structure of PPBQ-bound photosystem II complex
Entity
Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
1 | A, a | Photosystem II protein D1 | polymer | 344 | 38235.6 | 2 | UniProt (P51765) Pfam (PF00124) In PDB | Thermostichus vulcanus | PSII D1 protein,Photosystem II Q(B) protein |
2 | B, b | Photosystem II CP47 reaction center protein | polymer | 505 | 56068.7 | 2 | UniProt (D0VWR1) Pfam (PF00421) In PDB | Thermostichus vulcanus | PSII 47 kDa protein,Protein CP-47 |
3 | C, c | Photosystem II CP43 reaction center protein | polymer | 455 | 49668.8 | 2 | UniProt (D0VWR7) Pfam (PF00421) In PDB | Thermostichus vulcanus | PSII 43 kDa protein,Protein CP-43 |
4 | D, d | Photosystem II D2 protein | polymer | 342 | 38419.9 | 2 | UniProt (D0VWR8) Pfam (PF00124) In PDB | Thermostichus vulcanus | PSII D2 protein,Photosystem Q(A) protein |
5 | E, e | Cytochrome b559 subunit alpha | polymer | 83 | 9449.6 | 2 | UniProt (P12238) Pfam (PF00283) Pfam (PF00284) In PDB | Thermostichus vulcanus | PSII reaction center subunit V |
6 | F, f | Cytochrome b559 subunit beta | polymer | 44 | 4936.7 | 2 | UniProt (P12239) Pfam (PF00283) In PDB | Thermostichus vulcanus | PSII reaction center subunit VI |
7 | H, h | Photosystem II reaction center protein H | polymer | 63 | 7057.3 | 2 | UniProt (P19052) Pfam (PF00737) In PDB | Thermostichus vulcanus | PSII-H |
8 | I, i | Photosystem II reaction center protein I | polymer | 38 | 4438.3 | 2 | UniProt (P12240) Pfam (PF02532) In PDB | Thermostichus vulcanus | PSII-I,PSII 4.4 kDa protein |
9 | J, j | Photosystem II reaction center protein J | polymer | 40 | 4105.9 | 2 | UniProt (Q7DGD4) Pfam (PF01788) In PDB | Thermostichus vulcanus | PSII-J |
10 | K, k | Photosystem II reaction center protein K | polymer | 37 | 4101.9 | 2 | UniProt (P19054) Pfam (PF02533) In PDB | Thermostichus vulcanus | PSII-K |
11 | L, l | Photosystem II reaction center protein L | polymer | 37 | 4299.0 | 2 | UniProt (P12241) Pfam (PF02419) In PDB | Thermostichus vulcanus | PSII-L |
12 | M, m | Photosystem II reaction center protein M | polymer | 36 | 4009.7 | 2 | UniProt (P12312) Pfam (PF05151) In PDB | Thermostichus vulcanus | PSII-M |
13 | O, o | Photosystem II manganese-stabilizing polypeptide | polymer | 244 | 26651.7 | 2 | UniProt (D0VWR2) Pfam (PF01716) In PDB | Thermostichus vulcanus | MSP,Extrinsic protein O of oxygen-evolving complex |
14 | T, t | Photosystem II reaction center protein T | polymer | 32 | 3906.7 | 2 | UniProt (P12313) Pfam (PF01405) In PDB | Thermostichus vulcanus | PSII-Tc |
15 | U, u | Photosystem II 12 kDa extrinsic protein | polymer | 104 | 11656.0 | 2 | UniProt (P56152) Pfam (PF06514) In PDB | Thermostichus vulcanus | PS II complex 12 kDa extrinsic protein,PSII-U |
16 | V, v | Cytochrome c-550 | polymer | 137 | 15148.3 | 2 | UniProt (P0A387) Pfam (PF14495) In PDB | Thermostichus vulcanus | Cytochrome c550,Low-potential cytochrome c,Extrinsic protein V of oxygen-evolving complex |
17 | Y, y | Photosystem II reaction center protein Ycf12 | polymer | 30 | 3228.0 | 2 | UniProt (D0VWR3) Pfam (PF05969) In PDB | Thermostichus vulcanus | |
18 | X, x | Photosystem II reaction center protein X | polymer | 40 | 4191.0 | 2 | UniProt (D0VWR4) Pfam (PF06596) In PDB | Thermostichus vulcanus | |
19 | Z, z | Photosystem II reaction center protein Z | polymer | 62 | 6794.2 | 2 | UniProt (D0VWR5) Pfam (PF01737) In PDB | Thermostichus vulcanus | PSII-Z |
20 | R | Photosystem II protein Y | polymer | 41 | 4590.6 | 1 | UniProt (Q8DKM3) Pfam (PF06298) In PDB | Thermostichus vulcanus | |
21 | A, a | CA-MN4-O5 CLUSTER | non-polymer | 339.8 | 2 | Chemie (OEX) | |||
22 | a, A | FE (II) ION | non-polymer | 55.8 | 2 | Chemie (FE2) | |||
23 | a, A | CHLORIDE ION | non-polymer | 35.5 | 4 | Chemie (CL) | |||
24 | B, b, a, C, c... | CHLOROPHYLL A | non-polymer | 893.5 | 70 | Chemie (CLA) | |||
25 | a, D, A, d | PHEOPHYTIN A | non-polymer | 871.2 | 4 | Chemie (PHO) | |||
26 | B, k, T, a, D... | BETA-CAROTENE | non-polymer | 536.9 | 20 | Chemie (BCR) | |||
27 | a, f, D, L, A | 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL | non-polymer | 795.1 | 8 | Chemie (SQD) | |||
28 | c, B, d, C, a... | 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE | non-polymer | 787.2 | 10 | Chemie (LMG) | |||
29 | A, B, E, c, T... | DODECYL-BETA-D-MALTOSIDE | non-polymer | 510.6 | 17 | Chemie (LMT) | |||
30 | M, b, v, A, C... | GLYCEROL | non-polymer | 92.1 | 48 | Chemie (GOL) | |||
31 | D, b, j, A, E... | UNKNOWN LIGAND | non-polymer | 258.1 | 57 | Chemie (UNL) | |||
32 | A, a | 2-phenylcyclohexa-2,5-diene-1,4-dione | non-polymer | 184.2 | 2 | Chemie (K3C) | |||
33 | d, A, D, a | 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-BENZOQUINONE | non-polymer | 749.2 | 4 | Chemie (PL9) | |||
34 | a, A | BICARBONATE ION | non-polymer | 61.0 | 2 | Chemie (BCT) | |||
35 | O, F, B, c, f... | CALCIUM ION | non-polymer | 40.1 | 7 | Chemie (CA) | |||
36 | C, O, B, c, d... | heptyl 1-thio-beta-D-glucopyranoside | non-polymer | 294.4 | 21 | Chemie (HTG) | |||
37 | d, E, l, e, D... | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE | non-polymer | 723.0 | 10 | Chemie (LHG) | |||
38 | B, i, D, C, O... | DIMETHYL SULFOXIDE | non-polymer | 78.1 | 31 | Chemie (DMS) | |||
39 | c, H, D, h, C | DIGALACTOSYL DIACYL GLYCEROL (DGDG) | non-polymer | 949.3 | 9 | Chemie (DGD) | |||
40 | F, f | PROTOPORPHYRIN IX CONTAINING FE | non-polymer | 616.5 | 2 | Chemie (HEM) | |||
41 | H, h | (3R)-beta,beta-caroten-3-ol | non-polymer | 552.9 | 2 | Chemie (RRX) | |||
42 | j, J | MAGNESIUM ION | non-polymer | 24.3 | 2 | Chemie (MG) | |||
43 | v, V | HEME C | non-polymer | 618.5 | 2 | Chemie (HEC) | |||
44 | water | water | 18.0 | 3237 | Chemie (HOH) |
Sequence modifications
A, a: 1 - 344 (UniProt: P51765)
C, c: 23 - 473 (UniProt: D0VWR7)
K, k: 10 - 46 (UniProt: P19054)
M, m: 1 - 36 (UniProt: P12312)
PDB | External Database | Details |
---|---|---|
Pro 279 | Arg 279 | conflict |
PDB | External Database | Details |
---|---|---|
Asn 19 | - | expression tag |
Ser 20 | - | expression tag |
Ile 21 | - | expression tag |
Phe 22 | - | expression tag |
PDB | External Database | Details |
---|---|---|
Leu 33 | Phe 24 | conflict |
Trp 39 | Val 30 | conflict |
PDB | External Database | Details |
---|---|---|
Leu 8 | Phe 8 | conflict |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 39 |
Total formula weight | 597325.6 | |
Non-Polymers* | Number of molecules | 336 |
Total formula weight | 151516.1 | |
All* | Total formula weight | 748841.8 |