Research workbench
RT XFEL structure of Photosystem II 150 microseconds after the second illumination at 2.23 Angstrom resolution
Analyse RT XFEL structure of Photosystem II 150 microseconds after the second… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RF5
- Type
- protein
- Length
- 5,299 residues
- Chains
- 40
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.23
- Source
- Thermosynechococcus elongatus (strain BP-1)
- Molecule
- Photosystem II protein D1 1; Photosystem II CP47 reaction center protein; Photosystem II…
- EC
- 1.10.3.9
- UniProt
- P0A444, Q8DIQ1, Q8DIF8, Q8CM25, Q8DIP0, Q8DIN9, Q8DJ43, Q8DJZ6, P59087, Q9F1K9, Q8DIN8, Q8DHA7, P0A431, Q8DKM3, Q8DIQ0, Q9F1L5, P0A386, Q9F1R6, Q8DJI1, Q8DHJ2
- Ligands
- CLA, STE, BCR, LMG, LHG, SQD, PHO, PL9, OEY, OEX, BCT, HEM, HEC, DGD, FE2, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · resolution 2.23 · 26 distinct chains · 55% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Photosystem II protein D1 1 (EC 1.10.3.9) | protein | 334 | 61% helix, 4% strand | P0A444 |
| B, b | Photosystem II CP47 reaction center protein | protein | 505 | 50% helix, 11% strand | Q8DIQ1 |
| C | Photosystem II CP43 reaction center protein | protein | 442 | 58% helix, 6% strand | Q8DIF8 |
| D, d | Photosystem II D2 protein (EC 1.10.3.9) | protein | 341 | 63% helix, 4% strand | Q8CM25 |
| E, e | Cytochrome b559 subunit alpha | protein | 82 | 52% helix, 0% strand | Q8DIP0 |
| F, f | Cytochrome b559 subunit beta | protein | 34 | 68% helix, 0% strand | Q8DIN9 |
| H | Photosystem II reaction center protein H | protein | 65 | 55% helix, 3% strand | Q8DJ43 |
| I, i | Photosystem II reaction center protein I | protein | 36 | 72% helix, 0% strand | Q8DJZ6 |
| J, j | Photosystem II reaction center protein J | protein | 36 | 67% helix, 0% strand | P59087 |
| K, k | Photosystem II reaction center protein K | protein | 37 | 76% helix, 0% strand | Q9F1K9 |
| L | Photosystem II reaction center protein L | protein | 37 | 62% helix, 3% strand | Q8DIN8 |
| M | Photosystem II reaction center protein M | protein | 33 | 73% helix, 0% strand | Q8DHA7 |
| O, o | Photosystem II manganese-stabilizing polypeptide | protein | 244 | 6% helix, 47% strand | P0A431 |
| R, r | Photosystem II protein Y | protein | 28 | 93% helix, 0% strand | Q8DKM3 |
| T, t | Photosystem II reaction center protein T | protein | 30 | 70% helix, 0% strand | Q8DIQ0 |
| U, u | Photosystem II 12 kDa extrinsic protein | protein | 97 | 49% helix, 4% strand | Q9F1L5 |
| V, v | Cytochrome c-550 | protein | 137 | 47% helix, 6% strand | P0A386 |
| X | Photosystem II reaction center X protein | protein | 38 | 79% helix, 0% strand | Q9F1R6 |
| Y | Photosystem II reaction center protein Ycf12 | protein | 27 | 70% helix, 0% strand | Q8DJI1 |
| Z, z | Photosystem II reaction center protein Z | protein | 62 | 92% helix, 0% strand | Q8DHJ2 |
| c | Photosystem II CP43 reaction center protein | protein | 451 | 57% helix, 6% strand | Q8DIF8 |
| h | Photosystem II reaction center protein H | protein | 63 | 52% helix, 3% strand | Q8DJ43 |
| l | Photosystem II reaction center protein L | protein | 36 | 64% helix, 3% strand | Q8DIN8 |
| m | Photosystem II reaction center protein M | protein | 32 | 78% helix, 0% strand | Q8DHA7 |
| x | Photosystem II reaction center X protein | protein | 39 | 77% helix, 0% strand | Q9F1R6 |
| y | Photosystem II reaction center protein Ycf12 | protein | 30 | 80% helix, 0% strand | Q8DJI1 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, I, L, B, H, M, t, C, K, Y, Z, X, a, d, f, i, l, b, h, m, c, k, y, z, x
- STE · Stearic acid · ligand · 35 copies · chains B, M, m, t, H, a, C, A, I, J, L, l, E, R, T, b, D, X, Z, d, h, c, k, x, j
- BCR · Beta-carotene · ligand · 22 copies · chains A, I, B, M, t, C, D, F, J, K, Z, Y, T, b, H, X, a, i, m, c, k, z, d, f, j, h, x, y
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 13 copies · chains A, C, I, D, F, J, B, H, X, L, M, K, Y, a, i, o, b, c, k, y, d, f, j, l, m
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 10 copies · chains A, D, E, F, L, T, C, B, M, a, b, d, l, m, t, c, e, f, j
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 8 copies · chains A, C, D, J, K, T, b, B, L, l, m, t, E, F, X, a, c, d, j, k, M, e, f, r, x
- PHO · Pheophytin A · ligand · 4 copies · chains A, D, a, d
- PL9 · 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 · ligand · 4 copies · chains A, D, F, L, T, a, d, f, x, l, t
- OEY · Ca-MN4-O6 cluster · ligand · 2 copies · chains A, C, a, c
- OEX · Ca-MN4-O5 cluster · ligand · 2 copies · chains A, C, a, c
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, D, a, d
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains E, F, R, e, f, r
- HEC · Heme C · ligand · 2 copies · chains C, V, c, v
- DGD · Digalactosyl diacyl glycerol (dgdg) · sugar · 9 copies · chains A, I, O, b, C, J, D, V, B, H, a, c, j, d, v, h
- FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
- CL · Chloride ion · ion · 4 copies · chains A, D, C, a, d, c
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.87 | 0.87 | 76 | CLA, BCR |
| 2 | 1075 | 0.86 | 0.86 | 77 | CLA, BCR, STE |
| 3 | 976 | 0.85 | 0.86 | 83 | HEC |
| 4 | 1015 | 0.85 | 0.86 | 76 | HEC |
| 5 | 751 | 0.83 | 0.86 | 92 | LHG |
Interfaces
134 interfaces between chains.
- A–D · 5407 Ų buried · 67 hydrogen bonds · protein-protein
- a–d · 5401 Ų buried · 64 hydrogen bonds · protein-protein
- a–c · 3243 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 3237 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 3047 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 4 cofactor, 2 covalent, 2 disulfide (formylation, heme c attachment, covalent ligand, disulfide).
Compared structures
- Q8DIQ1 · AlphaFold monomer V2.0 prediction for photosystem II CP47 reaction center protein (Q8DIQ1) · a predicted model of the same protein · chain B against A, TM-score 1.00
- Q8DIF8 · AlphaFold monomer V2.0 prediction for photosystem II CP43 reaction center protein (Q8DIF8) · a predicted model of the same protein · chain C against A, TM-score 1.00
- Q8CM25 · AlphaFold monomer V2.0 prediction for photosystem II D2 protein (Q8CM25) · a predicted model of the same protein · chain D against A, TM-score 1.00
- P0A444 · AlphaFold monomer V2.0 prediction for photosystem II protein D1 1 (P0A444) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P0A431 · AlphaFold monomer V2.0 prediction for photosystem II manganese- stabilizing polypeptide… · a predicted model of the same protein · chain O against A, TM-score 1.00
- P0A386 · AlphaFold monomer V2.0 prediction for cytochrome C-550 (P0A386) · a predicted model of the same protein · chain V against A, TM-score 1.00
- Q9F1L5 · AlphaFold monomer V2.0 prediction for photosystem II 12 kda extrinsic protein (Q9F1L5) · a predicted model of the same protein · chain U against A, TM-score 0.99
- Q8DIP0 · AlphaFold monomer V2.0 prediction for cytochrome B559 subunit alpha (Q8DIP0) · a predicted model of the same protein · chain E against A, TM-score 0.94
- P59087 · AlphaFold monomer V2.0 prediction for photosystem II reaction center protein J (P59087) · a predicted model of the same protein · chain J against A, TM-score 0.94
- Q8DJ43 · AlphaFold monomer V2.0 prediction for photosystem II reaction center protein H (Q8DJ43) · a predicted model of the same protein · chain H against A, TM-score 0.94
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0A444
- Every structure of UniProt Q8DIQ1
- Every structure of UniProt Q8DIF8
- Every structure of UniProt Q8CM25
- Every structure of UniProt Q8DIP0
- Every structure of UniProt Q8DIN9
- Every structure of UniProt Q8DJ43
- Every structure of UniProt Q8DJZ6
- Every structure of UniProt P59087
- Every structure of UniProt Q9F1K9
- Every structure of UniProt Q8DIN8
- Every structure of UniProt Q8DHA7
- Every structure of UniProt P0A431
- Every structure of UniProt Q8DKM3
- Every structure of UniProt Q8DIQ0
- Every structure of UniProt Q9F1L5
- Every structure of UniProt P0A386
- Every structure of UniProt Q9F1R6
- Every structure of UniProt Q8DJI1
- Every structure of UniProt Q8DHJ2
- Elsewhere: RCSB PDB 7RF5 · PDBe 7RF5 · UniProt P0A444 · UniProt Q8DIQ1 · UniProt Q8DIF8 · UniProt Q8CM25 · UniProt Q8DIP0 · UniProt Q8DIN9 · UniProt Q8DJ43 · UniProt Q8DJZ6 · UniProt P59087 · UniProt Q9F1K9 · UniProt Q8DIN8 · UniProt Q8DHA7 · UniProt P0A431 · UniProt Q8DKM3 · UniProt Q8DIQ0 · UniProt Q9F1L5 · UniProt P0A386 · UniProt Q9F1R6 · UniProt Q8DJI1 · UniProt Q8DHJ2
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