MolNFT v1 · #68218 · protein
Cryo-EM structure of spinach psii-lhcii supercomplex at 3.2 ångström resolution
3JCU · Photosystem II protein D1: “Cryo-EM structure of spinach psii-lhcii supercomplex at 3.2 ångström resolution”. Electron microscopy, 17 ligands (CLA, CHL, BCR), 20 pockets (best druggability 0.85). MolNFT v1 #68218 on GenesisL1: 3D…
- PDB
- 3JCU
- Type
- protein
- Length
- 7,648 residues
- Chains
- 50
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem II protein D1; Photosystem II CP47 reaction center protein; Photosystem II…
- UniProt
- P69560, P04160, P06003, P06005, P69383, P60128, P12333, P05146, P62103, Q9M3L2, P12163, P60150, P62112, P12359, P12302, P12301, F2Z293, A0A0K9QUQ7, P61840, A0A0K9RHP1, Q41387, A0A0K9RTU3, Q9M3M6
- Ligands
- CLA, CHL, BCR, LHG, LUT, LMG, NEX, DGD, XAT, SQD, PHO, OEX, BCT, PL9, HEM, FE2…
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 23 distinct chains · 51% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Photosystem II protein D1 | protein | 334 | 58% helix, 4% strand | P69560 |
| B, b | Photosystem II CP47 reaction center protein | protein | 487 | 50% helix, 8% strand | P04160 |
| C, c | Photosystem II CP43 reaction center protein | protein | 449 | 57% helix, 4% strand | P06003 |
| D, d | Photosystem II D2 protein | protein | 340 | 60% helix, 2% strand | P06005 |
| E, e | Cytochrome B559 subunit alpha | protein | 79 | 62% helix, 3% strand | P69383 |
| F, f | Cytochrome B559 subunit beta | protein | 32 | 75% helix, 0% strand | P60128 |
| G, N, Y, g, n, y | Chlorophyll a-B binding protein, chloroplastic | protein | 218 | 55% helix, 1% strand | P12333 |
| H, h | Photosystem II reaction center protein H | protein | 59 | 56% helix, 3% strand | P05146 |
| I, i | Protein photosystem II reaction center protein I | protein | 35 | 74% helix, 0% strand | P62103 |
| J, j | Photosystem II reaction center protein J | protein | 34 | 68% helix, 0% strand | Q9M3L2 |
| K, k | Photosystem II reaction center protein K | protein | 37 | 73% helix, 0% strand | P12163 |
| L, l | Protein photosystem II reaction center protein L | protein | 37 | 62% helix, 5% strand | P60150 |
| M, m | Photosystem II reaction center protein M | protein | 33 | 82% helix, 0% strand | P62112 |
| O, o | Oxygen-evolving enhancer protein 1, chloroplastic | protein | 243 | 11% helix, 35% strand | P12359 |
| P, p | Oxygen-evolving enhancer protein 2, chloroplastic | protein | 172 | 19% helix, 33% strand | P12302 |
| Q, q | Oxygen-evolving enhancer protein 3, chloroplastic | protein | 148 | 61% helix, 0% strand | P12301 |
| R, r | Chlorophyll a-B binding protein 29 kd (CP29) | protein | 232 | 44% helix, 3% strand | F2Z293 |
| S, s | Chlorophyll a-B binding protein 26 kd (CP26) | protein | 214 | 46% helix, 0% strand | A0A0K9QUQ7 |
| T, t | Photosystem II reaction center protein tc | protein | 30 | 67% helix, 0% strand | P61840 |
| U, u | Photosystem II reaction center tn protein | protein | 25 | 52% helix, 0% strand | A0A0K9RHP1 |
| W, w | Photosystem II reaction center W protein, chloroplastic | protein | 54 | 41% helix, 0% strand | Q41387 |
| X, x | Photosystem II reaction center X protein | protein | 35 | 86% helix, 0% strand | A0A0K9RTU3 |
| Z, z | Photosystem II reaction center protein Z | protein | 61 | 90% helix, 0% strand | Q9M3M6 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 156 copies · chains A, D, L, T, I, W, B, H, M, t, C, S, K, Z, X, G, N, Y, R, a, d, l, i, w, b, h, m, c, s, k, z, x, g, n, y, r
- CHL · Chlorophyll B · ligand · 50 copies · chains G, Y, N, S, R, B, r, g, y, n, s, b
- BCR · Beta-carotene · ligand · 20 copies · chains A, I, b, B, M, t, C, J, K, Z, S, D, F, H, X, a, i, T, m, c, j, k, z, s, d, f, h, x
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 18 copies · chains A, B, D, L, T, C, G, M, N, R, S, Y, a, b, d, l, t, c, g, m, n, r, s, y
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 18 copies · chains G, N, R, S, Y, g, n, r, s, y
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 10 copies · chains A, C, I, W, B, D, L, M, J, K, F, S, Z, a, c, i, w, b, d, l, m, j, k, f, s, z
- NEX · (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R, 6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13, 15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol · ligand · 10 copies · chains G, N, S, R, y, Y, r, g, n, s
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 8 copies · chains A, C, J, D, B, E, H, U, a, c, j, d, b, e, h, u
- XAT · (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-beta,beta-carotene-3,3'-diol · ligand · 8 copies · chains G, Y, N, R, g, y, n, r
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 6 copies · chains A, C, D, K, T, b, h, B, L, l, m, t, a, c, d, k, H, M
- PHO · Pheophytin A · ligand · 4 copies · chains A, D, a, d
- OEX · Ca-MN4-O5 cluster · ligand · 2 copies · chains A, C, a, c
- BCT · Bicarbonate ion · ligand · 2 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 · 2 copies · chains A, D, L, T, a, d, l, t
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains E, F, e, f
- 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 | 966 | 0.85 | 0.86 | 105 | CLA, DGD |
| 2 | 872 | 0.85 | 0.86 | 101 | CLA, DGD |
| 3 | 806 | 0.83 | 0.85 | 93 | PL9, LHG |
| 4 | 1028 | 0.83 | 0.83 | 84 | DGD |
| 5 | 913 | 0.82 | 0.83 | 74 | CLA, BCR |
Interfaces
160 interfaces between chains.
- A–D · 5286 Ų buried · 61 hydrogen bonds · protein-protein
- a–d · 5286 Ų buried · 61 hydrogen bonds · protein-protein
- a–c · 3089 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 3085 Ų buried · 27 hydrogen bonds · protein-protein
- b–d · 2569 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 4 disulfide (covalent ligand, disulfide).
Compared structures
- 3JCU · Cryo-EM structure of spinach PSII-LHCII supercomplex at 3.2 Angstrom resolution · the same entry in another collection · chain K against K, TM-score 1.00
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 P69560
- Every structure of UniProt P04160
- Every structure of UniProt P06003
- Every structure of UniProt P06005
- Every structure of UniProt P69383
- Every structure of UniProt P60128
- Every structure of UniProt P12333
- Every structure of UniProt P05146
- Every structure of UniProt P62103
- Every structure of UniProt Q9M3L2
- Every structure of UniProt P12163
- Every structure of UniProt P60150
- Every structure of UniProt P62112
- Every structure of UniProt P12359
- Every structure of UniProt P12302
- Every structure of UniProt P12301
- Every structure of UniProt F2Z293
- Every structure of UniProt A0A0K9QUQ7
- Every structure of UniProt P61840
- Every structure of UniProt A0A0K9RHP1
- Every structure of UniProt Q41387
- Every structure of UniProt A0A0K9RTU3
- Every structure of UniProt Q9M3M6
- Elsewhere: RCSB PDB 3JCU · PDBe 3JCU · UniProt P69560 · UniProt P04160 · UniProt P06003 · UniProt P06005 · UniProt P69383 · UniProt P60128 · UniProt P12333 · UniProt P05146 · UniProt P62103 · UniProt Q9M3L2 · UniProt P12163 · UniProt P60150 · UniProt P62112 · UniProt P12359 · UniProt P12302 · UniProt P12301 · UniProt F2Z293 · UniProt A0A0K9QUQ7 · UniProt P61840 · UniProt A0A0K9RHP1 · UniProt Q41387 · UniProt A0A0K9RTU3 · UniProt Q9M3M6
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