Research workbench
Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions
Analyse Cryo-EM structure of the spinach chloroplast ribosome reveals the location of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MLC
- Type
- protein + RNA
- Length
- 6,385 residues
- Chains
- 32
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA, chloroplastic; 5S ribosomal RNA, chloroplastic; 4.8S ribosomal RNA…
- UniProt
- P06509, A0A0K9QEC7, O49937, P82192, A0A0K9R4N9, A0A0K9RQ91, P12629, P09596, A0A0K9QHT0, P17353, A0A0K9RLJ4, A0A0K9QQ60, P82413, P28803, P24613, P09594, Q9LWB5, P27683, A0A0K9R4I2, A0A0K9RD02, A0A0K9R7W8, P28804, P28805, P82244, P23326, P12230, P82231, P27684, P82411
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 32 distinct chains · 27% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 23S ribosomal RNA, chloroplastic | rna | 2750 | — | — |
| B | 5S ribosomal RNA, chloroplastic | rna | 120 | — | — |
| C | 4.8S ribosomal RNA, chloroplastic | rna | 93 | — | — |
| D | 50S ribosomal protein L2, chloroplastic | protein | 246 | 2% helix, 24% strand | P06509 |
| E | 50S ribosomal protein L3, chloroplastic | protein | 219 | 7% helix, 34% strand | A0A0K9QEC7 |
| F | 50S ribosomal protein L4, chloroplastic | protein | 205 | 31% helix, 6% strand | O49937 |
| G | 50S ribosomal protein L5, chloroplastic | protein | 179 | 30% helix, 19% strand | P82192 |
| H | 50S ribosomal protein L6, chloroplastic | protein | 178 | 20% helix, 17% strand | A0A0K9R4N9 |
| I | 50S ribosomal protein L9, chloroplastic | protein | 45 | 24% helix, 18% strand | A0A0K9RQ91 |
| L | 50S ribosomal protein L13, chloroplastic | protein | 196 | 30% helix, 13% strand | P12629 |
| M | 50S ribosomal protein L14, chloroplastic | protein | 120 | 8% helix, 38% strand | P09596 |
| N | 50S ribosomal protein L15, chloroplastic | protein | 182 | 23% helix, 6% strand | A0A0K9QHT0 |
| O | 50S ribosomal protein L16, chloroplastic | protein | 135 | 22% helix, 27% strand | P17353 |
| P | 50S ribosomal protein L17, chloroplastic | protein | 116 | 51% helix, 15% strand | A0A0K9RLJ4 |
| Q | 50S ribosomal protein L18, chloroplastic | protein | 118 | 41% helix, 15% strand | A0A0K9QQ60 |
| R | 50S ribosomal protein L19, chloroplastic | protein | 114 | 21% helix, 38% strand | P82413 |
| S | 50S ribosomal protein L20, chloroplastic | protein | 116 | 75% helix, 0% strand | P28803 |
| T | 50S ribosomal protein L21, chloroplastic | protein | 134 | 7% helix, 43% strand | P24613 |
| U | 50S ribosomal protein L22, chloroplastic | protein | 152 | 29% helix, 24% strand | P09594 |
| V | 50S ribosomal protein L23, chloroplastic | protein | 91 | 31% helix, 23% strand | Q9LWB5 |
| W | 50S ribosomal protein L24, chloroplastic | protein | 129 | 0% helix, 29% strand | P27683 |
| X | 50S ribosomal protein L27, chloroplastic | protein | 108 | 15% helix, 23% strand | A0A0K9R4I2 |
| Y | 50S ribosomal protein L28, chloroplastic | protein | 75 | 19% helix, 24% strand | A0A0K9RD02 |
| Z | 50S ribosomal protein L29, chloroplastic | protein | 94 | 61% helix, 0% strand | A0A0K9R7W8 |
| 2 | 50S ribosomal protein L32, chloroplastic | protein | 42 | 64% helix, 0% strand | P28804 |
| 3 | 50S ribosomal protein L33, chloroplastic | protein | 60 | 0% helix, 32% strand | P28805 |
| 4 | 50S ribosomal protein L34, chloroplastic | protein | 61 | 44% helix, 0% strand | P82244 |
| 5 | 50S ribosomal protein L35, chloroplastic | protein | 70 | 26% helix, 10% strand | P23326 |
| 6 | 50S ribosomal protein L36, chloroplastic | protein | 37 | 0% helix, 14% strand | P12230 |
| 9 | Ribosome-recycling factor, chloroplastic | protein | 107 | 83% helix, 0% strand | P82231 |
| 7 | PSRP5ALPHA, chloroplastic | protein | 46 | 72% helix, 0% strand | P27684 |
| 8 | PSRP6, chloroplastic | protein | 47 | 21% helix, 4% strand | P82411 |
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 | 951 | 0.89 | 0.92 | 99 | empty |
| 2 | 887 | 0.87 | 0.90 | 93 | empty |
| 3 | 887 | 0.87 | 0.90 | 77 | empty |
| 4 | 880 | 0.86 | 0.89 | 95 | empty |
| 5 | 893 | 0.86 | 0.88 | 65 | empty |
Interfaces
71 interfaces between chains.
- A–D · 6732 Ų buried · 144 hydrogen bonds · protein-nucleic
- A–N · 5515 Ų buried · 123 hydrogen bonds · protein-nucleic
- A–E · 4697 Ų buried · 87 hydrogen bonds · protein-nucleic
- A–F · 4612 Ų buried · 85 hydrogen bonds · protein-nucleic
- A–S · 4215 Ų buried · 106 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5MLC · Cryo-EM structure of the spinach chloroplast ribosome reveals the location of… · the same entry in another collection · chain M against M, 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 P06509
- Every structure of UniProt A0A0K9QEC7
- Every structure of UniProt O49937
- Every structure of UniProt P82192
- Every structure of UniProt A0A0K9R4N9
- Every structure of UniProt A0A0K9RQ91
- Every structure of UniProt P12629
- Every structure of UniProt P09596
- Every structure of UniProt A0A0K9QHT0
- Every structure of UniProt P17353
- Every structure of UniProt A0A0K9RLJ4
- Every structure of UniProt A0A0K9QQ60
- Every structure of UniProt P82413
- Every structure of UniProt P28803
- Every structure of UniProt P24613
- Every structure of UniProt P09594
- Every structure of UniProt Q9LWB5
- Every structure of UniProt P27683
- Every structure of UniProt A0A0K9R4I2
- Every structure of UniProt A0A0K9RD02
- Every structure of UniProt A0A0K9R7W8
- Every structure of UniProt P28804
- Every structure of UniProt P28805
- Every structure of UniProt P82244
- Every structure of UniProt P23326
- Every structure of UniProt P12230
- Every structure of UniProt P82231
- Every structure of UniProt P27684
- Every structure of UniProt P82411
- Elsewhere: RCSB PDB 5MLC · PDBe 5MLC · UniProt P06509 · UniProt A0A0K9QEC7 · UniProt O49937 · UniProt P82192 · UniProt A0A0K9R4N9 · UniProt A0A0K9RQ91 · UniProt P12629 · UniProt P09596 · UniProt A0A0K9QHT0 · UniProt P17353 · UniProt A0A0K9RLJ4 · UniProt A0A0K9QQ60 · UniProt P82413 · UniProt P28803 · UniProt P24613 · UniProt P09594 · UniProt Q9LWB5 · UniProt P27683 · UniProt A0A0K9R4I2 · UniProt A0A0K9RD02 · UniProt A0A0K9R7W8 · UniProt P28804 · UniProt P28805 · UniProt P82244 · UniProt P23326 · UniProt P12230 · UniProt P82231 · UniProt P27684 · UniProt P82411
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