MolNFT v1 · #184219 · protein + RNA
Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 1
7OI6 · 39S ribosomal protein L2, mitochondrial: “Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 1”. Electron microscopy, 3 ligands (4S8, MG, ZN), 20 pockets (best druggability 0.87). MolNFT v1 #184219 on…
- PDB
- 7OI6
- Type
- protein + RNA
- Length
- 9,867 residues
- Chains
- 52
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 39S ribosomal protein L2, mitochondrial; 39S ribosomal protein L3, mitochondrial; 39S…
- EC
- 3.1.26.-, 3.1.1.29, 3.6.4.13, 2.1.1.-
- UniProt
- Q5T653, P09001, Q9BYD3, Q9BYD2, Q9BYD1, Q6P1L8, Q9P015, Q9NX20, Q9NRX2, P49406, Q9BYC9, Q7Z2W9, Q9NWU5, Q16540, Q96A35, Q13084, Q9HD33, Q8TCC3, Q9BYC8, Q9BQ48, Q9BZE1, Q9NYK5, Q8IXM3, Q9Y6G3, Q8N983, Q9H9J2, Q9BRJ2, Q13405, Q8N5N7, Q4U2R6, Q86TS9, Q9BQC6, Q14197, Q8TAE8, Q9NVS2, Q9NP92, Q96EH3, L0R8F8, O14561, Q9NUL7, A4D1E9, Q9HC36, Q9H0U6, Q9P0M9, Q96DV4, Q7Z7H8, Q9Y3B7, Q96EL3, Q6P161
- Ligands
- 4S8, MG, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 52 distinct chains · 32% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 39S ribosomal protein L2, mitochondrial | protein | 220 | 3% helix, 27% strand | Q5T653 |
| E | 39S ribosomal protein L3, mitochondrial | protein | 285 | 15% helix, 26% strand | P09001 |
| F | 39S ribosomal protein L4, mitochondrial | protein | 250 | 28% helix, 9% strand | Q9BYD3 |
| H | 39S ribosomal protein L9, mitochondrial | protein | 95 | 32% helix, 24% strand | Q9BYD2 |
| K | 39S ribosomal protein L13, mitochondrial | protein | 177 | 36% helix, 9% strand | Q9BYD1 |
| L | 39S ribosomal protein L14, mitochondrial | protein | 115 | 11% helix, 21% strand | Q6P1L8 |
| M | 39S ribosomal protein L15, mitochondrial | protein | 257 | 33% helix, 8% strand | Q9P015 |
| N | 39S ribosomal protein L16, mitochondrial | protein | 205 | 26% helix, 21% strand | Q9NX20 |
| O | 39S ribosomal protein L17, mitochondrial | protein | 152 | 48% helix, 10% strand | Q9NRX2 |
| Q | 39S ribosomal protein L19, mitochondrial | protein | 217 | 24% helix, 21% strand | P49406 |
| R | 39S ribosomal protein L20, mitochondrial | protein | 140 | 66% helix, 0% strand | Q9BYC9 |
| S | 39S ribosomal protein L21, mitochondrial | protein | 156 | 13% helix, 36% strand | Q7Z2W9 |
| T | 39S ribosomal protein L22, mitochondrial | protein | 159 | 36% helix, 23% strand | Q9NWU5 |
| U | 39S ribosomal protein L23, mitochondrial | protein | 139 | 14% helix, 17% strand | Q16540 |
| V | 39S ribosomal protein L24, mitochondrial | protein | 192 | 9% helix, 25% strand | Q96A35 |
| X | 39S ribosomal protein L28, mitochondrial | protein | 243 | 43% helix, 13% strand | Q13084 |
| Y | 39S ribosomal protein L47, mitochondrial | protein | 176 | 60% helix, 7% strand | Q9HD33 |
| Z | 39S ribosomal protein L30, mitochondrial | protein | 120 | 23% helix, 13% strand | Q8TCC3 |
| 0 | 39S ribosomal protein L32, mitochondrial | protein | 108 | 28% helix, 13% strand | Q9BYC8 |
| 2 | 39S ribosomal protein L34, mitochondrial | protein | 43 | 53% helix, 0% strand | Q9BQ48 |
| 5 | 39S ribosomal protein L37, mitochondrial | protein | 387 | 24% helix, 22% strand | Q9BZE1 |
| 7 | 39S ribosomal protein L39, mitochondrial | protein | 287 | 34% helix, 24% strand | Q9NYK5 |
| 9 | 39S ribosomal protein L41, mitochondrial | protein | 117 | 22% helix, 8% strand | Q8IXM3 |
| a | 39S ribosomal protein L42, mitochondrial | protein | 82 | 18% helix, 12% strand | Q9Y6G3 |
| b | 39S ribosomal protein L43, mitochondrial | protein | 148 | 21% helix, 13% strand | Q8N983 |
| c | 39S ribosomal protein L44, mitochondrial (EC 3.1.26.-) | protein | 275 | 57% helix, 8% strand | Q9H9J2 |
| d | 39S ribosomal protein L45, mitochondrial | protein | 211 | 22% helix, 23% strand | Q9BRJ2 |
| g | 39S ribosomal protein L49, mitochondrial | protein | 129 | 26% helix, 21% strand | Q13405 |
| h | 39S ribosomal protein L50, mitochondrial | protein | 100 | 46% helix, 5% strand | Q8N5N7 |
| i | 39S ribosomal protein L51, mitochondrial | protein | 97 | 44% helix, 1% strand | Q4U2R6 |
| j | 39S ribosomal protein L52, mitochondrial | protein | 85 | 61% helix, 2% strand | Q86TS9 |
| o | Ribosomal protein 63, mitochondrial | protein | 79 | 56% helix, 1% strand | Q9BQC6 |
| p | Peptidyl-tRNA hydrolase ICT1, mitochondrial (EC 3.1.1.29) | protein | 107 | 30% helix, 18% strand | Q14197 |
| q | Growth arrest and DNA damage-inducible proteins-interacting protein 1 | protein | 99 | 57% helix, 1% strand | Q8TAE8 |
| r | 39S ribosomal protein S18A, mitochondrial | protein | 146 | 23% helix, 9% strand | Q9NVS2 |
| s | 39S ribosomal protein S30, mitochondrial | protein | 370 | 34% helix, 15% strand | Q9NP92 |
| u | Mitochondrial assembly of ribosomal large subunit protein 1 | protein | 111 | 37% helix, 20% strand | Q96EH3 |
| v | MIEF1 upstream open reading frame protein | protein | 69 | 65% helix, 3% strand | L0R8F8 |
| w | Acyl carrier protein, mitochondrial | protein | 79 | 61% helix, 0% strand | O14561 |
| A | 16S rRNA | rna | 1208 | — | — |
| x | Probable ATP-dependent RNA helicase DDX28 (EC 3.6.4.13) | protein | 374 | 42% helix, 15% strand | Q9NUL7 |
| y | GTP-binding protein 10 | protein | 331 | 18% helix, 18% strand | A4D1E9 |
| z | RRNA methyltransferase 3, mitochondrial (EC 2.1.1.-) | protein | 253 | 39% helix, 19% strand | Q9HC36 |
| B | Mitochondrial val tRNA | rna | 56 | — | — |
| P | 39S ribosomal protein L18, mitochondrial | protein | 133 | 32% helix, 13% strand | Q9H0U6 |
| W | 39S ribosomal protein L27, mitochondrial | protein | 98 | 9% helix, 39% strand | Q9P0M9 |
| 6 | 39S ribosomal protein L38, mitochondrial | protein | 325 | 26% helix, 18% strand | Q96DV4 |
| I | 39S ribosomal protein L10, mitochondrial | protein | 158 | 44% helix, 11% strand | Q7Z7H8 |
| J | 39S ribosomal protein L11, mitochondrial | protein | 140 | 41% helix, 11% strand | Q9Y3B7 |
| k | 39S ribosomal protein L53, mitochondrial | protein | 84 | 25% helix, 6% strand | Q96EL3 |
| l | 39S ribosomal protein L54, mitochondrial | protein | 23 | 87% helix, 0% strand | Q6P161 |
| 1 | RRNA methyltransferase 3, mitochondrial (EC 2.1.1.-) | protein | 257 | 36% helix, 19% strand | Q9HC36 |
Ligands and binding sites
- 4S8 · N~3~-{(2R)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-N-(2-sulfanylethyl)-beta-alaninamide · ligand · chains v, w
- MG · Magnesium ion · metal · 48 copies · chains F, A, g, x, U, R, W
- ZN · Zinc ion · metal · chains 0
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 | 996 | 0.87 | 0.89 | 110 | MG |
| 2 | 770 | 0.86 | 0.89 | 126 | empty |
| 3 | 1124 | 0.86 | 0.87 | 135 | MG |
| 4 | 1144 | 0.86 | 0.87 | 163 | MG |
| 5 | 946 | 0.85 | 0.87 | 142 | empty |
Interfaces
160 interfaces between chains.
- D–A · 2275 Ų buried · 34 hydrogen bonds · protein-nucleic
- E–A · 2000 Ų buried · 18 hydrogen bonds · protein-nucleic
- F–A · 1851 Ų buried · 13 hydrogen bonds · protein-nucleic
- R–A · 1428 Ų buried · 8 hydrogen bonds · protein-nucleic
- 5–A · 1279 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 7OI6 · Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 1 · the same entry in another collection · chain N against N, 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 Q5T653
- Every structure of UniProt P09001
- Every structure of UniProt Q9BYD3
- Every structure of UniProt Q9BYD2
- Every structure of UniProt Q9BYD1
- Every structure of UniProt Q6P1L8
- Every structure of UniProt Q9P015
- Every structure of UniProt Q9NX20
- Every structure of UniProt Q9NRX2
- Every structure of UniProt P49406
- Every structure of UniProt Q9BYC9
- Every structure of UniProt Q7Z2W9
- Every structure of UniProt Q9NWU5
- Every structure of UniProt Q16540
- Every structure of UniProt Q96A35
- Every structure of UniProt Q13084
- Every structure of UniProt Q9HD33
- Every structure of UniProt Q8TCC3
- Every structure of UniProt Q9BYC8
- Every structure of UniProt Q9BQ48
- Every structure of UniProt Q9BZE1
- Every structure of UniProt Q9NYK5
- Every structure of UniProt Q8IXM3
- Every structure of UniProt Q9Y6G3
- Every structure of UniProt Q8N983
- Every structure of UniProt Q9H9J2
- Every structure of UniProt Q9BRJ2
- Every structure of UniProt Q13405
- Every structure of UniProt Q8N5N7
- Every structure of UniProt Q4U2R6
- Every structure of UniProt Q86TS9
- Every structure of UniProt Q9BQC6
- Every structure of UniProt Q14197
- Every structure of UniProt Q8TAE8
- Every structure of UniProt Q9NVS2
- Every structure of UniProt Q9NP92
- Every structure of UniProt Q96EH3
- Every structure of UniProt L0R8F8
- Every structure of UniProt O14561
- Every structure of UniProt Q9NUL7
- Every structure of UniProt A4D1E9
- Every structure of UniProt Q9HC36
- Every structure of UniProt Q9H0U6
- Every structure of UniProt Q9P0M9
- Every structure of UniProt Q96DV4
- Every structure of UniProt Q7Z7H8
- Every structure of UniProt Q9Y3B7
- Every structure of UniProt Q96EL3
- Every structure of UniProt Q6P161
- Elsewhere: RCSB PDB 7OI6 · PDBe 7OI6 · UniProt Q5T653 · UniProt P09001 · UniProt Q9BYD3 · UniProt Q9BYD2 · UniProt Q9BYD1 · UniProt Q6P1L8 · UniProt Q9P015 · UniProt Q9NX20 · UniProt Q9NRX2 · UniProt P49406 · UniProt Q9BYC9 · UniProt Q7Z2W9 · UniProt Q9NWU5 · UniProt Q16540 · UniProt Q96A35 · UniProt Q13084 · UniProt Q9HD33 · UniProt Q8TCC3 · UniProt Q9BYC8 · UniProt Q9BQ48 · UniProt Q9BZE1 · UniProt Q9NYK5 · UniProt Q8IXM3 · UniProt Q9Y6G3 · UniProt Q8N983 · UniProt Q9H9J2 · UniProt Q9BRJ2 · UniProt Q13405 · UniProt Q8N5N7 · UniProt Q4U2R6 · UniProt Q86TS9 · UniProt Q9BQC6 · UniProt Q14197 · UniProt Q8TAE8 · UniProt Q9NVS2 · UniProt Q9NP92 · UniProt Q96EH3 · UniProt L0R8F8 · UniProt O14561 · UniProt Q9NUL7 · UniProt A4D1E9 · UniProt Q9HC36 · UniProt Q9H0U6 · UniProt Q9P0M9 · UniProt Q96DV4 · UniProt Q7Z7H8 · UniProt Q9Y3B7 · UniProt Q96EL3 · UniProt Q6P161
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