Research workbench
Cryo-EM structure of the human mtLSU assembly intermediate upon MRM2 depletion - class 4
Analyse Cryo-EM structure of the human mtLSU assembly intermediate upon MRM2 depletion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QH7
- Type
- protein + RNA
- Length
- 8,329 residues
- Chains
- 49
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.89
- Source
- Homo sapiens
- Molecule
- 39S ribosomal protein L2, mitochondrial; 39S ribosomal protein L3, mitochondrial; 39S…
- EC
- 3.1.26.-
- UniProt
- Q5T653, P09001, Q9BYD3, Q9BYD2, Q7Z7H8, Q9BYD1, Q6P1L8, Q9P015, Q9NX20, Q9NRX2, Q9H0U6, P49406, Q9BYC9, Q7Z2W9, Q9NWU5, Q96A35, Q9P0M9, Q13084, Q9HD33, Q8TCC3, Q9BYC8, O75394, Q9BQ48, Q9NZE8, Q9BZE1, Q9NYK5, Q8IXM3, Q8N983, Q9H9J2, Q9BRJ2, Q13405, Q8N5N7, Q4U2R6, Q86TS9, Q9BQC6, Q8TAE8, Q9NVS2, Q9NP92, Q96EH3, L0R8F8, O14561, Q9P0J6
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · resolution 2.89 · 49 distinct chains · 31% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 39S ribosomal protein L2, mitochondrial | protein | 215 | 5% helix, 28% strand | Q5T653 |
| E | 39S ribosomal protein L3, mitochondrial | protein | 304 | 14% helix, 26% strand | P09001 |
| F | 39S ribosomal protein L4, mitochondrial | protein | 250 | 30% helix, 15% strand | Q9BYD3 |
| H | 39S ribosomal protein L9, mitochondrial | protein | 95 | 25% helix, 29% strand | Q9BYD2 |
| I | 39S ribosomal protein L10, mitochondrial | protein | 30 | 40% helix, 0% strand | Q7Z7H8 |
| K | 39S ribosomal protein L13, mitochondrial | protein | 177 | 38% helix, 16% strand | Q9BYD1 |
| L | 39S ribosomal protein L14, mitochondrial | protein | 115 | 5% helix, 29% strand | Q6P1L8 |
| M | 39S ribosomal protein L15, mitochondrial | protein | 287 | 31% helix, 11% strand | Q9P015 |
| N | 39S ribosomal protein L16, mitochondrial | protein | 201 | 28% helix, 20% strand | Q9NX20 |
| O | 39S ribosomal protein L17, mitochondrial | protein | 152 | 49% helix, 10% strand | Q9NRX2 |
| P | 39S ribosomal protein L18, mitochondrial | protein | 141 | 33% helix, 17% strand | Q9H0U6 |
| Q | 39S ribosomal protein L19, mitochondrial | protein | 217 | 24% helix, 22% strand | P49406 |
| R | 39S ribosomal protein L20, mitochondrial | protein | 139 | 69% helix, 0% strand | Q9BYC9 |
| S | 39S ribosomal protein L21, mitochondrial | protein | 156 | 13% helix, 42% strand | Q7Z2W9 |
| T | 39S ribosomal protein L22, mitochondrial | protein | 155 | 34% helix, 19% strand | Q9NWU5 |
| U | 39S ribosomal protein L23, mitochondrial | protein | 125 | 10% helix, 21% strand | — |
| V | 39S ribosomal protein L24, mitochondrial | protein | 48 | 25% helix, 6% strand | Q96A35 |
| W | 39S ribosomal protein L27, mitochondrial | protein | 100 | 0% helix, 40% strand | Q9P0M9 |
| X | 39S ribosomal protein L28, mitochondrial | protein | 243 | 45% helix, 15% strand | Q13084 |
| Y | 39S ribosomal protein L47, mitochondrial | protein | 175 | 58% helix, 7% strand | Q9HD33 |
| Z | 39S ribosomal protein L30, mitochondrial | protein | 115 | 20% helix, 20% strand | Q8TCC3 |
| 0 | 39S ribosomal protein L32, mitochondrial | protein | 108 | 31% helix, 13% strand | Q9BYC8 |
| 1 | 39S ribosomal protein L33, mitochondrial | protein | 49 | 0% helix, 59% strand | O75394 |
| 2 | 39S ribosomal protein L34, mitochondrial | protein | 45 | 53% helix, 0% strand | Q9BQ48 |
| 3 | 39S ribosomal protein L35, mitochondrial | protein | 95 | 27% helix, 8% strand | Q9NZE8 |
| 5 | 39S ribosomal protein L37, mitochondrial | protein | 392 | 25% helix, 24% strand | Q9BZE1 |
| 6 | 39S ribosomal protein L38, mitochondrial | protein | 292 | 23% helix, 19% strand | — |
| 7 | 39S ribosomal protein L39, mitochondrial | protein | 287 | 33% helix, 24% strand | Q9NYK5 |
| 9 | 39S ribosomal protein L41, mitochondrial | protein | 117 | 26% helix, 9% strand | Q8IXM3 |
| a | 39S ribosomal protein L42, mitochondrial | protein | 80 | 25% helix, 14% strand | — |
| b | 39S ribosomal protein L43, mitochondrial | protein | 148 | 21% helix, 19% strand | Q8N983 |
| c | 39S ribosomal protein L44, mitochondrial (EC 3.1.26.-) | protein | 275 | 56% helix, 8% strand | Q9H9J2 |
| d | 39S ribosomal protein L45, mitochondrial | protein | 157 | 25% helix, 28% strand | Q9BRJ2 |
| f | 39S ribosomal protein L48, mitochondrial | protein | 17 | 18% helix, 0% strand | — |
| g | 39S ribosomal protein L49, mitochondrial | protein | 129 | 23% helix, 24% strand | Q13405 |
| h | 39S ribosomal protein L50, mitochondrial | protein | 101 | 44% helix, 8% strand | Q8N5N7 |
| i | 39S ribosomal protein L51, mitochondrial | protein | 97 | 44% helix, 1% strand | Q4U2R6 |
| j | 39S ribosomal protein L52, mitochondrial | protein | 86 | 60% helix, 5% strand | Q86TS9 |
| o | Ribosomal protein 63, mitochondrial | protein | 81 | 60% helix, 1% strand | Q9BQC6 |
| p | Peptidyl-tRNA hydrolase ICT1, mitochondrial | protein | 125 | 34% helix, 15% strand | — |
| q | Growth arrest and DNA damage-inducible proteins-interacting protein 1 | protein | 101 | 60% helix, 1% strand | Q8TAE8 |
| r | 39S ribosomal protein S18a, mitochondrial | protein | 129 | 23% helix, 5% strand | Q9NVS2 |
| s | 39S ribosomal protein S30, mitochondrial | protein | 370 | 29% helix, 18% strand | Q9NP92 |
| u | Mitochondrial assembly of ribosomal large subunit protein 1 | protein | 111 | 36% helix, 21% strand | Q96EH3 |
| v | MIEF1 upstream open reading frame protein | protein | 69 | 58% helix, 3% strand | L0R8F8 |
| w | Acyl carrier protein, mitochondrial | protein | 79 | 51% helix, 0% strand | O14561 |
| A | 16S ribosomal RNA | rna | 1256 | — | — |
| B | mitochondrial tRNAVal | rna | 56 | — | — |
| 4 | 39S ribosomal protein L36, mitochondrial | protein | 37 | 8% helix, 43% strand | Q9P0J6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 50 copies · chains E, A, F, Q, s, M, U, R
- ZN · Zinc ion · metal · 3 copies · chains 0, I, r, 4
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 | 779 | 0.88 | 0.92 | 94 | empty |
| 2 | 901 | 0.87 | 0.90 | 90 | MG |
| 3 | 936 | 0.86 | 0.88 | 78 | empty |
| 4 | 701 | 0.85 | 0.89 | 77 | empty |
| 5 | 858 | 0.83 | 0.86 | 89 | empty |
Interfaces
173 interfaces between chains.
- E–A · 5047 Ų buried · 91 hydrogen bonds · protein-nucleic
- M–A · 4079 Ų buried · 82 hydrogen bonds · protein-nucleic
- D–A · 3760 Ų buried · 88 hydrogen bonds · protein-nucleic
- F–A · 3609 Ų buried · 67 hydrogen bonds · protein-nucleic
- R–A · 3163 Ų buried · 62 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7QH7 · Cryo-EM structure of the human mtlsu assembly intermediate upon MRM2 depletion - class 4 · the same entry in another collection · chain B against B, 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 Q7Z7H8
- 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 Q9H0U6
- Every structure of UniProt P49406
- Every structure of UniProt Q9BYC9
- Every structure of UniProt Q7Z2W9
- Every structure of UniProt Q9NWU5
- Every structure of UniProt Q96A35
- Every structure of UniProt Q9P0M9
- Every structure of UniProt Q13084
- Every structure of UniProt Q9HD33
- Every structure of UniProt Q8TCC3
- Every structure of UniProt Q9BYC8
- Every structure of UniProt O75394
- Every structure of UniProt Q9BQ48
- Every structure of UniProt Q9NZE8
- Every structure of UniProt Q9BZE1
- Every structure of UniProt Q9NYK5
- Every structure of UniProt Q8IXM3
- 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 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 Q9P0J6
- Elsewhere: RCSB PDB 7QH7 · PDBe 7QH7 · UniProt Q5T653 · UniProt P09001 · UniProt Q9BYD3 · UniProt Q9BYD2 · UniProt Q7Z7H8 · UniProt Q9BYD1 · UniProt Q6P1L8 · UniProt Q9P015 · UniProt Q9NX20 · UniProt Q9NRX2 · UniProt Q9H0U6 · UniProt P49406 · UniProt Q9BYC9 · UniProt Q7Z2W9 · UniProt Q9NWU5 · UniProt Q96A35 · UniProt Q9P0M9 · UniProt Q13084 · UniProt Q9HD33 · UniProt Q8TCC3 · UniProt Q9BYC8 · UniProt O75394 · UniProt Q9BQ48 · UniProt Q9NZE8 · UniProt Q9BZE1 · UniProt Q9NYK5 · UniProt Q8IXM3 · UniProt Q8N983 · UniProt Q9H9J2 · UniProt Q9BRJ2 · UniProt Q13405 · UniProt Q8N5N7 · UniProt Q4U2R6 · UniProt Q86TS9 · UniProt Q9BQC6 · UniProt Q8TAE8 · UniProt Q9NVS2 · UniProt Q9NP92 · UniProt Q96EH3 · UniProt L0R8F8 · UniProt O14561 · UniProt Q9P0J6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.