MolNFT v1 · #166495 · protein + RNA
Cryo-EM structure of human CPSF160-WDR33-CPSF30-pas RNA-CSTF77 complex
6URO · Cleavage and polyadenylation specificity factor subunit 1: “Cryo-EM structure of human CPSF160-WDR33-CPSF30-pas RNA-CSTF77 complex”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.87). MolNFT v1 #166495 on…
- PDB
- 6URO
- Type
- protein + RNA
- Length
- 2,755 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cleavage and polyadenylation specificity factor subunit 1; Pre-mRNA 3' end processing…
- UniProt
- Q10570, Q9C0J8, O95639, Q12996
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 21% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cleavage and polyadenylation specificity factor subunit 1 | protein | 1199 | 5% helix, 43% strand | Q10570 |
| B | Pre-mRNA 3' end processing protein WDR33 | protein | 378 | 5% helix, 31% strand | Q9C0J8 |
| C | Cleavage and polyadenylation specificity factor subunit 4 | protein | 116 | 16% helix, 3% strand | O95639 |
| D | Pas RNA | rna | 8 | — | — |
| E, F | Cleavage stimulation factor subunit 3 | protein | 527 | 72% helix, 0% strand | Q12996 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains C, D
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 | 756 | 0.87 | 0.91 | 80 | empty |
| 2 | 1097 | 0.86 | 0.87 | 109 | empty |
| 3 | 597 | 0.85 | 0.90 | 68 | empty |
| 4 | 439 | 0.84 | 0.92 | 62 | empty |
| 5 | 441 | 0.83 | 0.91 | 42 | empty |
Interfaces
9 interfaces between chains.
- A–B · 4100 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 3159 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1825 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 882 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 728 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 6URO · Cryo-EM structure of human CPSF160-WDR33-CPSF30-PAS RNA-CstF77 complex · the same entry in another collection · chain E against E, TM-score 1.00
- Q9C0J8 · AlphaFold monomer V2.0 prediction for pre-mRNA 3' end processing protein WDR33 (Q9C0J8) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q10570 · AlphaFold monomer V2.0 prediction for cleavage and polyadenylation specificity factor… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q12996 · AlphaFold monomer V2.0 prediction for cleavage stimulation factor subunit 3 (Q12996) · a predicted model of the same protein · chain E against A, TM-score 0.99
- O95639 · AlphaFold monomer V2.0 prediction for cleavage and polyadenylation specificity factor… · a predicted model of the same protein · chain C against A, TM-score 0.93
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 Q10570
- Every structure of UniProt Q9C0J8
- Every structure of UniProt O95639
- Every structure of UniProt Q12996
- Elsewhere: RCSB PDB 6URO · PDBe 6URO · UniProt Q10570 · UniProt Q9C0J8 · UniProt O95639 · UniProt Q12996
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