Research workbench
Cryo-EM structure of the human CPSF160-WDR33-CPSF30 complex bound to the pas aauaaa motif at 3.1 ångström resolution
Analyse Cryo-EM structure of the human CPSF160-WDR33-CPSF30 complex bound to the pas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FBS
- Type
- protein + RNA
- Length
- 1,673 residues
- Chains
- 4
- 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
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cleavage and polyadenylation specificity factor subunit 1 | protein | 1181 | 5% helix, 47% strand | Q10570 |
| B | Pre-mRNA 3' end processing protein WDR33 | protein | 370 | 5% helix, 39% strand | Q9C0J8 |
| C | Cleavage and polyadenylation specificity factor subunit 4 | protein | 114 | 15% helix, 5% strand | O95639 |
| D | RNA (5'-R(P*AP*AP*UP*AP*AP*AP*GP*G)-3') | rna | 8 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.87 | 0.88 | 106 | empty |
| 2 | 978 | 0.87 | 0.88 | 94 | empty |
| 3 | 942 | 0.86 | 0.88 | 88 | empty |
| 4 | 783 | 0.84 | 0.87 | 58 | empty |
| 5 | 635 | 0.84 | 0.88 | 65 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3483 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 1754 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 783 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 764 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–D · 662 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 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
- 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 0.97
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
- Elsewhere: RCSB PDB 6FBS · PDBe 6FBS · UniProt Q10570 · UniProt Q9C0J8 · UniProt O95639
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