› 6en4

X-ray diffraction
3.08Å resolution

SF3b core in complex with a splicing modulator

Released:
DOI: 10.2210/pdb6en4/pdb
PDB entry 6en4 coloured by chain, front view.
PDB entry 6en4 coloured by chain, side view.
PDB entry 6en4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Basis of Splicing Modulation by Antitumor Macrolide Compounds.
Cretu C, Agrawal AA, Cook A, Will CL, Fekkes P, Smith PG, Lührmann R, Larsen N, Buonamici S, Pena V
Mol Cell 70 265-273.e8 (2018)
PMID: 29656923

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-131047 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Splicing factor 3B subunit 3 Chain: A
Molecule details ›
Chain: A
Length: 1209 amino acids
Theoretical weight: 135.02 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q15393 (Residues: 1-1217; Coverage: 99%)
Gene names: KIAA0017, SAP130, SF3B3
Sequence domains:
Splicing factor 3B subunit 5 Chain: B
Molecule details ›
Chain: B
Length: 85 amino acids
Theoretical weight: 10.02 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9BWJ5 (Residues: 2-86; Coverage: 99%)
Gene names: SF3B10, SF3B5
Sequence domains: Splicing factor 3B subunit 10 (SF3b10)
Splicing factor 3B subunit 1 Chain: C
Molecule details ›
Chain: C
Length: 852 amino acids
Theoretical weight: 96.62 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: O75533 (Residues: 453-1304; Coverage: 65%)
Gene names: SAP155, SF3B1
PHD finger-like domain-containing protein 5A Chain: D
Molecule details ›
Chain: D
Length: 108 amino acids
Theoretical weight: 11.67 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q7RTV0 (Residues: 1-98; Coverage: 89%)
Gene name: PHF5A
Sequence domains: PHF5-like protein

Ligands and Environments

2 bound ligands:
Ligand ZN 3 x ZN
Ligand BGZ 1 x BGZ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 106.067Å b: 154.568Å c: 210.207Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.232 0.232 0.266
Expression system: Trichoplusia ni

Quick links

Citations

25 review citations

Roles and mechanisms of alternative splicing in cancer - implications for care.
Bonnal et al. (2020)
24 more

9 mentions without citation

Structures of SF3b1 reveal a dynamic Achilles heel of spliceosome assembly: Implications for cancer-associated abnormalities and drug discovery.
Maji et al. (2019)
8 more