› 5ife

X-ray diffraction
3.1Å resolution

Crystal structure of the human SF3b core complex

Released:
DOI: 10.2210/pdb5ife/pdb
PDB entry 5ife coloured by chain, front view.
PDB entry 5ife coloured by chain, side view.
PDB entry 5ife coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular Architecture of SF3b and Structural Consequences of Its Cancer-Related Mutations.
Cretu C, Schmitzová J, Ponce-Salvatierra A, Dybkov O, De Laurentiis EI, Sharma K, Will CL, Urlaub H, Lührmann R, Pena V
Mol Cell 64 307-319 (2016)
PMID: 27720643

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 5 Chain: B
Molecule details ›
Chain: B
Length: 86 amino acids
Theoretical weight: 10.15 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9BWJ5 (Residues: 1-86; Coverage: 100%)
Gene names: SF3B10, SF3B5
Sequence domains: Splicing factor 3B subunit 10 (SF3b10)
Splicing factor 3B subunit 1 Chain: C
Molecule details ›
Chain: C
Length: 1304 amino acids
Theoretical weight: 146.02 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: O75533 (Residues: 1-1304; Coverage: 100%)
Gene names: SAP155, SF3B1
Sequence domains: Splicing factor 3B subunit 1
PHD finger-like domain-containing protein 5A Chain: D
Molecule details ›
Chain: D
Length: 120 amino acids
Theoretical weight: 13.31 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q7RTV0 (Residues: 1-110; Coverage: 100%)
Gene name: PHF5A
Sequence domains: PHF5-like protein
Splicing factor 3B subunit 3 Chain: A
Molecule details ›
Chain: A
Length: 1235 amino acids
Theoretical weight: 137.79 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q15393 (Residues: 1-1217; Coverage: 100%)
Gene names: KIAA0017, SAP130, SF3B3
Sequence domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 105.055Å b: 154.436Å c: 210.418Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.232 0.23 0.26
Expression system: Trichoplusia ni

Quick links

Citations

41 review citations

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

15 mentions without citation

Splicing Factor Mutations in Myelodysplasias: Insights from Spliceosome Structures.
Jenkins et al. (2017)
14 more