› 3vaf

X-ray diffraction
2.49Å resolution

Structure of U2AF65 variant with BrU3 DNA

Released:
DOI: 10.2210/pdb3vaf/pdb
PDB entry 3vaf coloured by chain, front view.
PDB entry 3vaf coloured by chain, side view.
PDB entry 3vaf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs.
Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf CL
Nucleic Acids Res 41 3859-73 (2013)
PMID: 23376934

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117040 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Splicing factor U2AF 65 kDa subunit Chains: A, B
Molecule details ›
Chains: A, B
Length: 174 amino acids
Theoretical weight: 19.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P26368 (Residues: 148-336; Coverage: 36%)
Gene names: U2AF2, U2AF65
Sequence domains: RNA recognition motif
Structure domains: Alpha-Beta Plaits
DNA 5'-D(*UP*UP*(BRU)P*(BRU)P*UP*UP*U)-3' Chains: E, P
Molecule details ›
Chains: E, P
Length: 7 nucleotides
Theoretical weight: 2.14 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand DIO 4 x DIO
Ligand SO4 6 x SO4
Ligand GOL 1 x GOL
Ligand CPQ 1 x CPQ
1 modified residue:
Ligand BRU 4 x BRU

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: C2
Unit cell:
a: 164.296Å b: 36.981Å c: 99.431Å
α: 90° β: 125.67° γ: 90°
R-values:
R R work R free
0.236 0.23 0.289
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

Mechanistic insights into precursor messenger RNA splicing by the spliceosome.
Shi Y. (2017)
6 more

3 mentions without citation

U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs.
Jenkins et al. (2013)
2 more