› 7c06

X-ray diffraction
3.02Å resolution

Crystal structure of yeast U2AF1 complex bound to 3' splice site RNA, 5'-UAGGU.

Released:
DOI: 10.2210/pdb7c06/pdb
PDB entry 7c06 coloured by chain, front view.
PDB entry 7c06 coloured by chain, side view.
PDB entry 7c06 coloured by chain, top view.
Source organism: Schizosaccharomyces pombe 972h-
Primary publication:
Elucidation of the aberrant 3' splice site selection by cancer-associated mutations on the U2AF1.
Yoshida H, Park SY, Sakashita G, Nariai Y, Kuwasako K, Muto Y, Urano T, Obayashi E
Nat Commun 11 4744 (2020)
PMID: 32958768

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153199 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (3 distinct):
Splicing factor U2AF 23 kDa subunit Chains: A, D, G, J, M, P, S, V, Y
Molecule details ›
Chains: A, D, G, J, M, P, S, V, Y
Length: 216 amino acids
Theoretical weight: 25.07 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli
UniProt:
  • Canonical: Q09176 (Residues: 1-216; Coverage: 100%)
Gene name: SPAP8A3.06
Sequence domains:
Splicing factor U2AF 59 kDa subunit Chains: B, E, H, K, N, Q, T, W, Z
Molecule details ›
Chains: B, E, H, K, N, Q, T, W, Z
Length: 69 amino acids
Theoretical weight: 7.83 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli
UniProt:
  • Canonical: P36629 (Residues: 93-161; Coverage: 13%)
Gene names: SPBC146.07, mis11, prp2
RNA (5'-R(*U*UP*AP*GP*GP*U)-3') Chains: 1, C, F, I, L, O, R, U, X
Molecule details ›
Chains: 1, C, F, I, L, O, R, U, X
Length: 6 nucleotides
Theoretical weight: 1.89 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 18 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P21
Unit cell:
a: 93.823Å b: 255.101Å c: 94.112Å
α: 90° β: 101.125° γ: 90°
R-values:
R R work R free
0.216 0.215 0.249
Expression system: Escherichia coli

Quick links

Citations

7 review citations

The Biological and Clinical Consequences of RNA Splicing Factor U2AF1 Mutation in Myeloid Malignancies.
Zhao et al. (2022)
6 more

2 mentions without citation

Elucidation of the aberrant 3' splice site selection by cancer-associated mutations on the U2AF1.
Yoshida et al. (2020)
1 more