› 4pkd

X-ray diffraction
2.5Å resolution

U1-70k in complex with U1 snRNA stem-loops 1 and U1-A RRM in complex with stem-loop 2

Released:
DOI: 10.2210/pdb4pkd/pdb
PDB entry 4pkd coloured by chain, front view.
PDB entry 4pkd coloured by chain, side view.
PDB entry 4pkd coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition.
Kondo Y, Oubridge C, van Roon AM, Nagai K
Elife 4 (2015)
PMID: 25555158

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140241 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
U1 small nuclear ribonucleoprotein 70 kDa; U1 small nuclear ribonucleoprotein A Chain: B
Molecule details ›
Chain: B
Length: 279 amino acids
Theoretical weight: 32.18 KDa
Source organisms: Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q06AA4 (Residues: 2-111; Coverage: 39%)
  • Canonical: P08621 (Residues: 60-215; Coverage: 36%)
Gene names: RNPU1Z, RPU1, SNRNP70, SNRP70, SNRPA, U1AP1
Sequence domains:
Structure domains: Alpha-Beta Plaits
U1 snRNA stem-loops 1 and 2 (55-MER) Chain: V
Molecule details ›
Chain: V
Length: 55 nucleotides
Theoretical weight: 17.79 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 3 x MG
Ligand IMD 1 x IMD
1 modified residue:
Ligand GTP 1 x GTP

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: C2
Unit cell:
a: 80.22Å b: 66.6Å c: 93.73Å
α: 90° β: 110.95° γ: 90°
R-values:
R R work R free
0.2 0.197 0.258
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

27 review citations

Specificity and nonspecificity in RNA-protein interactions.
Jankowsky et al. (2015)
26 more

13 mentions without citation

Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition.
Kondo et al. (2015)
12 more