› 5yki

X-ray diffraction
2.25Å resolution

Crystal structure of the engineered nine-repeat PUF domain in complex with cognate 9nt-RNA

Released:
DOI: 10.2210/pdb5yki/pdb
PDB entry 5yki coloured by chain, front view.
PDB entry 5yki coloured by chain, side view.
PDB entry 5yki coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Expanding RNA binding specificity and affinity of engineered PUF domains.
Zhao YY, Mao MW, Zhang WJ, Wang J, Li HT, Yang Y, Wang Z, Wu JW
OpenAccess logo Nucleic Acids Res 46 4771-4782 (2018)
PMID: 29490074

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-172073 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Pumilio homolog 1 Chain: A
Molecule details ›
Chain: A
Length: 415 amino acids
Theoretical weight: 48.06 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q14671 (Residues: 828-1016, 1017-1018, 1019-1176; Coverage: 29%)
Gene names: KIAA0099, PUM1, PUMH1
Sequence domains: Pumilio-family RNA binding repeat
RNA (5'-R(*UP*GP*UP*UP*GP*UP*AP*UP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 9 nucleotides
Theoretical weight: 2.83 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P212121
Unit cell:
a: 68.045Å b: 70.318Å c: 97.992Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.197 0.236
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms.
Corley et al. (2020)
5 more

1 mention without citation

Expanding RNA binding specificity and affinity of engineered PUF domains.
Zhao et al. (2018)