› 2p48

X-ray diffraction
2.3Å resolution

Complex of a camelid single-domain vhh antibody fragment with RNASE A at 2.3A resolution: SE5B-tetra crystal form with five se-met sites (L4M, M34, M51, F68M, M83) in vhh scaffold.

Released:
DOI: 10.2210/pdb2p48/pdb
PDB entry 2p48 coloured by chain, front view.
PDB entry 2p48 coloured by chain, side view.
PDB entry 2p48 coloured by chain, top view.
Source organisms:
Primary publication:
Toward chaperone-assisted crystallography: protein engineering enhancement of crystal packing and X-ray phasing capabilities of a camelid single-domain antibody (VHH) scaffold.
Tereshko V, Uysal S, Koide A, Margalef K, Koide S, Kossiakoff AA
Protein Sci 17 1175-87 (2008)
PMID: 18445622

Function and Biology Details

Reaction catalysed: 
(1a) an (RNA) containing cytidine = an (RNA)-3'-cytidine-2',3'-cyclophosphate + a 5'-hydroxy-ribonucleotide-3'-(RNA)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-211479 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ribonuclease pancreatic Chain: A
Molecule details ›
Chain: A
Length: 124 amino acids
Theoretical weight: 13.71 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P61823 (Residues: 27-150; Coverage: 100%)
Gene names: RNASE1, RNS1
Sequence domains: Pancreatic ribonuclease
Structure domains: Ribonuclease A-like domain
ANTIBODY CAB-RN05 Chain: B
Molecule details ›
Chain: B
Length: 123 amino acids
Theoretical weight: 13.34 KDa
Source organism: Camelus dromedarius
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand SO4 2 x SO4
1 modified residue:
Ligand MSE 5 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P43212
Unit cell:
a: 42.324Å b: 42.324Å c: 352.873Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.246 0.241 0.297
Expression system: Escherichia coli

Quick links

Citations

14 review citations

Nanobodies and recombinant binders in cell biology.
Helma et al. (2015)
13 more

2 mentions without citation

Cellular splicing factor RAF-2p48/NPI-5/BAT1/UAP56 interacts with the influenza virus nucleoprotein and enhances viral RNA synthesis.
Momose et al. (2001)
1 more