› 5e08

X-ray diffraction
2.38Å resolution

Specific Recognition of a Single-stranded RNA Sequence by an Engineered Synthetic Antibody Fragment

Released:
DOI: 10.2210/pdb5e08/pdb
PDB entry 5e08 coloured by chain, front view.
PDB entry 5e08 coloured by chain, side view.
PDB entry 5e08 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Specific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment.
Shao Y, Huang H, Qin D, Li NS, Koide A, Staley JP, Koide S, Kossiakoff AA, Piccirilli JA
J Mol Biol 428 4100-4114 (2016)
PMID: 27593161

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-230407 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (3 distinct):
Fab Heavy Chain Chain: H
Molecule details ›
Chain: H
Length: 233 amino acids
Theoretical weight: 24.96 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Fab Light Chain Chain: L
Molecule details ›
Chain: L
Length: 215 amino acids
Theoretical weight: 23.44 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
RNA Chain: N
Molecule details ›
Chain: N
Length: 12 nucleotides
Theoretical weight: 3.85 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: C2
Unit cell:
a: 199.515Å b: 63.401Å c: 57.061Å
α: 90° β: 97.51° γ: 90°
R-values:
R R work R free
0.211 0.209 0.234
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Protein Engineering: Advances in Phage Display for Basic Science and Medical Research.
Davydova EK. (2022)
6 other articles

3 mentions without citation

Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins.
Pal et al. (2019)
2 more