› 4zbn

X-ray diffraction
2.45Å resolution

Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor

Released:
DOI: 10.2210/pdb4zbn/pdb
PDB entry 4zbn coloured by chain, front view.
PDB entry 4zbn coloured by chain, side view.
PDB entry 4zbn coloured by chain, top view.
Source organisms:
Primary publication:
Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor.
Jarvis TC, Davies DR, Hisaminato A, Resnicow DI, Gupta S, Waugh SM, Nagabukuro A, Wadatsu T, Hishigaki H, Gawande B, Zhang C, Wolk SK, Mayfield WS, Nakaishi Y, Burgin AB, Stewart LJ, Edwards TE, Gelinas AD, Schneider DJ, Janjic N
Structure 23 1293-304 (2015)
PMID: 26027732

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118370 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Beta-nerve growth factor Chains: A, B
Molecule details ›
Chains: A, B
Length: 120 amino acids
Theoretical weight: 13.52 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01138 (Residues: 122-241; Coverage: 54%)
Gene names: NGF, NGFB
Sequence domains: Nerve growth factor family
Structure domains: Cystine-knot cytokines
DNA (28-MER) Chains: D, E
Molecule details ›
Chains: D, E
Length: 28 nucleotides
Theoretical weight: 9.8 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand EPE 1 x EPE
1 modified residue:
Ligand DUZ 18 x DUZ

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: C2
Unit cell:
a: 109.201Å b: 60.708Å c: 68.589Å
α: 90° β: 95.57° γ: 90°
R-values:
R R work R free
0.204 0.202 0.257
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

Embracing proteins: structural themes in aptamer-protein complexes.
Gelinas et al. (2016)
4 more

4 mentions without citation

The expanding world of DNA and RNA.
Chen et al. (2016)
3 more