› 3agv

X-ray diffraction
2.15Å resolution

Crystal structure of a human IgG-aptamer complex

Released:
DOI: 10.2210/pdb3agv/pdb
PDB entry 3agv coloured by chain, front view.
PDB entry 3agv coloured by chain, side view.
PDB entry 3agv coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Conformational plasticity of RNA for target recognition as revealed by the 2.15 A crystal structure of a human IgG-aptamer complex.
Nomura Y, Sugiyama S, Sakamoto T, Miyakawa S, Adachi H, Takano K, Murakami S, Inoue T, Mori Y, Nakamura Y, Matsumura H
Nucleic Acids Res 38 7822-9 (2010)
PMID: 20675355

Function and Biology Details

Biochemical function:
  • not assigned
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-134875 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (4 distinct):
Immunoglobulin heavy constant gamma 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 211 amino acids
Theoretical weight: 23.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01857 (Residues: 120-328; Coverage: 52%)
Gene name: IGHG1
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
5'-R(*GP*GP*AP*GP*GP*(UFT)P*GP*(CFZ)P*(UFT)P*(CFZ)P*(CFZ)P*GP*AP*AP*A*GP*GP*AP*AP*(CFZ)P*(UFT)P*(CFZ)P*(CFZ)P*A)-3' Chains: S, U
Molecule details ›
Chains: S, U
Length: 24 nucleotides
Theoretical weight: 7.79 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: MAN, NDG, GLA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: MAN, NDG, NAG, BMA, GAL, FUL
Carbohydrate polymer
1 bound ligand:
Ligand CA 2 x CA
2 modified residues:
Ligand UFT 6 x UFT
Ligand CFZ 12 x CFZ

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21212
Unit cell:
a: 83.587Å b: 107.238Å c: 79.458Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.237 0.237 0.277
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

25 review citations

Nucleic Acid Ligands With Protein-like Side Chains: Modified Aptamers and Their Use as Diagnostic and Therapeutic Agents.
Rohloff et al. (2014)
24 more

10 mentions without citation

Characterization of aptamer-protein complexes by X-ray crystallography and alternative approaches.
Ruigrok et al. (2012)
9 more