› 1i8m

X-ray diffraction
2.1Å resolution

CRYSTAL STRUCTURE OF A RECOMBINANT ANTI-SINGLE-STRANDED DNA ANTIBODY FRAGMENT COMPLEXED WITH DT5

Released:
DOI: 10.2210/pdb1i8m/pdb
PDB entry 1i8m coloured by chain, front view.
PDB entry 1i8m coloured by chain, side view.
PDB entry 1i8m coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Crystal structure of an antigen-binding fragment bound to single-stranded DNA.
Tanner JJ, Komissarov AA, Deutscher SL
J Mol Biol 314 807-22 (2001)
PMID: 11733999

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-218902 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
Ig-like domain-containing protein Chains: A, L
Molecule details ›
Chains: A, L
Length: 214 amino acids
Theoretical weight: 23.62 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7TS98 (Residues: 23-236; Coverage: 100%)
Sequence domains:
Structure domains: Immunoglobulins
Ig-like domain-containing protein Chains: B, H
Molecule details ›
Chains: B, H
Length: 224 amino acids
Theoretical weight: 24.15 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q924Q6 (Residues: 6-131; Coverage: 87%)
Gene names: Igh-6, Ighm, Slc25a30, VH186.2-D-J-C mu
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins
5'-D(*TP*TP*TP*TP*T)-3' Chain: T
Molecule details ›
Chain: T
Length: 5 nucleotides
Theoretical weight: 1.48 KDa
5'-D(P*TP*T)-3' Chain: D
Molecule details ›
Chain: D
Length: 2 nucleotides
Theoretical weight: 563 Da

Ligands and Environments

1 bound ligand:
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X8C, NSLS BEAMLINE X12B
Spacegroup: P6522
Unit cell:
a: 171.84Å b: 171.84Å c: 144.568Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.229 0.22 0.258
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Intramolecular immunological signal hypothesis revived--structural background of signalling revealed by using Congo Red as a specific tool.
Jagusiak et al. (2015)
30 other articles

6 mentions without citation

Length-independent structural similarities enrich the antibody CDR canonical class model.
Nowak et al. (2016)
5 more