› 3ru8

X-ray diffraction
2.07Å resolution

Structure of an HIV epitope scaffold in complex with neutralizing antibody b12 Fab

Released:
DOI: 10.2210/pdb3ru8/pdb
PDB entry 3ru8 coloured by chain, front view.
PDB entry 3ru8 coloured by chain, side view.
PDB entry 3ru8 coloured by chain, top view.
Source organisms:
Primary publication:
Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold.
Azoitei ML, Correia BE, Ban YE, Carrico C, Kalyuzhniy O, Chen L, Schroeter A, Huang PS, McLellan JS, Kwong PD, Baker D, Strong RK, Schief WR
Science 334 373-6 (2011)
PMID: 22021856

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208537 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Epitope Scaffold 2bodx43 Chain: X
Molecule details ›
Chain: X
Length: 282 amino acids
Theoretical weight: 30.04 KDa
Source organism: Human immunodeficiency virus
Expression system: Escherichia coli
Structure domains: 1, 4-beta cellobiohydrolase
Antibody b12, Heavy Chain Chain: H
Molecule details ›
Chain: H
Length: 230 amino acids
Theoretical weight: 24.94 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Immunoglobulin kappa constant Chain: L
Molecule details ›
Chain: L
Length: 215 amino acids
Theoretical weight: 23.71 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P01834 (Residues: 1-107; Coverage: 100%)
Gene name: IGKC
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P212121
Unit cell:
a: 90.453Å b: 93.097Å c: 94.373Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.168 0.203
Expression systems:
  • Escherichia coli
  • Homo sapiens

Quick links

Citations

44 review citations

The protein-folding problem, 50 years on.
Dill et al. (2012)
43 more

6 mentions without citation

Advances in structure-based vaccine design.
Kulp et al. (2013)
5 more