› 6d2p

X-ray diffraction
2.6Å resolution

Crystal structure of IOMA-class CLK31 Fab from an HIV-1 naive donor in complex with a germline-targeting gp120 engineered outer domain eOD-GT8 at 2.6 A

Released:
DOI: 10.2210/pdb6d2p/pdb
PDB entry 6d2p coloured by chain, front view.
PDB entry 6d2p coloured by chain, side view.
PDB entry 6d2p coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The human naive B cell repertoire contains distinct subclasses for a germline-targeting HIV-1 vaccine immunogen.
Havenar-Daughton C, Sarkar A, Kulp DW, Toy L, Hu X, Deresa I, Kalyuzhniy O, Kaushik K, Upadhyay AA, Menis S, Landais E, Cao L, Diedrich JK, Kumar S, Schiffner T, Reiss SM, Seumois G, Yates JR, Paulson JC, Bosinger SE, Wilson IA, Schief WR, Crotty S
Sci Transl Med 10 (2018)
PMID: 29973404

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-230993 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Germline-targeting HIV-1 gp120 engineered outer domain eOD-GT8 Chain: C
Molecule details ›
Chain: C
Length: 183 amino acids
Theoretical weight: 19.89 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
IOMAclass naive CLK31 Fab heavy chain Chain: H
Molecule details ›
Chain: H
Length: 221 amino acids
Theoretical weight: 23.7 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
IOMAclass naive CLK31 Fab light chain Chain: L
Molecule details ›
Chain: L
Length: 214 amino acids
Theoretical weight: 22.42 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand GOL 5 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P21212
Unit cell:
a: 134.3Å b: 66.636Å c: 76.518Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.213 0.268
Expression system: Homo sapiens

Quick links

Citations

19 review citations

Recent progress in broadly neutralizing antibodies to HIV.
Sok et al. (2018)
18 more

3 mentions without citation

The human naive B cell repertoire contains distinct subclasses for a germline-targeting HIV-1 vaccine immunogen.
Havenar-Daughton et al. (2018)
2 more