› 4laj

X-ray diffraction
2.14Å resolution

Crystal structure of HIV-1 YU2 envelope gp120 glycoprotein in complex with CD4-mimetic miniprotein, M48U1, and llama single-domain, broadly neutralizing, co-receptor binding site antibody, JM4

Released:
DOI: 10.2210/pdb4laj/pdb
PDB entry 4laj coloured by chain, front view.
PDB entry 4laj coloured by chain, side view.
PDB entry 4laj coloured by chain, top view.
Source organisms:
Primary publication:
Heavy chain-only IgG2b llama antibody effects near-pan HIV-1 neutralization by recognizing a CD4-induced epitope that includes elements of coreceptor- and CD4-binding sites.
Acharya P, Luongo TS, Georgiev IS, Matz J, Schmidt SD, Louder MK, Kessler P, Yang Y, McKee K, O'Dell S, Chen L, Baty D, Chames P, Martin L, Mascola JR, Kwong PD
J Virol 87 10173-81 (2013)
PMID: 23843638

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-106849 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Surface protein gp120 Chains: A, B, F, J
Molecule details ›
Chains: A, B, F, J
Length: 376 amino acids
Theoretical weight: 41.7 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: P35961 (Residues: 21-479; Coverage: 45%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
Structure domains: Human immunodeficiency virus 1, Gp160, envelope glycoprotein
CD4-mimetic miniprotein M48U1 Chains: C, D, G, K
Molecule details ›
Chains: C, D, G, K
Length: 28 amino acids
Theoretical weight: 3.06 KDa
Ig-like domain-containing protein Chains: H, I, L, M
Molecule details ›
Chains: H, I, L, M
Length: 129 amino acids
Theoretical weight: 14.01 KDa
Source organism: Lama glama
Expression system: Homo sapiens
UniProt:
  • Canonical: A2KD57 (Residues: 1-132; Coverage: 93%)
Gene name: hi113
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins

Ligands and Environments

3 bound ligands:
Ligand NAG 35 x NAG
Ligand EDO 7 x EDO
Ligand ACA 1 x ACA
2 modified residues:
Ligand DPR 4 x DPR
Ligand U2X 4 x U2X

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 96.772Å b: 86.221Å c: 144.848Å
α: 90° β: 102.88° γ: 90°
R-values:
R R work R free
0.188 0.185 0.227
Expression system: Homo sapiens

Quick links

Citations

6 review citations

Camelid nanobodies: killing two birds with one stone.
Desmyter et al. (2015)
5 more

7 mentions without citation

Single-Domain Antibodies As Therapeutics against Human Viral Diseases.
Wu et al. (2017)
6 more