› 4r2g

X-ray diffraction
3.28Å resolution

Crystal Structure of PGT124 Fab bound to HIV-1 JRCSF gp120 core and to CD4

Released:
DOI: 10.2210/pdb4r2g/pdb
PDB 4r2g coloured by chain and viewed from the front.
PDB 4r2g coloured by chain and viewed from the side.
PDB 4r2g coloured by chain and viewed from the top.
Source organisms:
Primary publication:
Structural Evolution of Glycan Recognition by a Family of Potent HIV Antibodies.
Garces F, Sok D, Kong L, McBride R, Kim HJ, Saye-Francisco KF, Julien JP, Hua Y, Cupo A, Moore JP, Paulson JC, Ward AB, Burton DR, Wilson IA
Cell 159 69-79 (2014)
PMID: 25259921

Function and Biology Details

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

Structure analysis Details

Assembly composition:
Non-polymer only tetramer (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (6 distinct):
Surface protein gp120 Chains: A, E, K, O
Molecule details ›
Chains: A, E, K, O
Length: 309 amino acids
Theoretical weight: 34.75 KDa
Source organism: Human immunodeficiency virus type 1 (JRCSF ISOLATE)
Expression system: Homo sapiens
UniProt:
  • Canonical: P20871 (Residues: 197-300, 308-484; Coverage: 33%)
Gene name: env
Structure domains: Human immunodeficiency virus 1, Gp160, envelope glycoprotein
T-cell surface glycoprotein CD4 Chains: B, F, H, L
Molecule details ›
Chains: B, F, H, L
Length: 184 amino acids
Theoretical weight: 20.42 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01730 (Residues: 26-208; Coverage: 42%)
Gene name: CD4
Sequence domains: Immunoglobulin C2-set domain
Structure domains: Immunoglobulins
PGT124 Light Chain Chains: C, I, M, P
Molecule details ›
Chains: C, I, M, P
Length: 214 amino acids
Theoretical weight: 23.06 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
PGT124 Heavy Chain Chains: D, J, N, Q
Molecule details ›
Chains: D, J, N, Q
Length: 236 amino acids
Theoretical weight: 25.46 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Ligand NAG 8 x NAG
Ligand BMA 4 x BMA
Ligand MAN 28 x MAN
Carbohydrate polymer : NEW Components: NAG
Ligand NAG 4 x NAG
3 bound ligands:
Ligand NAG 26 x NAG
Ligand CL 4 x CL
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P212121
Unit cell:
a: 164.406Å b: 165.438Å c: 229.712Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.207 0.262
Expression systems:
  • Homo sapiens
  • Escherichia coli

Quick links

Citations

29 review citations

Development of Protein- and Peptide-Based HIV Entry Inhibitors Targeting gp120 or gp41.
Pu et al. (2019)
28 more

8 mentions without citation

Structural evolution of glycan recognition by a family of potent HIV antibodies.
Garces et al. (2014)
7 more