› 4jm2

X-ray diffraction
3.1Å resolution

Crystal Structure of PGT 135 Fab in Complex with gp120 Core Protein from HIV-1 Strain JR-FL Bound to CD4 and 17b Fab

Released:
DOI: 10.2210/pdb4jm2/pdb
PDB entry 4jm2 coloured by chain, front view.
PDB entry 4jm2 coloured by chain, side view.
PDB entry 4jm2 coloured by chain, top view.
Source organisms:
Primary publication:
Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120.
Kong L, Lee JH, Doores KJ, Murin CD, Julien JP, McBride R, Liu Y, Marozsan A, Cupo A, Klasse PJ, Hoffenberg S, Caulfield M, King CR, Hua Y, Le KM, Khayat R, Deller MC, Clayton T, Tien H, Feizi T, Sanders RW, Paulson JC, Moore JP, Stanfield RL, Burton DR, Ward AB, Wilson IA
Nat Struct Mol Biol 20 796-803 (2013)
PMID: 23708606

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-208506 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (9 distinct):
PGT 135 Heavy chain Chain: A
Molecule details ›
Chain: A
Length: 236 amino acids
Theoretical weight: 25.58 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
Structure domains: Immunoglobulins
PGT 135 Light chain Chain: B
Molecule details ›
Chain: B
Length: 214 amino acids
Theoretical weight: 23.8 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
Structure domains: Immunoglobulins
17b Light chain Chain: C
Molecule details ›
Chain: C
Length: 214 amino acids
Theoretical weight: 23.4 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
Structure domains: Immunoglobulins
17b Heavy chain Chain: D
Molecule details ›
Chain: D
Length: 229 amino acids
Theoretical weight: 24.46 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
Structure domains: Immunoglobulins
Envelope glycoprotein gp160 Chain: E
Molecule details ›
Chain: E
Length: 321 amino acids
Theoretical weight: 35.99 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: Q75760 (Residues: 88-483; Coverage: 38%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
Structure domains: Human immunodeficiency virus 1, Gp160, envelope glycoprotein
T-cell surface glycoprotein CD4 Chain: F
Molecule details ›
Chain: F
Length: 185 amino acids
Theoretical weight: 20.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01730 (Residues: 26-208; Coverage: 42%)
Gene name: CD4
Sequence domains:
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
2 bound ligands:
Ligand PG4 1 x PG4
Ligand NAG 6 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: C2
Unit cell:
a: 218.409Å b: 92.146Å c: 88.187Å
α: 90° β: 104.75° γ: 90°
R-values:
R R work R free
0.241 0.238 0.285
Expression systems:
  • Spodoptera frugiperda
  • Homo sapiens
  • Escherichia coli

Quick links

Citations

63 review citations

Antibody responses to envelope glycoproteins in HIV-1 infection.
Burton et al. (2015)
62 more

22 mentions without citation

Targeting the N332-supersite of the HIV-1 envelope for vaccine design.
Moyo et al. (2020)
21 more