› 3tyg

X-ray diffraction
3.25Å resolution

Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with a glycosylated engineered gp120 outer domain with miniV3 (eODmV3)

Released:
DOI: 10.2210/pdb3tyg/pdb
PDB entry 3tyg coloured by chain, front view.
PDB entry 3tyg coloured by chain, side view.
PDB entry 3tyg coloured by chain, top view.
Source organisms:
Primary publication:
A potent and broad neutralizing antibody recognizes and penetrates the HIV glycan shield.
Pejchal R, Doores KJ, Walker LM, Khayat R, Huang PS, Wang SK, Stanfield RL, Julien JP, Ramos A, Crispin M, Depetris R, Katpally U, Marozsan A, Cupo A, Maloveste S, Liu Y, McBride R, Ito Y, Sanders RW, Ogohara C, Paulson JC, Feizi T, Scanlan CN, Wong CH, Moore JP, Olson WC, Ward AB, Poignard P, Schief WR, Burton DR, Wilson IA
Science 334 1097-103 (2011)
PMID: 21998254

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-134829 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (5 distinct):
Envelope glycoprotein gp160; Surface protein gp120 Chain: A
Molecule details ›
Chain: A
Length: 199 amino acids
Theoretical weight: 22.02 KDa
Source organisms: Expression system: Homo sapiens
UniProt:
  • Canonical: P04578 (Residues: 254-314, 340-401; Coverage: 14%)
  • Canonical: Q75760 (Residues: 317-335; Coverage: 2%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
Immunoglobulin lambda constant 2 Chain: L
Molecule details ›
Chain: L
Length: 211 amino acids
Theoretical weight: 22.21 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DOY2 (Residues: 1-106; Coverage: 100%)
Gene name: IGLC2
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Immunoglobulin heavy constant gamma 1 Chain: H
Molecule details ›
Chain: H
Length: 239 amino acids
Theoretical weight: 25.56 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P01857 (Residues: 1-104; Coverage: 26%)
Gene name: IGHG1
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
No bound ligands
1 modified residue:
Ligand PCA 2 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: P212121
Unit cell:
a: 50.791Å b: 73.512Å c: 241.447Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.207 0.257
Expression system: Homo sapiens

Quick links

Citations

119 review citations

Biological roles of glycans.
Varki A. (2017)
118 more

31 mentions without citation

Peptide-Based Vaccines: Current Progress and Future Challenges.
Malonis et al. (2020)
30 more