› 6mpg

Electron Microscopy
3.2Å resolution

Cryo-EM structure at 3.2 A resolution of HIV-1 fusion peptide-directed antibody, A12V163-b.01, elicited by vaccination of Rhesus macaques, in complex with stabilized HIV-1 Env BG505 DS-SOSIP, which was also bound to antibodies VRC03 and PGT122

Released:
DOI: 10.2210/pdb6mpg/pdb
PDB entry 6mpg coloured by chain, front view.
PDB entry 6mpg coloured by chain, side view.
PDB entry 6mpg coloured by chain, top view.
Source organisms:
Primary publication:
Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization.
Kong R, Duan H, Sheng Z, Xu K, Acharya P, Chen X, Cheng C, Dingens AS, Gorman J, Sastry M, Shen CH, Zhang B, Zhou T, Chuang GY, Chao CW, Gu Y, Jafari AJ, Louder MK, O'Dell S, Rowshan AP, Viox EG, Wang Y, Choi CW, Corcoran MM, Corrigan AR, Dandey VP, Eng ET, Geng H, Foulds KE, Guo Y, Kwon YD, Lin B, Liu K, Mason RD, Nason MC, Ohr TY, Ou L, Rawi R, Sarfo EK, Schön A, Todd JP, Wang S, Wei H, Wu W, Mullikin JC, Bailer RT, Doria-Rose NA, Karlsson Hedestam GB, Scorpio DG, Overbaugh J, Bloom JD, Carragher B, Potter CS, Shapiro L, Kwong PD, Mascola JR
Cell 178 567-584.e19 (2019)
PMID: 31348886
Related structures: EMD-8977

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 24-mer (preferred)
PDBe Complex ID:
PDB-CPX-212196 (preferred)
Entry contents:
8 distinct polypeptide molecules
Macromolecules (13 distinct):
A12V163-b.01 Light Chain Chains: 4, B, Y
Molecule details ›
Chains: 4, B, Y
Length: 113 amino acids
Theoretical weight: 12.33 KDa
Source organism: Macaca mulatta
Expression system: Homo sapiens
Transmembrane protein gp41 Chains: A, D, U
Molecule details ›
Chains: A, D, U
Length: 153 amino acids
Theoretical weight: 17.16 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: Q2N0S7 (Residues: 509-661; Coverage: 18%)
Gene name: env
Sequence domains: Retroviral envelope protein
Envelope glycoprotein gp160 Chains: 2, C, V
A12V163-b.01 Heavy Chain Chains: 3, W, X
PGT122 Heavy chain Chains: 5, M, m
PGT122 Light chain Chains: 6, N, n
VRC03 heavy chain Chains: 8, Q, q
VRC03 Light chain Chains: 7, R, r

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
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
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
1 bound ligand:
Ligand NAG 12 x NAG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.2Å
Relevant EMDB volumes: EMD-8977
Expression system: Homo sapiens

Quick links

Citations

10 review citations

Strategies for HIV-1 vaccines that induce broadly neutralizing antibodies.
Haynes et al. (2023)
9 more

3 mentions without citation

Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization.
Kong et al. (2019)
2 more