› 6mph

Electron Microscopy
3.8Å resolution

Cryo-EM structure at 3.8 A resolution of HIV-1 fusion peptide-directed antibody, DF1W-a.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/pdb6mph/pdb
PDB entry 6mph coloured by chain, front view.
PDB entry 6mph coloured by chain, side view.
PDB entry 6mph 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-9189

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-212197 (preferred)
Entry contents:
8 distinct polypeptide molecules
Macromolecules (13 distinct):
DF1W-a.01 heavy chain Chains: 1, 3, H
Molecule details ›
Chains: 1, 3, H
Length: 118 amino acids
Theoretical weight: 12.96 KDa
Source organism: Macaca mulatta
Expression system: Homo sapiens
DF1W-a.01 Light chain Chains: 2, 4, L
Molecule details ›
Chains: 2, 4, L
Length: 112 amino acids
Theoretical weight: 12.19 KDa
Source organism: Macaca mulatta
Expression system: Homo sapiens
Transmembrane protein gp41 Chains: 6, D, E
Molecule details ›
Chains: 6, D, E
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: A, B, C
Molecule details ›
Chains: A, B, C
Length: 473 amino acids
Theoretical weight: 52.99 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: Q2N0S6 (Residues: 30-502; Coverage: 55%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
PGT122 heavy chain Chains: M, X, Y
Molecule details ›
Chains: M, X, Y
Length: 132 amino acids
Theoretical weight: 14.84 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
PGT122 Light Chain Chains: N, Z, a
Molecule details ›
Chains: N, Z, a
Length: 107 amino acids
Theoretical weight: 11.59 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
VRC03 Heavy chain Chains: Q, f, g
Molecule details ›
Chains: Q, f, g
Length: 227 amino acids
Theoretical weight: 24.65 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
VRC03 Light Chain Chains: R, h, i
Molecule details ›
Chains: R, h, i
Length: 102 amino acids
Theoretical weight: 11.39 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
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 9 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-9189
Expression system: Homo sapiens

Quick links

Citations

8 review citations

Broadly neutralizing antibodies and vaccine design against HIV-1 infection.
Wang et al. (2020)
7 more

5 mentions without citation

Spectroscopy and kinetics of wild-type and mutant tyrosine hydroxylase: mechanistic insight into O2 activation.
Chow et al. (2009)
4 more