› 6nf5

Electron Microscopy
3.71Å resolution

BG505 MD64 N332-GT5 SOSIP trimer in complex with BG18-like precursor HMP1 fragmentantigen binding and base-binding RM20A3 fragment antigen binding

Released:
DOI: 10.2210/pdb6nf5/pdb
PDB entry 6nf5 coloured by chain, front view.
PDB entry 6nf5 coloured by chain, side view.
PDB entry 6nf5 coloured by chain, top view.
Source organisms:
Primary publication:
A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses.
Steichen JM, Lin YC, Havenar-Daughton C, Pecetta S, Ozorowski G, Willis JR, Toy L, Sok D, Liguori A, Kratochvil S, Torres JL, Kalyuzhniy O, Melzi E, Kulp DW, Raemisch S, Hu X, Bernard SM, Georgeson E, Phelps N, Adachi Y, Kubitz M, Landais E, Umotoy J, Robinson A, Briney B, Wilson IA, Burton DR, Ward AB, Crotty S, Batista FD, Schief WR
Science 366 (2019)
PMID: 31672916
Related structures: EMD-7884

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-212146 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (9 distinct):
Envelope glycoprotein gp160 Chains: A, C, J
Molecule details ›
Chains: A, C, J
Length: 481 amino acids
Theoretical weight: 54.24 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: Q2N0S6 (Residues: 30-508; Coverage: 56%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
Transmembrane protein gp41 Chains: B, D, M
Molecule details ›
Chains: B, D, M
Length: 162 amino acids
Theoretical weight: 18.25 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: Q2N0S6 (Residues: 509-661; Coverage: 18%)
Gene name: env
Sequence domains: Retroviral envelope protein
BG18-like precursor HMP1 fragment antigen binding heavy chain Chains: E, H, O
Molecule details ›
Chains: E, H, O
Length: 131 amino acids
Theoretical weight: 14.15 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
BG18-like precursor HMP1 fragment antigen binding light chain Chains: F, L, P
Molecule details ›
Chains: F, L, P
Length: 106 amino acids
Theoretical weight: 11.25 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
base-binding RM20A3 fragment antigen binding heavy chain Chains: G, K, Q
Molecule details ›
Chains: G, K, Q
Length: 125 amino acids
Theoretical weight: 13.51 KDa
Source organism: Macaca mulatta
Expression system: Homo sapiens
base-binding RM20A3 fragment antigen binding light chain Chains: I, N, R
Molecule details ›
Chains: I, N, R
Length: 128 amino acids
Theoretical weight: 13.51 KDa
Source organism: Macaca mulatta
Expression system: Homo sapiens

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
1 bound ligand:
Ligand NAG 33 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.71Å
Relevant EMDB volumes: EMD-7884
Expression system: Homo sapiens

Quick links

Citations

29 review citations

Factors in B cell competition and immunodominance.
Abbott et al. (2020)
28 more

1 mention without citation

A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses.
Steichen et al. (2019)