› 7ly9

Electron Microscopy
3.91Å resolution

Cryo-EM structure of 2909 Fab in complex with 3BNC117 Fab and CAP256.wk34.c80 SOSIP.RnS2 N160K HIV-1 Env trimer

Released:
DOI: 10.2210/pdb7ly9/pdb
PDB entry 7ly9 coloured by chain, front view.
PDB entry 7ly9 coloured by chain, side view.
PDB entry 7ly9 coloured by chain, top view.
Source organisms:
Primary publication:
Extended antibody-framework-to-antigen distance observed exclusively with broad HIV-1-neutralizing antibodies recognizing glycan-dense surfaces.
Lee M, Changela A, Gorman J, Rawi R, Bylund T, Chao CW, Lin BC, Louder MK, Olia AS, Zhang B, Doria-Rose NA, Zolla-Pazner S, Shapiro L, Chuang GY, Kwong PD
OpenAccess logo Nat Commun 12 6470 (2021)
PMID: 34753907
Related structures: EMD-23589

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetradecamer (preferred)
PDBe Complex ID:
PDB-CPX-278933 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (10 distinct):
2909 Light Chain Chain: L
Molecule details ›
Chain: L
Length: 211 amino acids
Theoretical weight: 22.58 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
2909 Heavy Chain Chain: H
Molecule details ›
Chain: H
Length: 231 amino acids
Theoretical weight: 25.07 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Envelope glycoprotein gp160 Chains: D, G, K
Molecule details ›
Chains: D, G, K
Length: 471 amino acids
Theoretical weight: 53.34 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: A0A0N9FF17 (Residues: 29-486; Coverage: 54%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
3BNC117 Heavy Chain Chains: A, B, E
Molecule details ›
Chains: A, B, E
Length: 226 amino acids
Theoretical weight: 24.66 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
3BNC117 Light Chain Chains: C, I, M
Molecule details ›
Chains: C, I, M
Length: 206 amino acids
Theoretical weight: 23.02 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Transmembrane protein gp41 Chains: F, J, N
Molecule details ›
Chains: F, J, N
Length: 154 amino acids
Theoretical weight: 17.36 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: W6HZ60 (Residues: 513-666; Coverage: 18%)
Gene name: env
Sequence domains: Retroviral envelope protein

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
1 bound ligand:
Ligand NAG 54 x NAG
1 modified residue:
Ligand TYS 2 x TYS

Experiments and Validation Details

Entry percentile scores
Resolution: 3.91Å
Relevant EMDB volumes: EMD-23589
Expression system: Homo sapiens

Quick links

Citations

3 citation in other articles

HIV-1 neutralizing antibodies elicited in humans by a prefusion-stabilized envelope trimer form a reproducible class targeting fusion peptide.
Wang et al. (2023)
2 more