› 7mdt

Electron Microscopy
3.6Å resolution

BG505 SOSIP.v5.2 in complex with the monoclonal antibody Rh4O9.8 (as Fab fragment)

Released:
DOI: 10.2210/pdb7mdt/pdb
PDB entry 7mdt coloured by chain, front view.
PDB entry 7mdt coloured by chain, side view.
PDB entry 7mdt coloured by chain, top view.
Source organisms:
Primary publication:
From structure to sequence: Antibody discovery using cryoEM.
Antanasijevic A, Bowman CA, Kirchdoerfer RN, Cottrell CA, Ozorowski G, Upadhyay AA, Cirelli KM, Carnathan DG, Enemuo CA, Sewall LM, Nogal B, Zhao F, Groschel B, Schief WR, Sok D, Silvestri G, Crotty S, Bosinger SE, Ward AB
OpenAccess logo Sci Adv 8 eabk2039 (2022)
PMID: 35044813
Related structures: EMD-23779

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-212181 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (7 distinct):
Envelope glycoprotein gp160 Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 513 amino acids
Theoretical weight: 57.78 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, F
Molecule details ›
Chains: B, D, F
Length: 153 amino acids
Theoretical weight: 17.18 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
Rh4O9.8 monoclonal antibody Light Chain Chain: L
Rh4O9.8 monoclonal antibody Heavy Chain Chain: H

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
1 bound ligand:
Ligand NAG 31 x NAG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.6Å
Relevant EMDB volumes: EMD-23779
Expression system: Homo sapiens

Quick links

Citations

5 review citations

Applications and prospects of cryo-EM in drug discovery.
Zhu et al. (2023)
4 more

1 mention without citation

From structure to sequence: Antibody discovery using cryoEM.
Antanasijevic et al. (2022)