› 7upx

Electron Microscopy
3.2Å resolution

Three RBD-down state of SARS-CoV-2 D614G spike in complex with the SP1-77 neutralizing antibody Fab fragment (local refinement of the RBD and Fab variable domains)

Released:
DOI: 10.2210/pdb7upx/pdb
PDB entry 7upx coloured by chain, front view.
PDB entry 7upx coloured by chain, side view.
PDB entry 7upx coloured by chain, top view.
Source organisms:
Primary publication:
An antibody from single human VH-rearranging mouse neutralizes all SARS-CoV-2 variants through BA.5 by inhibiting membrane fusion.
Luo S, Zhang J, Kreutzberger AJB, Eaton A, Edwards RJ, Jing C, Dai HQ, Sempowski GD, Cronin K, Parks R, Ye AY, Mansouri K, Barr M, Pishesha N, Williams AC, Vieira Francisco L, Saminathan A, Peng H, Batra H, Bellusci L, Khurana S, Alam SM, Montefiori DC, Saunders KO, Tian M, Ploegh H, Kirchhausen T, Chen B, Haynes BF, Alt FW
OpenAccess logo Sci Immunol 7 eadd5446 (2022)
PMID: 35951767
Related structures: EMD-26677

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-534951 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Spike glycoprotein Chain: A
Molecule details ›
Chain: A
Length: 1310 amino acids
Theoretical weight: 144.86 KDa
Source organism: Severe acute respiratory syndrome coronavirus
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 1-1273; Coverage: 100%)
Gene names: 2, S
Sequence domains:
SP1-77 Fab heavy chain Chain: H
Molecule details ›
Chain: H
Length: 451 amino acids
Theoretical weight: 49.67 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
SP1-77 Fab light chain Chain: L
Molecule details ›
Chain: L
Length: 213 amino acids
Theoretical weight: 23.29 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-26677
Expression system: Homo sapiens

Quick links

Citations

7 review citations

Broadly neutralizing antibodies to SARS-CoV-2 and other human coronaviruses.
Chen et al. (2023)
6 more

1 mention without citation

Structural basis for broad neutralization of human antibody against Omicron sublineages and evasion by XBB variant.
Sun et al. (2023)