› 8dgx

X-ray diffraction
2.89Å resolution

Crystal structure of MERS-CoV spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC68.109 isolated from a vaccinated COVID-19 convalescent

Released:
DOI: 10.2210/pdb8dgx/pdb
PDB entry 8dgx coloured by chain, front view.
PDB entry 8dgx coloured by chain, side view.
PDB entry 8dgx coloured by chain, top view.
Source organisms:
Primary publication:
Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause deadly disease.
Zhou P, Song G, Liu H, Yuan M, He WT, Beutler N, Zhu X, Tse LV, Martinez DR, Schäfer A, Anzanello F, Yong P, Peng L, Dueker K, Musharrafieh R, Callaghan S, Capozzola T, Limbo O, Parren M, Garcia E, Rawlings SA, Smith DM, Nemazee D, Jardine JG, Safonova Y, Briney B, Rogers TF, Wilson IA, Baric RS, Gralinski LE, Burton DR, Andrabi R
OpenAccess logo Immunity (2023)
PMID: 36889306

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-516636 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Antibody CC68.109 Fab heavy chain Chains: A, H
Molecule details ›
Chains: A, H
Length: 221 amino acids
Theoretical weight: 23.61 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Antibody CC68.109 Fab light chain Chains: B, L
Molecule details ›
Chains: B, L
Length: 218 amino acids
Theoretical weight: 23.87 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Spike protein S2' Chains: C, D
Molecule details ›
Chains: C, D
Length: 27 amino acids
Theoretical weight: 2.99 KDa
Source organism: Betacoronavirus England 1
Expression system: Not provided
UniProt:
  • Canonical: K9N5Q8 (Residues: 1221-1247; Coverage: 2%)
Gene names: 3, S

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P21
Unit cell:
a: 68.997Å b: 66.499Å c: 94.386Å
α: 90° β: 107.76° γ: 90°
R-values:
R R work R free
0.235 0.233 0.28
Expression systems:
  • Homo sapiens
  • Not provided

Quick links

Citations

13 review citations

Monoclonal antibody therapies against SARS-CoV-2.
Focosi et al. (2022)
12 more

1 mention without citation

Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause deadly disease.
Zhou et al. (2023)