› 7e3o

X-ray diffraction
2.51Å resolution

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody nCoV617

Released:
DOI: 10.2210/pdb7e3o/pdb
PDB entry 7e3o coloured by chain, front view.
PDB entry 7e3o coloured by chain, side view.
PDB entry 7e3o coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis of a Human Neutralizing Antibody Specific to the SARS-CoV-2 Spike Protein Receptor-Binding Domain.
Yang M, Li J, Huang Z, Li H, Wang Y, Wang X, Kang S, Huang X, Wu C, Liu T, Jia Z, Liang J, Yuan X, He S, Chen X, Zhou Z, Chen Q, Liu S, Li J, Zheng H, Liu X, Li K, Yao X, Lang B, Liu L, Liao HX, Chen S
OpenAccess logo Microbiol Spectr 9 e0135221 (2021)
PMID: 34643438

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-209741 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
nCoV617 Light Chain Chain: L
Molecule details ›
Chain: L
Length: 215 amino acids
Theoretical weight: 22.55 KDa
Source organism: Homo sapiens
Expression system: Mammalian expression vector HA-MCS-pcDNA3.1
nCoV617 Heigh Chain Chain: H
Molecule details ›
Chain: H
Length: 227 amino acids
Theoretical weight: 24.28 KDa
Source organism: Homo sapiens
Expression system: Mammalian expression vector HA-MCS-pcDNA3.1
Spike protein S1 Chain: R
Molecule details ›
Chain: R
Length: 199 amino acids
Theoretical weight: 22.55 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: unidentified baculovirus
UniProt:
  • Canonical: P0DTC2 (Residues: 337-527; Coverage: 15%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 165.093Å b: 60.367Å c: 77.296Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.204 0.259
Expression systems:
  • Mammalian expression vector HA-MCS-pcDNA3.1
  • unidentified baculovirus

Quick links

Citations

2 review citations

SARS-CoV-2: Recent Variants and Clinical Efficacy of Antibody-Based Therapy.
Singh et al. (2022)
1 more

5 mentions without citation

Main and papain-like proteases as prospective targets for pharmacological treatment of coronavirus SARS-CoV-2.
Yevsieieva et al. (2023)
4 more