› 5y9c

X-ray diffraction
3.44Å resolution

Crystal structure of HPV58 pentamer in complex with the Fab fragment of antibody A12A3

Released:
DOI: 10.2210/pdb5y9c/pdb
PDB entry 5y9c coloured by chain, front view.
PDB entry 5y9c coloured by chain, side view.
PDB entry 5y9c coloured by chain, top view.
Source organisms:
Primary publication:
Crystal Structures of Two Immune Complexes Identify Determinants for Viral Infectivity and Type-Specific Neutralization of Human Papillomavirus.
Li Z, Wang D, Gu Y, Song S, He M, Shi J, Liu X, Wei S, Li J, Yu H, Zheng Q, Yan X, Baker TS, Zhang J, McLellan JS, Li S, Xia N
mBio 8 (2017)
PMID: 28951471

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-210908 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Major capsid protein L1 Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 490 amino acids
Theoretical weight: 55.25 KDa
Source organism: human papillomavirus 58
Expression system: Escherichia coli
UniProt:
  • Canonical: P26535 (Residues: 36-524; Coverage: 93%)
Gene name: L1
Sequence domains: L1 (late) protein
Structure domains: Major capsid L1 (late) superfamily, Papillomavirus
heavy chain of Fab fragment of antibody A12A3 Chain: H
Molecule details ›
Chain: H
Length: 216 amino acids
Theoretical weight: 23.37 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins
light chain of Fab fragment of antibody A12A3 Chain: L
Molecule details ›
Chain: L
Length: 213 amino acids
Theoretical weight: 23.73 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P21
Unit cell:
a: 121.571Å b: 102.6Å c: 138.032Å
α: 90° β: 114.52° γ: 90°
R-values:
R R work R free
0.205 0.202 0.249
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Virus-like particles: preparation, immunogenicity and their roles as nanovaccines and drug nanocarriers.
Nooraei et al. (2021)
2 more

2 mentions without citation

Crystal Structures of Two Immune Complexes Identify Determinants for Viral Infectivity and Type-Specific Neutralization of Human Papillomavirus.
Li et al. (2017)
1 more