› 6ml8

X-ray diffraction
2.92Å resolution

Crystal structure of hemagglutinin from H1N1 Influenza A virus A/Denver/57 bound to the C05 antibody

Released:
DOI: 10.2210/pdb6ml8/pdb
PDB entry 6ml8 coloured by chain, front view.
PDB entry 6ml8 coloured by chain, side view.
PDB entry 6ml8 coloured by chain, top view.
Source organisms:
Primary publication:
Structural characterisation of hemagglutinin from seven Influenza A H1N1 strains reveal diversity in the C05 antibody recognition site.
Ghafoori SM, Petersen GF, Conrady DG, Calhoun BM, Stigliano MZZ, Baydo RO, Grice R, Abendroth J, Lorimer DD, Edwards TE, Forwood JK
Sci Rep 13 6940 (2023)
PMID: 37117205

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-233666 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (7 distinct):
Hemagglutinin HA1 chain Chain: A
Molecule details ›
Chain: A
Length: 330 amino acids
Theoretical weight: 37 KDa
Source organism: Influenza A virus (A/Denver/1957(H1N1))
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q2IBI1 (Residues: 18-343; Coverage: 58%)
Gene name: HA
Sequence domains: Haemagglutinin
Structure domains:
Hemagglutinin HA2 chain Chain: B
Molecule details ›
Chain: B
Length: 165 amino acids
Theoretical weight: 18.95 KDa
Source organism: Influenza A virus (A/Denver/1957(H1N1))
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q2IBI1 (Residues: 344-508; Coverage: 29%)
Gene name: HA
Sequence domains: Haemagglutinin
Structure domains: Hemagglutinin Ectodomain; Chain B
C05 antibody Fab heavy chain Chain: H
Molecule details ›
Chain: H
Length: 247 amino acids
Theoretical weight: 26.32 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
C05 antibody Fab light chain Chain: L
Molecule details ›
Chain: L
Length: 214 amino acids
Theoretical weight: 23.37 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P321
Unit cell:
a: 118.46Å b: 118.46Å c: 162.44Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.204 0.201 0.264
Expression systems:
  • Trichoplusia ni
  • Homo sapiens

Quick links

Citations

3 mentions without citation

iBRAB: In silico based-designed broad-spectrum Fab against H1N1 influenza A virus.
Do et al. (2020)
2 more