5UMN

Crystal structure of C05 VPGSGW mutant bound to H3 influenza hemagglutinin, HA1 subunit

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

In vitro evolution of an influenza broadly neutralizing antibody is modulated by hemagglutinin receptor specificity.

Wu, N.C., Grande, G., Turner, H.L., Ward, A.B., Xie, J., Lerner, R.A., Wilson, I.A.

(2017) Nat Commun 8: 15371-15371

  • DOI: 10.1038/ncomms15371
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • The relatively recent discovery and characterization of human broadly neutralizing antibodies (bnAbs) against influenza virus provide valuable insights into antiviral and vaccine development. However, the factors that influence the evolution of high- ...

    The relatively recent discovery and characterization of human broadly neutralizing antibodies (bnAbs) against influenza virus provide valuable insights into antiviral and vaccine development. However, the factors that influence the evolution of high-affinity bnAbs remain elusive. We therefore explore the functional sequence space of bnAb C05, which targets the receptor-binding site (RBS) of influenza haemagglutinin (HA) via a long CDR H3. We combine saturation mutagenesis with yeast display to enrich for C05 variants of CDR H3 that bind to H1 and H3 HAs. The C05 variants evolve up to 20-fold higher affinity but increase specificity to each HA subtype used in the selection. Structural analysis reveals that the fine specificity is strongly influenced by a highly conserved substitution that regulates receptor binding in different subtypes. Overall, this study suggests that subtle natural variations in the HA RBS between subtypes and species may differentially influence the evolution of high-affinity bnAbs.

    Organizational Affiliation: 

    The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HemagglutininA, B274Influenza A virus (A/Hong Kong/1/1968(H3N2))Mutation(s): 0 
Gene Names: HA
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2))
Explore Q91MA7 
Go to UniProtKB:  Q91MA7
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antibody C05 VPGSGW mutant, heavy chainC, E247Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Antibody C05, light chainD, F214Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE
Download CCD File 
A, B
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N		 Ligand Interaction
NAG
Query on NAG
Download CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
FLC
Query on FLC
Download CCD File 
C
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K		 Ligand Interaction
NA
Query on NA
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.344α = 90
b = 88.344β = 90
c = 255.038γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-01-27 
  • Released Date: 2017-05-24 
    • Deposition Author(s): Wu, N.C., Wilson, I.A.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR56 AI117675

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-05-31
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary