4EEF

Crystal structure of the designed inhibitor protein F-HB80.4 in complex with the 1918 influenza virus hemagglutinin.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

wwPDB Validation 3D Report Full Report



Literature

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing.

Whitehead, T.A., Chevalier, A., Song, Y., Dreyfus, C., Fleishman, S.J., De Mattos, C., Myers, C.A., Kamisetty, H., Blair, P., Wilson, I.A., Baker, D.

(2012) Nat Biotechnol 30: 543-548

  • DOI: 10.1038/nbt.2214
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • We show that comprehensive sequence-function maps obtained by deep sequencing can be used to reprogram interaction specificity and to leapfrog over bottlenecks in affinity maturation by combining many individually small contributions not detectable i ...

    We show that comprehensive sequence-function maps obtained by deep sequencing can be used to reprogram interaction specificity and to leapfrog over bottlenecks in affinity maturation by combining many individually small contributions not detectable in conventional approaches. We use this approach to optimize two computationally designed inhibitors against H1N1 influenza hemagglutinin and, in both cases, obtain variants with subnanomolar binding affinity. The most potent of these, a 51-residue protein, is broadly cross-reactive against all influenza group 1 hemagglutinins, including human H2, and neutralizes H1N1 viruses with a potency that rivals that of several human monoclonal antibodies, demonstrating that computational design followed by comprehensive energy landscape mapping can generate proteins with potential therapeutic utility.

    Organizational Affiliation: 

    Department of Biochemistry, University of Washington, Seattle, Washington, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA1 chain
A, C, E
331Influenza A virus (A/Brevig Mission/1/1918(H1N1))Mutation(s): 0 
Gene Names: HA, hemagglutinin
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1))
Go to UniProtKB:  Q9WFX3
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA2 chain
B, D, F
179Influenza A virus (A/Brevig Mission/1/1918(H1N1))Mutation(s): 0 
Gene Names: HA, hemagglutinin
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1))
Go to UniProtKB:  Q9WFX3
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
F-HB80.4, DESIGNED HEMAGGLUTININ BINDING PROTEIN
G, H, I
74synthetic constructMutation(s): 0 
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download CCD File 
A, C, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
BMA
Query on BMA
Download CCD File 
A, C, E
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.333α = 90
b = 126.151β = 90
c = 243.29γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
XPREPdata reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-27
    Type: Initial release