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: 2.704 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

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

  • 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 (strain A/Brevig Mission/1/1918 H1N1)Mutation(s): 0 
Gene Names: HA
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1))
Go to UniProtKB:  Q9WFX3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA2 chain
B, D, F
179Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)Mutation(s): 0 
Gene Names: HA
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1))
Go to UniProtKB:  Q9WFX3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
F-HB80.4, DESIGNED HEMAGGLUTININ BINDING PROTEIN
G, H, I
74N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA
Download SDF File 
Download CCD File 
A, C, E
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, C, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.704 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.333α = 90.00
b = 126.151β = 90.00
c = 243.290γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XPREPdata reduction
Blu-Icedata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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