5W5U

Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP141037 (P4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

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This is version 2.0 of the entry. See complete history


Literature

Potent peptidic fusion inhibitors of influenza virus.

Kadam, R.U.Juraszek, J.Brandenburg, B.Buyck, C.Schepens, W.B.G.Kesteleyn, B.Stoops, B.Vreeken, R.J.Vermond, J.Goutier, W.Tang, C.Vogels, R.Friesen, R.H.E.Goudsmit, J.van Dongen, M.J.P.Wilson, I.A.

(2017) Science 358: 496-502

  • DOI: 10.1126/science.aan0516
  • Primary Citation of Related Structures:  
    5W5S, 5W5U, 5W6I, 5W6R, 5W6T, 5W6U

  • PubMed Abstract: 
  • Influenza therapeutics with new targets and mechanisms of action are urgently needed to combat potential pandemics, emerging viruses, and constantly mutating strains in circulation. We report here on the design and structural characterization of potent peptidic inhibitors of influenza hemagglutinin ...

    Influenza therapeutics with new targets and mechanisms of action are urgently needed to combat potential pandemics, emerging viruses, and constantly mutating strains in circulation. We report here on the design and structural characterization of potent peptidic inhibitors of influenza hemagglutinin. The peptide design was based on complementarity-determining region loops of human broadly neutralizing antibodies against the hemagglutinin (FI6v3 and CR9114). The optimized peptides exhibit nanomolar affinity and neutralization against influenza A group 1 viruses, including the 2009 H1N1 pandemic and avian H5N1 strains. The peptide inhibitors bind to the highly conserved stem epitope and block the low pH-induced conformational rearrangements associated with membrane fusion. These peptidic compounds and their advantageous biological properties should accelerate the development of new small molecule- and peptide-based therapeutics against influenza virus.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HemagglutininA326Influenza A virus (A/Puerto Rico/8/1934(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for P03452 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Explore P03452 
Go to UniProtKB:  P03452
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03452
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HemagglutininB176Influenza A virus (A/Puerto Rico/8/1934(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for P03452 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Explore P03452 
Go to UniProtKB:  P03452
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03452
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ACE-PH8-ORN-MLE-GLU-TYR-PHE-GLU-TRP-LEU-SER-BALC [auth D]12synthetic constructMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth C]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MLE
Query on MLE
C [auth D]L-PEPTIDE LINKINGC7 H15 N O2LEU
ORN
Query on ORN
C [auth D]L-PEPTIDE LINKINGC5 H12 N2 O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.362α = 90
b = 161.362β = 90
c = 161.362γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR56 AI117675

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-10-25
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Database references
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary