5W6R

Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP141099 (P6)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.731 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 pote ...

    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

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
A, C, E, G
326Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)Mutation(s): 0 
Gene Names: HA
Find proteins for P03452 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Go to UniProtKB:  P03452
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
B, D, F, H
176Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)Mutation(s): 0 
Gene Names: HA
Find proteins for P03452 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Go to UniProtKB:  P03452
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ACE-PH8-ORN-LEU-GLU-TYR-PHE-GLU-TRP-LEU-SER-9WV
M, O, N, Q
12N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
9WV
Query on 9WV
M, N, O, Q
L-peptide linkingC6 H13 N3 O3ALA
PH8
Query on PH8
M, N, O, Q
L-PEPTIDE LINKINGC11 H15 N O2

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ORN
Query on ORN
M, N, O, Q
L-PEPTIDE LINKINGC5 H12 N2 O2ALA
ACE
Query on ACE
M, N, O, Q
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.731 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.198 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 234.461α = 90.00
b = 234.461β = 90.00
c = 144.560γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR56 AI117675

Revision History 

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-10-25
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Database references