Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 59673.55 
• Atom Count: 4115 
• Residue Count: 514 
• Unique protein chains: 3

5W5U

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

• DOI: 10.2210/pdb5W5U/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
• Expression System: Trichoplusia ni


• Deposited: 2017-06-15 Released: 2017-10-04 
• Deposition Author(s): Wilson, I.A., Kadam, R.U.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.461 Å
• R-Value Free: 0.251 
• R-Value Work: 0.210 

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

• PubMed: 28971971 
• DOI: 10.1126/science.aan0516
• Primary Citation of Related Structures:  
  5W6U, 5W6T, 5W6R, 5W6I, 5W5S


• 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. 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Hemagglutinin	A	326	Influenza 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
Molecule	Chains	Sequence Length	Organism	Details
Hemagglutinin	B	176	Influenza 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
Molecule	Chains	Sequence Length	Organism	Details
ACE-PH8-ORN-MLE-GLU-TYR-PHE-GLU-TRP-LEU-SER-BAL	D	12	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NAG	A, B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BAL	D	peptide-like	C3 H7 N O2		--
MLE	D	L-PEPTIDE LINKING	C7 H15 N O2		LEU
PH8	D	L-PEPTIDE LINKING	C11 H15 N O2		--
ORN	D	L-PEPTIDE LINKING	C5 H12 N2 O2		ALA
ACE	D	NON-POLYMER	C2 H4 O		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.461 Å
• R-Value Free: 0.251 
• R-Value Work: 0.210 
• Space Group: I 2₁ 3

Unit Cell:

Length (Å)	Angle (°)
a = 161.362	α = 90.00
b = 161.362	β = 90.00
c = 161.362	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-06-15 
• Released Date: 2017-10-04 
• Deposition Author(s): Wilson, I.A., Kadam, R.U.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases	United States	R56 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