Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 9-mer - A3B3C3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A3B3C1D1E1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 59.66 kDa 
• Atom Count: 4172 
• Modelled Residue Count: 505 
• Deposited 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)

• PDB DOI: 10.2210/pdb5W5U/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Puerto Rico/8/1934(H1N1)), synthetic construct
• Expression System: Trichoplusia ni
• Mutation(s): No 


• 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 (NIH/NIAID)

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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 

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:  
  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. 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: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A	326	Influenza 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B	176	Influenza 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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-PH8-ORN-MLE-GLU-TYR-PHE-GLU-TRP-LEU-SER-BAL	C [auth D]	12	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], G [auth A], H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CL	I [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLE	C [auth D]	L-PEPTIDE LINKING	C7 H15 N O2		LEU
ORN	C [auth D]	L-PEPTIDE LINKING	C5 H12 N2 O2		ALA

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 = 161.362	α = 90
b = 161.362	β = 90
c = 161.362	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
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 (NIH/NIAID)	United States	R56 AI117675

Revision History  

• 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