5W5U

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

• PDB DOI: https://doi.org/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 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
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: 4,172 
• Modelled Residue Count: 505 
• Deposited Residue Count: 514 
• Unique protein chains: 3

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	Length	2D Diagram	Glycosylation	3D Interactions
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

• 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
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2023-11-15
  Changes: Data collection