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 

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

Macromolecule Content

• Total Structure Weight: 68.42 kDa 
• Atom Count: 4608 
• Modelled Residue Count: 575 
• Deposited Residue Count: 603 
• Unique protein chains: 3

3R2X

Crystal structure of the de novo designed binding protein HB36.3 in complex the the 1918 influenza virus hemagglutinin

• PDB DOI: 10.2210/pdb3R2X/pdb

• Classification: VIRAL PROTEIN/DE NOVO PROTEIN
• Organism(s): Influenza A virus (A/Brevig Mission/1/1918(H1N1)), synthetic construct
• Expression System: Trichoplusia ni, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-03-14 Released: 2011-05-11 
• Deposition Author(s): Ekiert, D.C., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 

Literature

Computational design of proteins targeting the conserved stem region of influenza hemagglutinin.

Fleishman, S.J., Whitehead, T.A., Ekiert, D.C., Dreyfus, C., Corn, J.E., Strauch, E.M., Wilson, I.A., Baker, D.

(2011) Science 332: 816-821

• PubMed: 21566186 
• DOI: 10.1126/science.1202617
• Primary Citation of Related Structures:  
  3R2X


• PubMed Abstract: 
  

We describe a general computational method for designing proteins that bind a surface patch of interest on a target macromolecule. Favorable interactions between disembodied amino acid residues and the target surface are identified and used to anchor de novo designed interfaces. The method was used to design proteins that bind a conserved surface patch on the stem of the influenza hemagglutinin (HA) from the 1918 H1N1 pandemic virus. After affinity maturation, two of the designed proteins, HB36 and HB80, bind H1 and H5 HAs with low nanomolar affinity. Further, HB80 inhibits the HA fusogenic conformational changes induced at low pH. The crystal structure of HB36 in complex with 1918/H1 HA revealed that the actual binding interface is nearly identical to that in the computational design model. Such designed binding proteins may be useful for both diagnostics and therapeutics.

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Organizational Affiliation: 

Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A	331	Influenza A virus (A/Brevig Mission/1/1918(H1N1))	Mutation(s): 0  Gene Names: HA, hemagglutinin
UniProt
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)) Explore Q9WFX3  Go to UniProtKB:  Q9WFX3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B	179	Influenza A virus (A/Brevig Mission/1/1918(H1N1))	Mutation(s): 0  Gene Names: HA, hemagglutinin
UniProt
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)) Explore Q9WFX3  Go to UniProtKB:  Q9WFX3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HB36.3, designed hemagglutinin binding protein	C	93	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.054	α = 90
b = 130.054	β = 90
c = 313.735	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
XPREP	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-03-14 
• Released Date: 2011-05-11 
Deposition Author(s): Ekiert, D.C., Wilson, I.A.

Revision History  

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary