5KUY

Influenza hemagglutinin H3 A/Hong Kong/1/1968 in complex with designed inhibitor protein HSB.2A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

wwPDB Validation 3D Report Full Report



Literature

Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site.

Strauch, E.M.Bernard, S.M.La, D.Bohn, A.J.Lee, P.S.Anderson, C.E.Nieusma, T.Holstein, C.A.Garcia, N.K.Hooper, K.A.Ravichandran, R.Nelson, J.W.Sheffler, W.Bloom, J.D.Lee, K.K.Ward, A.B.Yager, P.Fuller, D.H.Wilson, I.A.Baker, D.

(2017) Nat Biotechnol 35: 667-671

  • DOI: 10.1038/nbt.3907
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Many viral surface glycoproteins and cell surface receptors are homo-oligomers, and thus can potentially be targeted by geometrically matched homo-oligomers that engage all subunits simultaneously to attain high avidity and/or lock subunits together. ...

    Many viral surface glycoproteins and cell surface receptors are homo-oligomers, and thus can potentially be targeted by geometrically matched homo-oligomers that engage all subunits simultaneously to attain high avidity and/or lock subunits together. The adaptive immune system cannot generally employ this strategy since the individual antibody binding sites are not arranged with appropriate geometry to simultaneously engage multiple sites in a single target homo-oligomer. We describe a general strategy for the computational design of homo-oligomeric protein assemblies with binding functionality precisely matched to homo-oligomeric target sites. In the first step, a small protein is designed that binds a single site on the target. In the second step, the designed protein is assembled into a homo-oligomer such that the designed binding sites are aligned with the target sites. We use this approach to design high-avidity trimeric proteins that bind influenza A hemagglutinin (HA) at its conserved receptor binding site. The designed trimers can both capture and detect HA in a paper-based diagnostic format, neutralizes influenza in cell culture, and completely protects mice when given as a single dose 24 h before or after challenge with influenza.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA1A, C, E323Influenza A virus (A/Hong Kong/1/1968(H3N2))Mutation(s): 0 
Gene Names: HA
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2))
Explore Q91MA7 
Go to UniProtKB:  Q91MA7
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA2B, D, F177Influenza A virus (A/Hong Kong/1/1968(H3N2))Mutation(s): 1 
Gene Names: HA
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2))
Explore Q91MA7 
Go to UniProtKB:  Q91MA7
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Designed influenza inhibitor HSB.2AG, H, I97synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J, K, L, M, O
2 N-Glycosylation
Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
N
3 N-Glycosylation
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B, D, E
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.259α = 90
b = 219.322β = 117.78
c = 104.524γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR56 AI117675

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 1.2: 2017-07-26
    Changes: Author supporting evidence, Database references
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary