4HG4

Crystal structure of Fab 2G1 in complex with a H2N2 influenza virus hemagglutinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 

wwPDB Validation 3D Report Full Report



Literature

A recurring motif for antibody recognition of the receptor-binding site of influenza hemagglutinin.

Xu, R.Krause, J.C.McBride, R.Paulson, J.C.Crowe, J.E.Wilson, I.A.

(2013) Nat Struct Mol Biol 20: 363-370

  • DOI: 10.1038/nsmb.2500
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Influenza virus hemagglutinin (HA) mediates receptor binding and viral entry during influenza infection. The development of receptor analogs as viral-entry blockers has not been successful, which suggests that sialic acid may not be an ideal scaffold ...

    Influenza virus hemagglutinin (HA) mediates receptor binding and viral entry during influenza infection. The development of receptor analogs as viral-entry blockers has not been successful, which suggests that sialic acid may not be an ideal scaffold to obtain broad, potent HA inhibitors. Here, we report crystal structures of Fab fragments from three human antibodies that neutralize the 1957 pandemic H2N2 influenza virus in complex with H2 HA. All three antibodies use an aromatic residue to plug a conserved cavity in the HA receptor-binding site. Each antibody interacts with the absolutely conserved HA1 Trp153 at the cavity base through π-π stacking with the signature Phe54 of two VH1-69-encoded antibodies or a tyrosine from HCDR3 in the other antibody. This highly conserved interaction can be used as a starting point to design inhibitors targeting this conserved hydrophobic pocket in influenza viruses.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA1A, B, C, D, E, F, G, H, I327Influenza A virus (A/Japan/305+/1957(H2N2))Mutation(s): 0 
Gene Names: HA
Find proteins for P03451 (Influenza A virus (strain A/Japan/305/1957 H2N2))
Explore P03451 
Go to UniProtKB:  P03451
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA2a, b, c, d, e, f, g, h, i174Influenza A virus (A/Japan/305+/1957(H2N2))Mutation(s): 0 
Gene Names: HA
Find proteins for P03451 (Influenza A virus (strain A/Japan/305/1957 H2N2))
Explore P03451 
Go to UniProtKB:  P03451
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab 2G1 heavy chainJ, L, N, P, R, T, V, X, Z223Homo sapiensMutation(s): 0 
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Fab 2G1 light chainK, M, O, Q, S, U, W, Y, z214Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
j, k, m, n, o, q, r, s, t
2 N-Glycosylation
Entity ID: 6
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
l, p
3 N-Glycosylation
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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A, C, E, F
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: 3.20 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.842α = 90
b = 133.143β = 90
c = 812.99γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2012-10-06 
  • Released Date: 2013-02-13 
  • Deposition Author(s): Xu, R., Wilson, I.A.

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary