4HLZ

Crystal Structure of Fab C179 in Complex with a H2N2 influenza virus hemagglutinin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

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Literature

Structure of a classical broadly neutralizing stem antibody in complex with a pandemic h2 influenza virus hemagglutinin.

Dreyfus, C., Ekiert, D.C., Wilson, I.A.

(2013) J Virol 87: 7149-7154

  • DOI: 10.1128/JVI.02975-12
  • Primary Citation of Related Structures:  
    4HLZ

  • PubMed Abstract: 

    • We report the structural characterization of the first antibody identified to cross-neutralize multiple subtypes of influenza A viruses. The crystal structure of mouse antibody C179 bound to the pandemic 1957 H2N2 hemagglutinin (HA) reveals that it targets an epitope on the HA stem similar to those targeted by the recently identified human broadly neutralizing antibodies ...

    We report the structural characterization of the first antibody identified to cross-neutralize multiple subtypes of influenza A viruses. The crystal structure of mouse antibody C179 bound to the pandemic 1957 H2N2 hemagglutinin (HA) reveals that it targets an epitope on the HA stem similar to those targeted by the recently identified human broadly neutralizing antibodies. C179 also inhibits the low-pH conformational change of the HA but uses a different angle of approach and both heavy and light chains.

    Organizational Affiliation: 

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA1A, C, E327Influenza A virus (A/Japan/305/1957(H2N2))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for C7S226 (Influenza A virus (strain A/Japan/305/1957 H2N2))
Explore C7S226 
Go to UniProtKB:  C7S226
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7S226
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA2B, D, F174Influenza A virus (A/Japan/305/1957(H2N2))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for C7S226 (Influenza A virus (strain A/Japan/305/1957 H2N2))
Explore C7S226 
Go to UniProtKB:  C7S226
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7S226
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab C179 heavy chainG, I, K229Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Fab C179 light chainH, J, L214Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM, P 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseN 4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseO, Q 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
R [auth A],
S [auth A],
U [auth B],
W [auth E],
Z [auth F]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
SO4
Query on SO4
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AA [auth H],
BA [auth J],
DA [auth L],
T [auth B],
V [auth D],
AA [auth H],
BA [auth J],
DA [auth L],
T [auth B],
V [auth D],
X [auth E],
Y [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
CA [auth J]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.58α = 90
b = 150.78β = 90
c = 217.78γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary