4FQR

Crystal structure of broadly neutralizing antibody C05 bound to H3 influenza hemagglutinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.309 
  • R-Value Observed: 0.310 

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Ligand Structure Quality Assessment 


This is version 3.1 of the entry. See complete history


Literature

Cross-neutralization of influenza A viruses mediated by a single antibody loop.

Ekiert, D.C.Kashyap, A.K.Steel, J.Rubrum, A.Bhabha, G.Khayat, R.Lee, J.H.Dillon, M.A.O'Neil, R.E.Faynboym, A.M.Horowitz, M.Horowitz, L.Ward, A.B.Palese, P.Webby, R.Lerner, R.A.Bhatt, R.R.Wilson, I.A.

(2012) Nature 489: 526-532

  • DOI: 10.1038/nature11414
  • Primary Citation of Related Structures:  
    4FQR, 4FNL, 4FNK, 4FP8

  • PubMed Abstract: 
  • Immune recognition of protein antigens relies on the combined interaction of multiple antibody loops, which provide a fairly large footprint and constrain the size and shape of protein surfaces that can be targeted. Single protein loops can mediate extremely high-affinity binding, but it is unclear whether such a mechanism is available to antibodies ...

    Immune recognition of protein antigens relies on the combined interaction of multiple antibody loops, which provide a fairly large footprint and constrain the size and shape of protein surfaces that can be targeted. Single protein loops can mediate extremely high-affinity binding, but it is unclear whether such a mechanism is available to antibodies. Here we report the isolation and characterization of an antibody called C05, which neutralizes strains from multiple subtypes of influenza A virus, including H1, H2 and H3. X-ray and electron microscopy structures show that C05 recognizes conserved elements of the receptor-binding site on the haemagglutinin surface glycoprotein. Recognition of the haemagglutinin receptor-binding site is dominated by a single heavy-chain complementarity-determining region 3 loop, with minor contacts from heavy-chain complementarity-determining region 1, and is sufficient to achieve nanomolar binding with a minimal footprint. Thus, binding predominantly with a single loop can allow antibodies to target small, conserved functional sites on otherwise hypervariable antigens.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA1 chain
A, C, E, G, I, K, M, O
A, C, E, G, I, K, M, O, Q, S, U, W
323Influenza A virus (A/Hong Kong/1/1968(H3N2))Mutation(s): 0 
Gene Names: HA
UniProt
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
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA2 chain
B, D, F, H, J, L, N, P
B, D, F, H, J, L, N, P, R, T, V, X
174Influenza A virus (A/Hong Kong/1/1968(H3N2))Mutation(s): 0 
Gene Names: HA
UniProt
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
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Broadly neutralizing antibody C05, heavy chain241Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Broadly neutralizing antibody C05, light chain214Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AB [auth 0], CB [auth 2], EB [auth 4], GB [auth 6], IB [auth 8], KB [auth AA], MB [auth CA], OB [auth EA]
AB [auth 0], CB [auth 2], EB [auth 4], GB [auth 6], IB [auth 8], KB [auth AA], MB [auth CA], OB [auth EA], QB [auth GA], SB [auth IA], WA [auth Y], YA [auth y]
4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BB [auth 1], DB [auth 3], FB [auth 5], HB [auth 7], JB [auth 9], LB [auth BA], NB [auth DA], PB [auth FA]
BB [auth 1], DB [auth 3], FB [auth 5], HB [auth 7], JB [auth 9], LB [auth BA], NB [auth DA], PB [auth FA], RB [auth HA], TB [auth JA], XA [auth Z], ZA [auth z]
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AC [auth G] , BC [auth G] , CC [auth H] , DC [auth I] , EC [auth J] , FC [auth K] , GC [auth L] , HC [auth M] , 
AC [auth G],  BC [auth G],  CC [auth H],  DC [auth I],  EC [auth J],  FC [auth K],  GC [auth L],  HC [auth M],  IC [auth M],  JC [auth N],  KC [auth O],  LC [auth O],  MC [auth P],  NC [auth Q],  OC [auth Q],  PC [auth R],  QC [auth S],  RC [auth S],  SC [auth T],  TC [auth U],  UB [auth A],  UC [auth U],  VB [auth B],  VC [auth V],  WB [auth C],  WC [auth W],  XB [auth D],  XC [auth X],  YB [auth E],  ZB [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
AA [auth c] , CA [auth e] , EA [auth g] , GA [auth i] , IA [auth k] , KA [auth m] , MA [auth o] , OA [auth q] , 
AA [auth c],  CA [auth e],  EA [auth g],  GA [auth i],  IA [auth k],  KA [auth m],  MA [auth o],  OA [auth q],  QA [auth s],  SA [auth u],  UA [auth w],  Y [auth a]
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.309 
  • R-Value Observed: 0.310 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.02α = 89.95
b = 158.62β = 85.44
c = 178.5γ = 84.37
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
XPREPdata reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2012-10-03
    Changes: Database references
  • Version 1.2: 2012-10-10
    Changes: Database references
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Polymer sequence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 3.1: 2021-05-19
    Changes: Derived calculations, Source and taxonomy, Structure summary