5UGY

Influenza hemagglutinin in complex with a neutralizing antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.260 

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Literature

Broadly neutralizing human antibody that recognizes the receptor-binding pocket of influenza virus hemagglutinin.

Whittle, J.R.Zhang, R.Khurana, S.King, L.R.Manischewitz, J.Golding, H.Dormitzer, P.R.Haynes, B.F.Walter, E.B.Moody, M.A.Kepler, T.B.Liao, H.X.Harrison, S.C.

(2011) Proc Natl Acad Sci U S A 108: 14216-14221

  • DOI: 10.1073/pnas.1111497108
  • Primary Citation of Related Structures:  
    5UGY

  • PubMed Abstract: 
  • Seasonal antigenic drift of circulating influenza virus leads to a requirement for frequent changes in vaccine composition, because exposure or vaccination elicits human antibodies with limited cross-neutralization of drifted strains. We describe a human monoclonal antibody, CH65, obtained by isolating rearranged heavy- and light-chain genes from sorted single plasma cells, coming from a subject immunized with the 2007 trivalent influenza vaccine ...

    Seasonal antigenic drift of circulating influenza virus leads to a requirement for frequent changes in vaccine composition, because exposure or vaccination elicits human antibodies with limited cross-neutralization of drifted strains. We describe a human monoclonal antibody, CH65, obtained by isolating rearranged heavy- and light-chain genes from sorted single plasma cells, coming from a subject immunized with the 2007 trivalent influenza vaccine. The crystal structure of a complex of the hemagglutinin (HA) from H1N1 strain A/Solomon Islands/3/2006 with the Fab of CH65 shows that the tip of the CH65 heavy-chain complementarity determining region 3 (CDR3) inserts into the receptor binding pocket on HA1, mimicking in many respects the interaction of the physiological receptor, sialic acid. CH65 neutralizes infectivity of 30 out of 36 H1N1 strains tested. The resistant strains have a single-residue insertion near the rim of the sialic-acid pocket. We conclude that broad neutralization of influenza virus can be achieved by antibodies with contacts that mimic those of the receptor.


    Organizational Affiliation

    Laboratory of Molecular Medicine, Children's Hospital, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA 02115, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA1A, C, E323Influenza A virus (A/Solomon Islands/3/2006(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A7Y8A6 (Influenza A virus)
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Go to UniProtKB:  A7Y8A6
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UniProt GroupA7Y8A6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA2B, D, F173Influenza A virus (A/Solomon Islands/3/2006(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A7Y8I1 (Influenza A virus)
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UniProt GroupA7Y8I1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CH65 heavy chainG [auth H],
H [auth I],
I [auth J]
227Homo sapiensMutation(s): 0 
UniProt
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UniProt GroupS6C4S0
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CH65 light chainJ [auth L],
K [auth M],
L [auth N]
210Homo sapiensMutation(s): 0 
Gene Names: IGL@
UniProt
Find proteins for Q8N355 (Homo sapiens)
Explore Q8N355 
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UniProt GroupQ8N355
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Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M [auth G],
O,
P,
R,
S,
M [auth G],
O,
P,
R,
S,
U
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseN [auth K],
Q,
T
3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth E],
V [auth A],
W [auth A],
X [auth C],
Y [auth C],
AA [auth E],
V [auth A],
W [auth A],
X [auth C],
Y [auth C],
Z [auth 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: 2.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.260 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.824α = 90
b = 192.19β = 90
c = 333.219γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary