5W42

Crystal structure of human monoclonal antibody H3v-47 in complex with influenza virus hemagglutinin from A/Minnesota/11/2010 (H3N2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.57 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A multifunctional human monoclonal neutralizing antibody that targets a unique conserved epitope on influenza HA.

Bangaru, S.Zhang, H.Gilchuk, I.M.Voss, T.G.Irving, R.P.Gilchuk, P.Matta, P.Zhu, X.Lang, S.Nieusma, T.Richt, J.A.Albrecht, R.A.Vanderven, H.A.Bombardi, R.Kent, S.J.Ward, A.B.Wilson, I.A.Crowe, J.E.

(2018) Nat Commun 9: 2669-2669

  • DOI: 10.1038/s41467-018-04704-9
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The high rate of antigenic drift in seasonal influenza viruses necessitates frequent changes in vaccine composition. Recent seasonal H3 vaccines do not protect against swine-origin H3N2 variant (H3N2v) strains that recently have caused severe human i ...

    The high rate of antigenic drift in seasonal influenza viruses necessitates frequent changes in vaccine composition. Recent seasonal H3 vaccines do not protect against swine-origin H3N2 variant (H3N2v) strains that recently have caused severe human infections. Here, we report a human V H 1-69 gene-encoded monoclonal antibody (mAb) designated H3v-47 that exhibits potent cross-reactive neutralization activity against human and swine H3N2 viruses that circulated since 1989. The crystal structure and electron microscopy reconstruction of H3v-47 Fab with the H3N2v hemagglutinin (HA) identify a unique epitope spanning the vestigial esterase and receptor-binding subdomains that is distinct from that of any known neutralizing antibody for influenza A H3 viruses. MAb H3v-47 functions largely by blocking viral egress from infected cells. Interestingly, H3v-47 also engages Fcγ receptor and mediates antibody dependent cellular cytotoxicity (ADCC). This newly identified conserved epitope can be used in design of novel immunogens for development of broadly protective H3 vaccines.


    Organizational Affiliation

    Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA. james.crowe@vanderbilt.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
A
329Influenza A virus (A/swine/Minnesota/A01134337/2010(H3N2))Mutation(s): 0 
Gene Names: HA
Find proteins for I0AXC3 (Influenza A virus)
Go to UniProtKB:  I0AXC3
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
B
174Influenza A virus (A/swine/Minnesota/A01134337/2010(H3N2))Mutation(s): 0 
Gene Names: HA
Find proteins for I0AXC3 (Influenza A virus)
Go to UniProtKB:  I0AXC3
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab H3v-47 heavy chain
H
236Homo sapiensMutation(s): 0 
Gene Names: DKFZp686P15220
Find proteins for Q6N089 (Homo sapiens)
Go to UniProtKB:  Q6N089
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Fab H3v-47 light chain
L
214Homo sapiensMutation(s): 0 
Find proteins for Q8TCD0 (Homo sapiens)
Go to UniProtKB:  Q8TCD0
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.57 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 194.622α = 90
b = 194.622β = 90
c = 194.622γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data 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 StatesU19 AI117905

Revision History 

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Author supporting evidence