6TVB

Crystal structure of the haemagglutinin from a transmissible H10N7 seal influenza virus isolated in Netherland in complex with human receptor analogue 6'-SLN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 

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Ligand Structure Quality Assessment 


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Literature

Hemagglutinin Traits Determine Transmission of Avian A/H10N7 Influenza Virus between Mammals.

Herfst, S.Zhang, J.Richard, M.McBride, R.Lexmond, P.Bestebroer, T.M.Spronken, M.I.J.de Meulder, D.van den Brand, J.M.Rosu, M.E.Martin, S.R.Gamblin, S.J.Xiong, X.Peng, W.Bodewes, R.van der Vries, E.Osterhaus, A.D.M.E.Paulson, J.C.Skehel, J.J.Fouchier, R.A.M.

(2020) Cell Host Microbe 28: 602-613.e7

  • DOI: 10.1016/j.chom.2020.08.011
  • Primary Citation of Related Structures:  
    6TJW, 6TJY, 6TVA, 6TVB, 6TVC, 6TVD, 6TVF, 6TVR, 6TVS, 6TVT, 6TWH, 6TWI, 6TWS, 6TWV, 6TXO, 6TY1

  • PubMed Abstract: 
  • In 2014, an outbreak of avian A/H10N7 influenza virus occurred among seals along North-European coastal waters, significantly impacting seal populations. Here, we examine the cross-species transmission and mammalian adaptation of this influenza A virus, revealing changes in the hemagglutinin surface protein that increase stability and receptor binding ...

    In 2014, an outbreak of avian A/H10N7 influenza virus occurred among seals along North-European coastal waters, significantly impacting seal populations. Here, we examine the cross-species transmission and mammalian adaptation of this influenza A virus, revealing changes in the hemagglutinin surface protein that increase stability and receptor binding. The seal A/H10N7 virus was aerosol or respiratory droplet transmissible between ferrets. Compared with avian H10 hemagglutinin, seal H10 hemagglutinin showed stronger binding to the human-type sialic acid receptor, with preferential binding to α2,6-linked sialic acids on long extended branches. In X-ray structures, changes in the 220-loop of the receptor-binding pocket caused similar interactions with human receptor as seen for pandemic strains. Two substitutions made seal H10 hemagglutinin more stable than avian H10 hemagglutinin and similar to human hemagglutinin. Consequently, identification of avian-origin influenza viruses across mammals appears critical to detect influenza A viruses posing a major threat to humans and other mammals.


    Organizational Affiliation

    Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC University Medical Center, 3015GE, Rotterdam, the Netherlands. Electronic address: r.fouchier@erasmusmc.nl.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA1A, C, E325Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A0A7HR51 (Influenza A virus)
Explore A0A0A7HR51 
Go to UniProtKB:  A0A0A7HR51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A7HR51
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA2B, D, F177Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A0A7HR51 (Influenza A virus)
Explore A0A0A7HR51 
Go to UniProtKB:  A0A0A7HR51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A7HR51
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG, H, I 3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G73578JC
GlyCosmos:  G73578JC
GlyGen:  G73578JC
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
L [auth B],
M [auth B],
X [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth F],
BA [auth F],
CA [auth F],
J [auth A],
K [auth A],
AA [auth F],
BA [auth F],
CA [auth F],
J [auth A],
K [auth A],
N [auth B],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
Y [auth D],
Z [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.46α = 90
b = 213.11β = 98.28
c = 76.58γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release