4XKF

Crystal structure of hemagglutinin from Taiwan (2013) H6N1 influenza virus in complex with LSTa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structure and Receptor Binding of the Hemagglutinin from a Human H6N1 Influenza Virus.

Tzarum, N.de Vries, R.P.Zhu, X.Yu, W.McBride, R.Paulson, J.C.Wilson, I.A.

(2015) Cell Host Microbe 17: 369-376

  • DOI: 10.1016/j.chom.2015.02.005
  • Primary Citation of Related Structures:  
    4XKD, 4XKE, 4XKF, 4XKG

  • PubMed Abstract: 
  • Avian influenza viruses that cause infection and are transmissible in humans involve changes in the receptor binding site (RBS) of the viral hemagglutinin (HA) that alter receptor preference from α2-3-linked (avian-like) to α2-6-linked (human-like) sialosides ...

    Avian influenza viruses that cause infection and are transmissible in humans involve changes in the receptor binding site (RBS) of the viral hemagglutinin (HA) that alter receptor preference from α2-3-linked (avian-like) to α2-6-linked (human-like) sialosides. A human case of avian-origin H6N1 influenza virus was recently reported, but the molecular mechanisms contributing to it crossing the species barrier are unknown. We find that, although the H6 HA RBS contains D190V and G228S substitutions that potentially promote human receptor binding, recombinant H6 HA preferentially binds α2-3-linked sialosides, indicating no adaptation to human receptors. Crystal structures of H6 HA with avian and human receptor analogs reveal that H6 HA preferentially interacts with avian receptor analogs. This binding mechanism differs from other HA subtypes due to a unique combination of RBS residues, highlighting additional variation in HA-receptor interactions and the challenges in predicting which influenza strains and subtypes can infect humans and cause pandemics.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address: wilson@scripps.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA1 chainA, C, E333H6N1 subtypeMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A0J9X268 (H6N1 subtype)
Explore A0A0J9X268 
Go to UniProtKB:  A0A0J9X268
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0J9X268
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA2 chainB, D, F180H6N1 subtypeMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A0J9X267 (H6N1 subtype)
Explore A0A0J9X267 
Go to UniProtKB:  A0A0J9X267
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0J9X267
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranoseG 3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G46776WR
GlyCosmos:  G46776WR
GlyGen:  G46776WR
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth D],
K [auth E],
L [auth E],
H [auth A],
I [auth A],
J [auth D],
K [auth E],
L [auth E],
M [auth F]
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: 2.45 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.735α = 90
b = 99.271β = 126.45
c = 133.437γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXmodel building
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2015-04-01
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Derived calculations, Refinement description, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary