6PCX

Crystal Structure of a H5N1 influenza virus hemagglutinin at pH 6.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification of a pH sensor in Influenza hemagglutinin using X-ray crystallography.

Antanasijevic, A.Durst, M.A.Lavie, A.Caffrey, M.

(2020) J.Struct.Biol. 209: 107412-107412

  • DOI: 10.1016/j.jsb.2019.107412
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Hemagglutnin (HA) mediates entry of influenza virus through a series of conformational changes triggered by the low pH of the endosome. The residue or combination of residues acting as pH sensors has not yet been fully elucidated. In this work, we as ...

    Hemagglutnin (HA) mediates entry of influenza virus through a series of conformational changes triggered by the low pH of the endosome. The residue or combination of residues acting as pH sensors has not yet been fully elucidated. In this work, we assay pH effects on the structure of H5 HA by soaking HA crystallized at pH 6.5 in a series of buffers with lower pH, mimicking the conditions of the endosome. We find that HA1-H38, which is conserved in Group 1 HA, undergoes a striking change in side chain conformation, which we attribute to its protonation and cation-cation repulsion with conserved HA1-H18. This work suggests that x-ray crystallography can be applied for studying small-scale pH-induced conformational changes providing valuable information on the location of pH sensors in HA. Importantly, the observed change in HA1-H38 conformation is further evidence that the pH-induced conformational changes of HA are the result of a series of protonation events to conserved and non-conserved pH sensors.


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland Ave, 60607 Chicago, USA.,Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland Ave, 60607 Chicago, USA. Electronic address: lavie@uic.edu.,Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland Ave, 60607 Chicago, USA. Electronic address: caffrey@uic.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
A
526Influenza A virusMutation(s): 0 
Gene Names: HA
Find proteins for Q1KHJ9 (Influenza A virus)
Go to UniProtKB:  Q1KHJ9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.207 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 108.537α = 90.00
b = 108.537β = 90.00
c = 419.790γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2019-11-20
    Type: Database references
  • Version 1.2: 2020-01-22
    Type: Database references