3QQB

Crystal structure of HA2 R106H mutant of H2 hemagglutinin, neutral pH form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structural Characterization of an Early Fusion Intermediate of Influenza Virus Hemagglutinin.

Xu, R., Wilson, I.A.

(2011) J.Virol. 85: 5172-5182

  • DOI: 10.1128/JVI.02430-10
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The hemagglutinin (HA) envelope protein of influenza virus mediates viral entry through membrane fusion in the acidic environment of the endosome. Crystal structures of HA in pre- and postfusion states have laid the foundation for proposals for a gen ...

    The hemagglutinin (HA) envelope protein of influenza virus mediates viral entry through membrane fusion in the acidic environment of the endosome. Crystal structures of HA in pre- and postfusion states have laid the foundation for proposals for a general fusion mechanism for viral envelope proteins. The large-scale conformational rearrangement of HA at low pH is triggered by a loop-to-helix transition of an interhelical loop (B loop) within the fusion domain and is often referred to as the "spring-loaded" mechanism. Although the receptor-binding HA1 subunit is believed to act as a "clamp" to keep the B loop in its metastable prefusion state at neutral pH, the "pH sensors" that are responsible for the clamp release and the ensuing structural transitions have remained elusive. Here we identify a mutation in the HA2 fusion domain from the influenza virus H2 subtype that stabilizes the HA trimer in a prefusion-like state at and below fusogenic pH. Crystal structures of this putative early intermediate state reveal reorganization of ionic interactions at the HA1-HA2 interface at acidic pH and deformation of the HA1 membrane-distal domain. Along with neutralization of glutamate residues on the B loop, these changes cause a rotation of the B loop and solvent exposure of conserved phenylalanines, which are key residues at the trimer interface of the postfusion structure. Thus, our study reveals the possible initial structural event that leads to release of the B loop from its prefusion conformation, which is aided by unexpected structural changes within the membrane-distal HA1 domain at low pH.

    Organizational Affiliation: 

    Department of Molecular Biology, BCC-206, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
A
327Influenza A virus (strain A/Japan/305/1957 H2N2)Mutation(s): 0 
Gene Names: HA
Find proteins for C7S226 (Influenza A virus (strain A/Japan/305/1957 H2N2))
Go to UniProtKB:  C7S226
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
B
174Influenza A virus (strain A/Japan/305/1957 H2N2)Mutation(s): 1 
Gene Names: HA
Find proteins for C7S226 (Influenza A virus (strain A/Japan/305/1957 H2N2))
Go to UniProtKB:  C7S226
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG
Download SDF File 
Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 70.288α = 90.00
b = 70.288β = 90.00
c = 237.136γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2011-02-15 
  • Released Date: 2011-03-09 
  • Deposition Author(s): Xu, R., Wilson, I.A.

Revision History 

  • Version 1.0: 2011-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description