4WEG

influenza virus neuraminidase N9 in complex 2,3-difluorosialic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Catalytic mechanism and novel receptor binding sites of human parainfluenza virus type 3 hemagglutinin-neuraminidase (hPIV3 HN)

Streltsov, V.A.Pilling, P.Barrett, S.McKimm-Breschkin, J.L.

(2015) Antiviral Res 123: 216-223

  • DOI: https://doi.org/10.1016/j.antiviral.2015.08.014
  • Primary Citation of Related Structures:  
    4WEF, 4WEG

  • PubMed Abstract: 

    The human parainfluenza virus type 3 (hPIV3) hemagglutinin-neuraminidase (HN) has opposing functions of binding sialic acid receptors and cleaving them, facilitating virus release. The crystal structure of hPIV3 HN complexed with the substrate analogue difluorosialic acid (DFSA) revealed that catalysis by HN involves the formation of a covalently linked sialosyl-enzyme intermediate which was trapped along with a transition-state analogue resembling an oxocarbenium ion. This mechanism of enzyme catalysis was also confirmed in the crystal structure of the influenza N9 neuraminidase complexed with DFSA. Additionally, novel secondary receptor binding sites were identified in the hPIV3 HN-DFSA complex including one near the catalytic cavity which upon binding DFSA imposes subtle changes and may help the HN balance the opposing functions. Multiple receptor binding sites may increase avidity to facilitate cell binding and fusion promotion. The secondary receptor binding sites in the paramyxoviruses are so far unique to each virus type.


  • Organizational Affiliation

    CSIRO Manufacturing, 343 Royal Parade, Parkville, Victoria 3052, Australia. Electronic address: victor.streltsov@csiro.au.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuraminidase388Influenza A virus (A/tern/Australia/G70C/1975(H11N9))Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for P03472 (Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9))
Explore P03472 
Go to UniProtKB:  P03472
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03472
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G83582BK
GlyCosmos:  G83582BK
GlyGen:  G83582BK
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SFJ
Query on SFJ

Download Ideal Coordinates CCD File 
D [auth A](2R,3R,4R,5R,6R)-5-acetamido-2,3-difluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxylic acid
C11 H17 F2 N O8
HMALKZAXODOYOP-DAXAGCIGSA-N
FSI
Query on FSI

Download Ideal Coordinates CCD File 
H [auth A]5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid
C11 H18 F N O9
ALJLGESFXXDPKH-RISWTRDCSA-N
DF4
Query on DF4

Download Ideal Coordinates CCD File 
G [auth A](3R,4R,5R,6R)-5-(acetylamino)-3-fluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-3,4,5,6-tetrahydropyranium-2-carboxylate
C11 H16 F N O8
OXSMZBYWMIZHJQ-LNSOWFDVSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.146 
  • Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.194α = 90
b = 181.194β = 90
c = 181.194γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data processing
PHASERphasing
PDB_EXTRACTdata extraction
HKLdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2015-10-07
    Changes: Database references
  • Version 1.2: 2015-11-18
    Changes: Database references
  • Version 1.3: 2017-10-04
    Changes: Advisory, Data collection, Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary