4GDJ | pdb_00004gdj

A subtype N10 neuraminidase-like protein of A/little yellow-shouldered bat/Guatemala/060/2010


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.226 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Crystal structures of two subtype N10 neuraminidase-like proteins from bat influenza A viruses reveal a diverged putative active site.

Zhu, X.Yang, H.Guo, Z.Yu, W.Carney, P.J.Li, Y.Chen, L.M.Paulson, J.C.Donis, R.O.Tong, S.Stevens, J.Wilson, I.A.

(2012) Proc Natl Acad Sci U S A 109: 18903-18908

  • DOI: https://doi.org/10.1073/pnas.1212579109
  • Primary Citation Related Structures: 
    4GDI, 4GDJ, 4GEZ

  • PubMed Abstract: 

    Recently, we reported a unique influenza A virus subtype H17N10 from little yellow-shouldered bats. Its neuraminidase (NA) gene encodes a protein that appears to be highly divergent from all known influenza NAs and was assigned as a new subtype N10. To provide structural and functional insights on the bat H17N10 virus, X-ray structures were determined for N10 NA proteins from influenza A viruses A/little yellow-shouldered bat/Guatemala/164/2009 (GU09-164) in two crystal forms at 1.95 Å and 2.5 Å resolution and A/little yellow-shouldered bat/Guatemala/060/2010 (GU10-060) at 2.0 Å. The overall N10 structures are similar to each other and to other known influenza NA structures, with a single highly conserved calcium binding site in each monomer. However, the region corresponding to the highly conserved active site of influenza A N1-N9 NA subtypes and influenza B NA differs substantially. In particular, most of the amino acid residues required for NA activity are substituted, and the putative active site is much wider because of displacement of the 150-loop and 430-loop. These structural features and the fact that the recombinant N10 protein exhibits no, or extremely low, NA activity suggest that it may have a different function than the NA proteins of other influenza viruses. Accordingly, we propose that the N10 protein be termed an NA-like protein until its function is elucidated.


  • Organizational Affiliation
    • Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 171.29 kDa 
  • Atom Count: 10,915 
  • Modeled Residue Count: 1,266 
  • Deposited Residue Count: 1,492 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neuraminidase
A, B, C, D
373Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for H6QM95 (Influenza A virus)
Explore H6QM95 
Go to UniProtKB:  H6QM95
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH6QM95
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G62810GW
GlyCosmos: G62810GW
GlyGen: G62810GW

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
L [auth B]
M [auth B]
O [auth C]
I [auth A],
J [auth A],
L [auth B],
M [auth B],
O [auth C],
Q [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
K [auth A],
N [auth B],
P [auth C],
R [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.226 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.902α = 90
b = 107.902β = 90
c = 345.21γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-26
    Type: Initial release
  • Version 1.1: 2012-10-10
    Changes: Database references
  • Version 1.2: 2012-11-28
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-11-20
    Changes: Data collection, Database references, Structure summary