4MC5 | pdb_00004mc5

Crystal structure of a subtype H18 hemagglutinin homologue from A/flat-faced bat/Peru/033/2010 (H18N11)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 
    0.204 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4MC5

Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

New world bats harbor diverse influenza a viruses.

Tong, S.Zhu, X.Li, Y.Shi, M.Zhang, J.Bourgeois, M.Yang, H.Chen, X.Recuenco, S.Gomez, J.Chen, L.M.Johnson, A.Tao, Y.Dreyfus, C.Yu, W.McBride, R.Carney, P.J.Gilbert, A.T.Chang, J.Guo, Z.Davis, C.T.Paulson, J.C.Stevens, J.Rupprecht, C.E.Holmes, E.C.Wilson, I.A.Donis, R.O.

(2013) PLoS Pathog 9: e1003657-e1003657

  • DOI: https://doi.org/10.1371/journal.ppat.1003657
  • Primary Citation Related Structures: 
    4K3X, 4K3Y, 4MC5, 4MC7

  • PubMed Abstract: 

    Aquatic birds harbor diverse influenza A viruses and are a major viral reservoir in nature. The recent discovery of influenza viruses of a new H17N10 subtype in Central American fruit bats suggests that other New World species may similarly carry divergent influenza viruses. Using consensus degenerate RT-PCR, we identified a novel influenza A virus, designated as H18N11, in a flat-faced fruit bat (Artibeus planirostris) from Peru. Serologic studies with the recombinant H18 protein indicated that several Peruvian bat species were infected by this virus. Phylogenetic analyses demonstrate that, in some gene segments, New World bats harbor more influenza virus genetic diversity than all other mammalian and avian species combined, indicative of a long-standing host-virus association. Structural and functional analyses of the hemagglutinin and neuraminidase indicate that sialic acid is not a ligand for virus attachment nor a substrate for release, suggesting a unique mode of influenza A virus attachment and activation of membrane fusion for entry into host cells. Taken together, these findings indicate that bats constitute a potentially important and likely ancient reservoir for a diverse pool of influenza viruses.


  • Organizational Affiliation
    • Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.

Macromolecule Content 

  • Total Structure Weight: 179.8 kDa 
  • Atom Count: 13,219 
  • Modeled Residue Count: 1,485 
  • Deposited Residue Count: 1,530 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin
A, B, C
510Influenza A virusMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
E, G
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G26299SM
GlyCosmos: G26299SM
GlyGen: G26299SM
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, H, J
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
I
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G04825SN
GlyCosmos: G04825SN
GlyGen: G04825SN

Small Molecules

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

Query on NAG



Download:Ideal Coordinates CCD File
L [auth A]
M [auth A]
O [auth B]
P [auth B]
Q [auth B]
L [auth A],
M [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth C],
T [auth C],
U [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
FUC

Query on FUC



Download:Ideal Coordinates CCD File
K [auth A],
N [auth B],
S [auth C]
alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free:  0.204 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 239.093α = 90
b = 239.093β = 90
c = 161.228γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-11-20
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-30
    Changes: Data collection, Database references, Structure summary