4POQ

Structure of unliganded VP1 pentamer of Human Polyomavirus 9

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Crystallographic and glycan microarray analysis of human polyomavirus 9 VP1 identifies N-glycolyl neuraminic acid as a receptor candidate.

Khan, Z.M., Liu, Y., Neu, U., Gilbert, M., Ehlers, B., Feizi, T., Stehle, T.

(2014) J Virol 88: 6100-6111

  • DOI: 10.1128/JVI.03455-13
  • Primary Citation of Related Structures:  
    4POQ, 4POR, 4POS, 4POT

  • PubMed Abstract: 

    • Human polyomavirus 9 (HPyV9) is a closely related homologue of simian B-lymphotropic polyomavirus (LPyV). In order to define the architecture and receptor binding properties of HPyV9, we solved high-resolution crystal structures of its major capsid protein, VP1, in complex with three putative oligosaccharide receptors identified by glycan microarray screening ...

    Human polyomavirus 9 (HPyV9) is a closely related homologue of simian B-lymphotropic polyomavirus (LPyV). In order to define the architecture and receptor binding properties of HPyV9, we solved high-resolution crystal structures of its major capsid protein, VP1, in complex with three putative oligosaccharide receptors identified by glycan microarray screening. Comparison of the properties of HPyV9 VP1 with the known structure and glycan-binding properties of LPyV VP1 revealed that both viruses engage short sialylated oligosaccharides, but small yet important differences in specificity were detected. Surprisingly, HPyV9 VP1 preferentially binds sialyllactosamine compounds terminating in 5-N-glycolyl neuraminic acid (Neu5Gc) over those terminating in 5-N-acetyl neuraminic acid (Neu5Ac), whereas LPyV does not exhibit such a preference. The structural analysis demonstrated that HPyV9 makes specific contacts, via hydrogen bonds, with the extra hydroxyl group present in Neu5Gc. An equivalent hydrogen bond cannot be formed by LPyV VP1.

    Organizational Affiliation: 

    Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VP1
A, B, C, D, E, F, G, H, I, J
A, B, C, D, E, F, G, H, I, J
278Human polyomavirus 9Mutation(s): 0 
Gene Names: gp3, vp1
UniProt
Find proteins for E9NQ90 (Human polyomavirus 9)
Explore E9NQ90 
Go to UniProtKB:  E9NQ90
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9NQ90
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth F],
BA [auth F],
EA [auth G],
FA [auth G],
KA [auth I],
AA [auth F],
BA [auth F],
EA [auth G],
FA [auth G],
KA [auth I],
L [auth A],
NA [auth J],
O [auth B],
R [auth C],
U [auth D],
X [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
IPA
Query on IPA
Download Ideal Coordinates CCD File 
CA [auth F],
GA [auth G],
IA [auth H],
LA [auth I],
M [auth A],
CA [auth F],
GA [auth G],
IA [auth H],
LA [auth I],
M [auth A],
OA [auth J],
P [auth B],
S [auth C],
V [auth D],
Y [auth E]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
DA [auth G],
HA [auth H],
JA [auth I],
K [auth A],
MA [auth J],
DA [auth G],
HA [auth H],
JA [auth I],
K [auth A],
MA [auth J],
N [auth B],
Q [auth C],
T [auth D],
W [auth E],
Z [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.33α = 90
b = 180.09β = 90
c = 199.39γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2014-02-26 
  • Released Date: 2014-04-09 
    • Deposition Author(s): Khan, Z.M., Stehle, T.

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-11-26
    Changes: Database references