4POR

Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 2.0 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VP1
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J
278Human polyomavirus 9Mutation(s): 0 
Gene Names: gp3vp1
UniProt
Find proteins for E9NQ90 (Human polyomavirus 9)
Explore E9NQ90 
Go to UniProtKB:  E9NQ90
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
K, L, M, N, O, P, Q, R
K, L, M, N, O, P, Q, R, S
3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G91237TK
GlyCosmos:  G91237TK
GlyGen:  G91237TK
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B] , BA [auth B] , BB [auth G] , CB [auth G] , DB [auth G] , EA [auth C] , EB [auth G] , FA [auth C] , 
AA [auth B], BA [auth B], BB [auth G], CB [auth G], DB [auth G], EA [auth C], EB [auth G], FA [auth C], GA [auth C], HA [auth C], HB [auth H], IB [auth H], JB [auth H], KA [auth D], KB [auth H], LA [auth D], MA [auth D], NA [auth D], NB [auth I], OB [auth I], PB [auth I], QA [auth E], RA [auth E], SA [auth E], SB [auth J], TA [auth E], U [auth A], V [auth A], W [auth A], WA [auth F], XA [auth F], YA [auth F], Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download Ideal Coordinates CCD File 
CA [auth B] , FB [auth G] , IA [auth C] , LB [auth H] , OA [auth D] , QB [auth I] , TB [auth J] , UA [auth E] , 
CA [auth B], FB [auth G], IA [auth C], LB [auth H], OA [auth D], QB [auth I], TB [auth J], UA [auth E], X [auth A], ZA [auth F]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
AB [auth G] , DA [auth C] , GB [auth H] , JA [auth D] , MB [auth I] , PA [auth E] , RB [auth J] , T [auth A] , 
AB [auth G], DA [auth C], GB [auth H], JA [auth D], MB [auth I], PA [auth E], RB [auth J], T [auth A], VA [auth F], Y [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.01α = 90
b = 180.4β = 90
c = 199.66γ = 90
Software Package:
Software NamePurpose
RemDAqdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report




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
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary