1SIE

MURINE POLYOMAVIRUS COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE

• PDB DOI: https://doi.org/10.2210/pdb1SIE/pdb

• Classification: VIRUS
• Organism(s): Mouse polyomavirus (strain p16 small-plaque)
• Mutation(s): No 


• Deposited: 1995-12-12 Released: 1996-06-20 
• Deposition Author(s): Stehle, T., Harrison, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.65 Å
• R-Value Free: 0.264 
• R-Value Work: 0.244 
• R-Value Observed: 0.244 

Literature

Crystal structures of murine polyomavirus in complex with straight-chain and branched-chain sialyloligosaccharide receptor fragments.

Stehle, T., Harrison, S.C.

(1996) Structure 4: 183-194

• PubMed: 8805524 
• DOI: https://doi.org/10.1016/s0969-2126(96)00021-4
• Primary Citation of Related Structures:  
  1SID, 1SIE


• PubMed Abstract: 
  

  Murine polyomavirus recognizes (alpha2,3)-linked alpha-5-N-acetylneuraminic acid (sialic acid) on the surface of susceptible cells. While all strains bind to straight-chain receptors terminating in (alpha2,3)-linked sialic acid, some strains also bind to branched oligosaccharides that carry a second, (alpha2,6)-linked sialic acid. The ability to bind to these branched-chain receptors correlates with a single amino acid mutation at position 91 on the outer surface of the major capsid protein, VP1, and with a significant decrease in tumorigenicity.

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Organizational Affiliation: 

Howard Hughes Medical Institute and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 360-mer - A360 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 260.23 kDa 
• Atom Count: 17,141 
• Modelled Residue Count: 2,151 
• Deposited Residue Count: 2,298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POLYOMAVIRUS COAT PROTEIN VP1	A, B, C, D, E, F	383	Mouse polyomavirus (strain p16 small-plaque)	Mutation(s): 0
UniProt
Find proteins for P49302 (Murine polyomavirus (strain P16 small-plaque)) Explore P49302  Go to UniProtKB:  P49302

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I, J, K, L	4		N/A
Glycosylation Resources
GlyTouCan:  G14000ZZ GlyCosmos:  G14000ZZ GlyGen:  G14000ZZ

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.65 Å
• R-Value Free: 0.264 
• R-Value Work: 0.244 
• R-Value Observed: 0.244 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 570	α = 90
b = 570	β = 90
c = 570	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-06-20 
Deposition Author(s): Stehle, T., Harrison, S.C.

Revision History  

• Version 1.0: 1996-06-20
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Structure summary