5TIP

The Structure of the Major Capsid protein of PBCV-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.183 

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This is version 2.0 of the entry. See complete history


Literature

Structure of the chlorovirus PBCV-1 major capsid glycoprotein determined by combining crystallographic and carbohydrate molecular modeling approaches.

De Castro, C.Klose, T.Speciale, I.Lanzetta, R.Molinaro, A.Van Etten, J.L.Rossmann, M.G.

(2018) Proc Natl Acad Sci U S A 115: E44-E52

  • DOI: 10.1073/pnas.1613432115
  • Primary Citation of Related Structures:  
    5TIP, 5TIQ

  • PubMed Abstract: 
  • The glycans of the major capsid protein (Vp54) of Paramecium bursaria chlorella virus (PBCV-1) were recently described and found to be unusual. This prompted a reexamination of the previously reported Vp54 X-ray structure. A detailed description of the complete glycoprotein was achieved by combining crystallographic data with molecular modeling ...

    The glycans of the major capsid protein (Vp54) of Paramecium bursaria chlorella virus (PBCV-1) were recently described and found to be unusual. This prompted a reexamination of the previously reported Vp54 X-ray structure. A detailed description of the complete glycoprotein was achieved by combining crystallographic data with molecular modeling. The crystallographic data identified most of the monosaccharides located close to the protein backbone, but failed to detect those further from the glycosylation sites. Molecular modeling complemented this model by adding the missing monosaccharides and examined the conformational preference of the whole molecule, alone or within the crystallographic environment. Thus, combining X-ray crystallography with carbohydrate molecular modeling resulted in determining the complete glycosylated structure of a glycoprotein. In this case, it is the chlorovirus PBCV-1 major capsid protein.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-2032; decastro@unina.it jvanetten1@unl.edu mr@purdue.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major capsid proteinA, B, C, D436Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A430L
UniProt
Find proteins for P30328 (Paramecium bursaria Chlorella virus 1)
Explore P30328 
Go to UniProtKB:  P30328
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30328
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose-(1-2)-beta-L-rhamnopyranose-(1-4)-beta-D-xylopyranose-(1-4)-[alpha-D-mannopyranose-(1-3)-alpha-D-rhamnopyranose-(1-3)][alpha-D-galactopyranose-(1-2)]alpha-L-fucopyranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-glucopyranoseE, F, J, N, Q 9N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G08707KI
GlyCosmos:  G08707KI
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-rhamnopyranose-(1-3)-[alpha-D-galactopyranose-(1-2)][beta-D-xylopyranose-(1-4)]alpha-L-fucopyranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-glucopyranoseG, K, M, O, R 7N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22683EH
GlyCosmos:  G22683EH
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-3)-beta-D-glucopyranoseH, L, S 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G08796XG
GlyCosmos:  G08796XG
GlyGen:  G08796XG
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-L-rhamnopyranose-(1-4)-beta-D-xylopyranose-(1-4)-[alpha-D-galactopyranose-(1-2)][alpha-D-rhamnopyranose-(1-3)]alpha-L-fucopyranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-glucopyranoseI 7N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G08201UK
GlyCosmos:  G08201UK
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-rhamnopyranose-(1-3)-[beta-L-rhamnopyranose-(1-4)-beta-D-xylopyranose-(1-4)][alpha-D-galactopyranose-(1-2)]alpha-L-fucopyranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-glucopyranoseP 8N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G88961XM
GlyCosmos:  G88961XM
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download Ideal Coordinates CCD File 
T [auth A],
U [auth B],
V [auth C],
X [auth D]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

Download Ideal Coordinates CCD File 
W [auth C]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.183 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 188.792α = 90
b = 188.792β = 90
c = 188.792γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI011219
National Science Foundation (NSF, United States)United StatesEPS-1004049
Stanley Medical Research InstituteUnited States11R-003
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesP20-RR15635

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-12-20
    Changes: Database references
  • Version 1.2: 2018-01-03
    Changes: Database references
  • Version 1.3: 2018-01-17
    Changes: Database references
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence, Data collection, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary