5TIQ

The Structure of the Major Capsid protein of PBCV-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.537 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 1J5Q - determined by Nandhagopal, N., Simpson, A.A., Gurnon, J.R., Yan, X., Baker, T.S., Graves, M.V., Van Etten, J.L., Rossmann, M.G.  

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

  • 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 t ...

    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 Agricultural Sciences, University of Napoli, 80055 Portici, Italy; decastro@unina.it jvanetten1@unl.edu mr@purdue.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major capsid protein
A, B
436Paramecium bursaria Chlorella virus 1N/A
Find proteins for P30328 (Paramecium bursaria Chlorella virus 1)
Go to UniProtKB:  P30328
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BGC
Query on BGC

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Download CCD File 
A, B
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
XXR
Query on XXR

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Download CCD File 
A, B
6-deoxy-alpha-D-mannopyranose
D-Rhamnose
C6 H12 O5
SHZGCJCMOBCMKK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
7CV
Query on 7CV

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Download CCD File 
A, B
6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose
C8 H16 O5
SXWBIRCAXZNEGK-TVNFTVLESA-N
 Ligand Interaction
XYP
Query on XYP

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Download CCD File 
A, B
BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
GLA
Query on GLA

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Download CCD File 
A, B
ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
HG
Query on HG

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Download CCD File 
A, B
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
RM4
Query on RM4

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Download CCD File 
A, B
6-deoxy-beta-L-mannopyranose
C6 H12 O5
SHZGCJCMOBCMKK-YJRYQGEOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.537 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 
  • Space Group: P 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 188.763α = 90.00
b = 188.763β = 90.00
c = 188.763γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI011219

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-12-20
    Type: Advisory, Database references
  • Version 1.2: 2018-01-03
    Type: Database references
  • Version 1.3: 2018-01-17
    Type: Database references