5TIP

The Structure of the Major Capsid protein of PBCV-1

• PDB DOI: https://doi.org/10.2210/pdb5TIP/pdb
• Entry: 5TIP supersedes: 1M3Y

• Classification: VIRAL PROTEIN
• Organism(s): Paramecium bursaria Chlorella virus 1
• Mutation(s): No 


• Deposited: 2016-10-03 Released: 2017-10-18 
• Deposition Author(s): Klose, T., De Castro, C., Speciale, I., Molinaro, A., Van Etten, J.L., Rossmann, M.G.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Science Foundation (NSF, United States), Stanley Medical Research Institute, National Institutes of Health/National Center for Research Resources (NIH/NCRR)

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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 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 208.7 kDa 
• Atom Count: 15,788 
• Modelled Residue Count: 1,744 
• Deposited Residue Count: 1,744 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A, B, C, D	436	Paramecium bursaria Chlorella virus 1	Mutation(s): 0
UniProt
Find proteins for P30328 (Paramecium bursaria Chlorella virus 1) Explore P30328  Go to UniProtKB:  P30328

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-glucopyranose	E, F, J, N, Q	9		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G08707KI GlyCosmos:  G08707KI

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-glucopyranose	G, K, M, O, R	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22683EH GlyCosmos:  G22683EH

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-beta-D-glucopyranose	H, L, S	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G08796XG GlyCosmos:  G08796XG GlyGen:  G08796XG

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-glucopyranose	I	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G08201UK GlyCosmos:  G08201UK

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-glucopyranose	P	8		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G88961XM GlyCosmos:  G88961XM

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	T [auth A], U [auth B], V [auth C], X [auth D]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
BGC	W [auth C]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N

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 = 188.792	α = 90
b = 188.792	β = 90
c = 188.792	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-10-18 
Deposition Author(s): Klose, T., De Castro, C., Speciale, I., Molinaro, A., Van Etten, J.L., Rossmann, M.G.
• This entry supersedes: 1M3Y

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI011219
National Science Foundation (NSF, United States)	United States	EPS-1004049
Stanley Medical Research Institute	United States	11R-003
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	P20-RR15635

Revision History  

• 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