3T4R | pdb_00003t4r

Lettuce Necrotic Yellow Virus Phosphoprotein C-Terminal Domain

• PDB DOI: https://doi.org/10.2210/pdb3T4R/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Lettuce necrotic yellows virus isolate 318
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-07-26 Released: 2013-01-30 
• Deposition Author(s): Martinez, N., Tarbouriech, N., Jamin, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.294 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Literature

Structure of the C-terminal domain of lettuce necrotic yellows virus phosphoprotein.

Martinez, N., Ribeiro, E.A., Leyrat, C., Tarbouriech, N., Ruigrok, R.W., Jamin, M.

(2013) J Virol 87: 9569-9578

• PubMed: 23785215 
• DOI: https://doi.org/10.1128/JVI.00999-13
• Primary Citation Related Structures: 
  3T4R


• PubMed Abstract: 
  

  Lettuce necrotic yellows virus (LNYV) is a prototype of the plant-adapted cytorhabdoviruses. Through a meta-prediction of disorder, we localized a folded C-terminal domain in the amino acid sequence of its phosphoprotein. This domain consists of an autonomous folding unit that is monomeric in solution. Its structure, solved by X-ray crystallography, reveals a lollipop-shaped structure comprising five helices. The structure is different from that of the corresponding domains of other Rhabdoviridae, Filoviridae, and Paramyxovirinae; only the overall topology of the polypeptide chain seems to be conserved, suggesting that this domain evolved under weak selective pressure and varied in size by the acquisition or loss of functional modules.

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Organizational Affiliation: 
• Université Grenoble Alpes, UVHCI, Grenoble, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.58 kDa 
• Atom Count: 610 
• Modeled Residue Count: 72 
• Deposited Residue Count: 81 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoprotein	A	81	Lettuce necrotic yellows virus isolate 318	Mutation(s): 0  Gene Names: P
UniProt
Find proteins for Q9E7N7 (Lettuce necrotic yellows virus (isolate 318)) Explore Q9E7N7  Go to UniProtKB:  Q9E7N7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.294 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.28	α = 90
b = 43.28	β = 90
c = 89.38	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
SHELXD	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-30 
Deposition Author(s): Martinez, N., Tarbouriech, N., Jamin, M.

Revision History  

• Version 1.0: 2013-01-30
  Type: Initial release
  
• Version 1.1: 2014-03-26
  Changes: Database references
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary