6YPT | pdb_00006ypt

X-ray structure of Turnip Yellow Mosaic Virus PRO/DUB in complex with Ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb6YPT/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Turnip yellow mosaic virus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-16 Released: 2020-08-05 
• Deposition Author(s): Fieulaine, S., Bressanelli, S.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.66 Å
• R-Value Free: 
  0.283 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of Turnip Yellow Mosaic Virus PRO/DUB in complex with Ubiquitin

Fieulaine, S., Bressanelli, S.

(2020) J Biological Chem 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 55.26 kDa 
• Atom Count: 3,480 
• Modeled Residue Count: 440 
• Deposited Residue Count: 490 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA replicase polyprotein	A, C	160	Turnip yellow mosaic virus	Mutation(s): 0  EC: 2.1.1 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.6.4 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P10358 (Turnip yellow mosaic virus) Explore P10358  Go to UniProtKB:  P10358

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-C	B, D	85	Homo sapiens	Mutation(s): 0  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48 GTEx:  ENSG00000150991

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GVE	E [auth A], F [auth C]	METHYL 4-AMINOBUTANOATE C5 H11 N O2 KVQGGLZHHFGHPU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.66 Å
• R-Value Free:  0.283 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.93	α = 90
b = 51.86	β = 98.37
c = 125.25	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-05 
Deposition Author(s): Fieulaine, S., Bressanelli, S.

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Funding Organization	Location	Grant Number
French National Research Agency	France	11-BSV8-011

Revision History  

• Version 1.0: 2020-08-05
  Type: Initial release
  
• Version 2.0: 2023-03-15
  Changes: Advisory, Database references, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations, Refinement description
• Version 3.1: 2024-02-07
  Changes: Refinement description