Macromolecule Content

Total Structure Weight: 55.38 kDa
Atom Count: 3480
Modelled Residue Count: 440
Deposited Residue Count: 492
Unique protein chains: 2

6YPT

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

DOI: 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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.66 Å
R-Value Free: 0.283
R-Value Work: 0.206
R-Value Observed: 0.209

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

Fieulaine, S., Bressanelli, S.

(2020) J Biol Chem

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

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)
Find proteins for P10358 (Turnip yellow mosaic virus) Explore P10358 Go to UniProtKB: P10358
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-C	B, D	86	Homo sapiens	Mutation(s): 0 Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48 Go to UniProtKB: P0CG48
NIH Common Fund Data Resources
PHAROS: P0CG48
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GVE Query on GVE Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain F [C] MOL2 format, chain E [A] MOL2 format, chain F [C]	A, C	METHYL 4-AMINOBUTANOATE C₅ H₁₁ N O₂ KVQGGLZHHFGHPU-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.66 Å
R-Value Free: 0.283
R-Value Work: 0.206
R-Value Observed: 0.209
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2020-04-16
Released Date: 2020-08-05

Deposition Author(s):

Bressanelli, S.

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

Revision History (Full details and data files)

Version 1.0: 2020-08-05
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.