6Q1M

Crystal structure of the wheat dwarf virus Rep domain

• PDB DOI: https://doi.org/10.2210/pdb6Q1M/pdb

• Classification: REPLICATION
• Organism(s): Wheat dwarf virus
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-08-05 Released: 2019-12-11 
• Deposition Author(s): Litzau, L.A., Everett, B.A., Evans III, R.L., Shi, K., Tompkins, K., Gordon, W.R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 0.166 
• R-Value Work: 0.158 
• R-Value Observed: 0.158 

Starting Model: experimental

Literature

Crystal structure of the Wheat dwarf virus Rep domain.

Everett, B.A., Litzau, L.A., Tompkins, K., Shi, K., Nelson, A., Aihara, H., Evans Iii, R.L., Gordon, W.R.

(2019) Acta Crystallogr F Struct Biol Commun 75: 744-749

• PubMed: 31797816 
• DOI: https://doi.org/10.1107/S2053230X19015796
• Primary Citation of Related Structures:  
  6Q1M


• PubMed Abstract: 
  

  The Rep domain of Wheat dwarf virus (WDV Rep) is an HUH endonuclease involved in rolling-circle replication. HUH endonucleases coordinate a metal ion to enable the nicking of a specific ssDNA sequence and the subsequent formation of an intermediate phosphotyrosine bond. This covalent protein-ssDNA adduct makes HUH endonucleases attractive fusion tags (HUH-tags) in a diverse number of biotechnological applications. Solving the structure of an HUH endonuclease in complex with ssDNA will provide critical information about ssDNA recognition and sequence specificity, thus enabling rationally engineered protein-DNA interactions that are programmable. The structure of the WDV Rep domain reported here was solved in the apo state from a crystal diffracting to 1.24 Å resolution and represents an initial step in the direction of solving the structure of a protein-ssDNA complex.

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Organizational Affiliation: 

Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 15.98 kDa 
• Atom Count: 1,198 
• Modelled Residue Count: 119 
• Deposited Residue Count: 137 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication-associated protein	A	137	Wheat dwarf virus	Mutation(s): 0  Gene Names: repA EC: 3.1.21 (PDB Primary Data), 2.7.7 (UniProt)
UniProt
Find proteins for Q67622 (Wheat dwarf virus (isolate Sweden)) Explore Q67622  Go to UniProtKB:  Q67622

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 0.166 
• R-Value Work: 0.158 
• R-Value Observed: 0.158 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.566	α = 90
b = 49.566	β = 90
c = 145.653	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-12-11 
Deposition Author(s): Litzau, L.A., Everett, B.A., Evans III, R.L., Shi, K., Tompkins, K., Gordon, W.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM119483
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118047

Revision History  

• Version 1.0: 2019-12-11
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2020-04-29
  Changes: Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description