6Q1M

Crystal structure of the wheat dwarf virus Rep domain


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 

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This is version 1.2 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Replication-associated proteinA137Wheat dwarf virusMutation(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
Protein Feature View
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  • Reference Sequence
Small Molecules
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 = 49.566α = 90
b = 49.566β = 90
c = 145.653γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM119483
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118047

Revision History  (Full details and data files)

  • 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