6WE0

Wheat dwarf virus Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site

• PDB DOI:  https://doi.org/10.2210/pdb6WE0/pdb
• NAKB: 6WE0

• Classification: REPLICATION/DNA
• Organism(s): Wheat dwarf virus
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2020-04-01 Released: 2020-12-16 
• Deposition Author(s): Tompkins, K., Litzau, L.A., Shi, K., Nelson, A., Evans III, R.L., 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: 1.80 Å
• R-Value Free: 0.216 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Literature

Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering.

Tompkins, K.J., Houtti, M., Litzau, L.A., Aird, E.J., Everett, B.A., Nelson, A.T., Pornschloegl, L., Limon-Swanson, L.K., Evans, R.L., Evans, K., Shi, K., Aihara, H., Gordon, W.R.

(2021) Nucleic Acids Res 49: 1046-1064

• PubMed: 33410911 
• DOI: https://doi.org/10.1093/nar/gkaa1248
• Primary Citation of Related Structures:  
  6WDZ, 6WE0, 6WE1


• PubMed Abstract: 
  

Replication initiator proteins (Reps) from the HUH-endonuclease superfamily process specific single-stranded DNA (ssDNA) sequences to initiate rolling circle/hairpin replication in viruses, such as crop ravaging geminiviruses and human disease causing parvoviruses. In biotechnology contexts, Reps are the basis for HUH-tag bioconjugation and a critical adeno-associated virus genome integration tool. We solved the first co-crystal structures of Reps complexed to ssDNA, revealing a key motif for conferring sequence specificity and for anchoring a bent DNA architecture. In combination, we developed a deep sequencing cleavage assay, termed HUH-seq, to interrogate subtleties in Rep specificity and demonstrate how differences can be exploited for multiplexed HUH-tagging. Together, our insights allowed engineering of only four amino acids in a Rep chimera to predictably alter sequence specificity. These results have important implications for modulating viral infections, developing Rep-based genomic integration tools, and enabling massively parallel HUH-tag barcoding and bioconjugation applications.

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Organizational Affiliation: 

Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 18.82 kDa 
• Atom Count: 1,161 
• Modelled Residue Count: 129 
• Deposited Residue Count: 147 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication-associated protein	A	137	Wheat dwarf virus	Mutation(s): 1  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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*AP*TP*AP*TP*TP*AP*CP*C)-3')	B [auth C]	10	Wheat dwarf virus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	C [auth A], D [auth C], E [auth C], F [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.216 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.572	α = 90
b = 50.01	β = 90
c = 73.441	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
PHASER	phasing
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Tompkins, K., Litzau, L.A., Shi, K., Nelson, A., Evans III, R.L., 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: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2021-03-17
  Changes: Database references