8FR5 | pdb_00008fr5

Crystal structure of the Human Smacovirus 1 Rep domain

• PDB DOI: https://doi.org/10.2210/pdb8FR5/pdb

• Classification: REPLICATION
• Organism(s): Human smacovirus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-01-06 Released: 2023-12-27 
• Deposition Author(s): Limon, L.K., Shi, K., Dao, A., Rugloski, J., Tompkins, K.J., Aihara, H., Gordon, W.R., Evans IIII, R.L.
• 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: 1.33 Å
• R-Value Free: 
  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: in silico

Literature

The crystal structure of the human smacovirus 1 Rep domain.

Limon, L.K., Shi, K., Dao, A., Rugloski, J., Tompkins, K.J., Aihara, H., Gordon, W.R., Evans 3rd, R.L.

(2023) Acta Crystallogr F Struct Biol Commun 79: 295-300

• PubMed: 38051309 
• DOI: https://doi.org/10.1107/S2053230X23009536
• Primary Citation of Related Structures:  
  8FR5


• PubMed Abstract: 
  

  Replication initiator proteins (Reps) from the HUH endonuclease family process specific single-stranded DNA sequences to initiate rolling-circle replication in viruses. Here, the first crystal structure of the apo state of a Rep domain from the smacovirus family is reported. The structure of the human smacovirus 1 Rep domain was obtained at 1.33 Å resolution and represents an expansion of the HUH endonuclease superfamily, allowing greater diversity in bioconjugation-tag applications.

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Organizational Affiliation: 
• Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 11.63 kDa 
• Atom Count: 784 
• Modeled Residue Count: 92 
• Deposited Residue Count: 97 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rep	A	97	Human smacovirus 1	Mutation(s): 1  Gene Names: Rep

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free:  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.16	α = 90
b = 49.37	β = 110.301
c = 31.38	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Limon, L.K., Shi, K., Dao, A., Rugloski, J., Tompkins, K.J., Aihara, H., Gordon, W.R., Evans IIII, R.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM119483

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release