6DKU | pdb_00006dku

Crystal structure of Myotis VP35 mutant of interferon inhibitory domain

• PDB DOI: https://doi.org/10.2210/pdb6DKU/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Myotis lucifugus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-05-30 Released: 2018-07-18 
• Deposition Author(s): Liu, H., Ginell, G.M., Keefe, L.J., Leung, D.W., Amarasinghe, G.K.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.223 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.171 (Depositor) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Conservation of Structure and Immune Antagonist Functions of Filoviral VP35 Homologs Present in Microbat Genomes.

Edwards, M.R., Liu, H., Shabman, R.S., Ginell, G.M., Luthra, P., Ramanan, P., Keefe, L.J., Kollner, B., Amarasinghe, G.K., Taylor, D.J., Leung, D.W., Basler, C.F.

(2018) Cell Rep 24: 861-872.e6

• PubMed: 30044983 
• DOI: https://doi.org/10.1016/j.celrep.2018.06.045
• Primary Citation Related Structures: 
  6DKU


• PubMed Abstract: 
  

  Non-retroviral integrated RNA viral sequences (NIRVs) potentially encoding ∼280 amino acid homologs to filovirus VP35 proteins are present across the Myotis genus of bats. These are estimated to have been maintained for ∼18 million years, indicating their co-option. To address the reasons for co-option, 16 Myotis VP35s were characterized in comparison to VP35s from the extant filoviruses Ebola virus and Marburg virus, in which VP35s play critical roles in immune evasion and RNA synthesis. The Myotis VP35s demonstrated a conserved suppression of innate immune signaling, albeit with reduced potency, in either human or Myotis cells. Their attenuation reflects a lack of dsRNA binding that in the filoviral VP35s correlates with potent suppression of interferon responses. Despite divergent function, evolution has preserved in Myotis the structure of the filoviral VP35s, indicating that this structure is critical for co-opted function, possibly as a regulator of innate immune signaling.

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Organizational Affiliation: 
• Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA.
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Cornell College, Mt. Vernon, IA 52314, USA; Industrial Macromolecular Crystallography Association-Collaborative Access Team, Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA.
Industrial Macromolecular Crystallography Association-Collaborative Access Team, Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA.
Institute of Immunology, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Südufer 10, 17493 Greifswald-Insel Riems, Germany.
Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY 14260, USA. Electronic address: [e-mail].
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address: [e-mail].
Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA. Electronic address: [e-mail].

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: light scattering

Macromolecule Content 

• Total Structure Weight: 14.51 kDa 
• Atom Count: 998 
• Modeled Residue Count: 125 
• Deposited Residue Count: 128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP35	A	128	Myotis lucifugus	Mutation(s): 9
UniProt
Find proteins for G9JKD1 (Myotis lucifugus) Explore G9JKD1  Go to UniProtKB:  G9JKD1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.223 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.171 (Depositor) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.126	α = 90
b = 78.126	β = 90
c = 43.471	γ = 120

Software Package:

Software Name	Purpose
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
autoPROC	data scaling
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-07-18 
Deposition Author(s): Liu, H., Ginell, G.M., Keefe, L.J., Leung, D.W., Amarasinghe, G.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI109945

Revision History  

• Version 1.0: 2018-07-18
  Type: Initial release
  
• Version 1.1: 2018-08-08
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description