4I1S

Melanoma differentiation associated protein-5 Helicase domain complex with inhibitor Non-structural protein V

• PDB DOI: https://doi.org/10.2210/pdb4I1S/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Sus scrofa, Simian virus 5 (strain W3)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-11-21 Released: 2013-01-30 
• Deposition Author(s): Motz, C., Witte, G., Hopfner, K.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.230 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 

Literature

Paramyxovirus V proteins disrupt the fold of the RNA sensor MDA5 to inhibit antiviral signaling.

Motz, C., Schuhmann, K.M., Kirchhofer, A., Moldt, M., Witte, G., Conzelmann, K.K., Hopfner, K.P.

(2013) Science 339: 690-693

• PubMed: 23328395 
• DOI: https://doi.org/10.1126/science.1230949
• Primary Citation of Related Structures:  
  4I1S


• PubMed Abstract: 
  

  The retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) melanoma differentiation-associated protein 5 (MDA5) senses cytoplasmic viral RNA and activates antiviral innate immunity. To reveal how paramyxoviruses counteract this response, we determined the crystal structure of the MDA5 adenosine 5'-triphosphate (ATP)-hydrolysis domain in complex with the viral inhibitor V protein. The V protein unfolded the ATP-hydrolysis domain of MDA5 via a β-hairpin motif and recognized a structural motif of MDA5 that is normally buried in the conserved helicase fold. This leads to disruption of the MDA5 ATP-hydrolysis site and prevention of RNA-bound MDA5 filament formation. The structure explains why V proteins inactivate MDA5, but not RIG-I, and mutating only two amino acids in RIG-I induces robust V protein binding. Our results suggest an inhibition mechanism of RLR signalosome formation by unfolding of receptor and inhibitor.

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Organizational Affiliation: 

Department of Biochemistry and Gene Center, Ludwig-Maximilians-University, Munich, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 34.56 kDa 
• Atom Count: 2,489 
• Modelled Residue Count: 290 
• Deposited Residue Count: 295 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Melanoma differentiation associated protein-5	A	243	Sus scrofa	Mutation(s): 0  Gene Names: MDA5
UniProt
Find proteins for A7LCX1 (Sus scrofa) Explore A7LCX1  Go to UniProtKB:  A7LCX1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein V	B	52	Simian virus 5 (strain W3)	Mutation(s): 0  Gene Names: P/V
UniProt
Find proteins for P11207 (Parainfluenza virus 5 (strain W3)) Explore P11207  Go to UniProtKB:  P11207

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth B], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.230 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.07	α = 90
b = 52.49	β = 90
c = 120.79	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
SHARP	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-30 
Deposition Author(s): Motz, C., Witte, G., Hopfner, K.P.

Revision History  

• Version 1.0: 2013-01-30
  Type: Initial release
  
• Version 1.1: 2013-02-20
  Changes: Database references
• Version 1.2: 2017-07-26
  Changes: Advisory, Refinement description, Source and taxonomy