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- PDB-4o9f: crystal structure of horse MAVS card domain mutant R64C -

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Basic information

Entry
Database: PDB / ID: 4o9f
Titlecrystal structure of horse MAVS card domain mutant R64C
Componentsmitochondrial antiviral signaling protein (MAVS)
KeywordsANTIVIRAL PROTEIN
Function / homology
Function and homology information


membrane => GO:0016020 / defense response to virus / mitochondrion
Similarity search - Function
Mitochondrial antiviral-signalling protein, metazoan / Death Domain, Fas / Death Domain, Fas / Caspase recruitment domain / Caspase recruitment domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mitochondrial antiviral signaling protein
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.348 Å
AuthorsZhang, X. / He, X.
CitationJournal: Elife / Year: 2014
Title: Structural basis for the prion-like MAVS filaments in antiviral innate immunity.
Authors: Hui Xu / Xiaojing He / Hui Zheng / Lily J Huang / Fajian Hou / Zhiheng Yu / Michael Jason de la Cruz / Brian Borkowski / Xuewu Zhang / Zhijian J Chen / Qiu-Xing Jiang /
Abstract: Mitochondrial antiviral signaling (MAVS) protein is required for innate immune responses against RNA viruses. In virus-infected cells MAVS forms prion-like aggregates to activate antiviral signaling ...Mitochondrial antiviral signaling (MAVS) protein is required for innate immune responses against RNA viruses. In virus-infected cells MAVS forms prion-like aggregates to activate antiviral signaling cascades, but the underlying structural mechanism is unknown. Here we report cryo-electron microscopic structures of the helical filaments formed by both the N-terminal caspase activation and recruitment domain (CARD) of MAVS and a truncated MAVS lacking part of the proline-rich region and the C-terminal transmembrane domain. Both structures are left-handed three-stranded helical filaments, revealing specific interfaces between individual CARD subunits that are dictated by electrostatic interactions between neighboring strands and hydrophobic interactions within each strand. Point mutations at multiple locations of these two interfaces impaired filament formation and antiviral signaling. Super-resolution imaging of virus-infected cells revealed rod-shaped MAVS clusters on mitochondria. These results elucidate the structural mechanism of MAVS polymerization, and explain how an α-helical domain uses distinct chemical interactions to form self-perpetuating filaments. DOI: http://dx.doi.org/10.7554/eLife.01489.001.
History
DepositionJan 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mitochondrial antiviral signaling protein (MAVS)


Theoretical massNumber of molelcules
Total (without water)11,2471
Polymers11,2471
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.816, 52.029, 35.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein mitochondrial antiviral signaling protein (MAVS)


Mass: 11246.693 Da / Num. of mol.: 1 / Fragment: card domain, UNP residues 1-94 / Mutation: R64C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: MAVS / Plasmid: modified pET28a with a preScission protease site / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F6QPU3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris, 25% PEG 3350, 0.20 M ammonium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5481 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 13, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5481 Å / Relative weight: 1
ReflectionResolution: 2.348→50 Å / Num. all: 4287 / Num. obs: 4212 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.35→2.39 Å / % possible all: 84.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
CCP4model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VGQ

2vgq


Resolution: 2.348→36.354 Å / SU ML: 0.27 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 210 5 %RANDOM
Rwork0.1633 ---
obs0.1666 4196 98.89 %-
all-4406 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.348→36.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms765 0 0 74 839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007781
X-RAY DIFFRACTIONf_angle_d0.961058
X-RAY DIFFRACTIONf_dihedral_angle_d14.108281
X-RAY DIFFRACTIONf_chiral_restr0.073119
X-RAY DIFFRACTIONf_plane_restr0.003134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3484-2.95860.27851010.16951920X-RAY DIFFRACTION98
2.9586-36.3580.20341090.16022066X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.8766 Å / Origin y: 6.3355 Å / Origin z: 9.2752 Å
111213212223313233
T0.1106 Å2-0.0151 Å2-0.0195 Å2-0.1215 Å20.0164 Å2--0.0927 Å2
L0.9933 °2-0.844 °20.0016 °2-3.2388 °20.7485 °2--1.2506 °2
S-0.0212 Å °0.0182 Å °0.0676 Å °0.1015 Å °-0.0071 Å °0.1374 Å °-0.0721 Å °-0.064 Å °0.0403 Å °
Refinement TLS groupSelection details: chain A

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