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- PDB-4i1s: Melanoma differentiation associated protein-5 Helicase domain com... -

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Basic information

Entry
Database: PDB / ID: 4i1s
TitleMelanoma differentiation associated protein-5 Helicase domain complex with inhibitor Non-structural protein V
Components
  • Melanoma differentiation associated protein-5
  • Non-structural protein V
KeywordsHydrolase/Hydrolase Inhibitor / SF2-ATPase / Helicase / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / ubiquitin-like ligase-substrate adaptor activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / defense response to virus / host cell cytoplasm / RNA helicase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / innate immune response ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / ubiquitin-like ligase-substrate adaptor activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / defense response to virus / host cell cytoplasm / RNA helicase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / innate immune response / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Rhinovirus 14, subunit 4 - #340 / Paramyxovirinae protein V, zinc-binding domain / Zinc-binding domain of Paramyxoviridae V protein / phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain ...Rhinovirus 14, subunit 4 - #340 / Paramyxovirinae protein V, zinc-binding domain / Zinc-binding domain of Paramyxoviridae V protein / phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / Caspase recruitment domain / Caspase recruitment domain / Rhinovirus 14, subunit 4 / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Death-like domain superfamily / Helicase conserved C-terminal domain / Few Secondary Structures / Irregular / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA helicase / Non-structural protein V
Similarity search - Component
Biological speciesSus scrofa (pig)
Simian virus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.293 Å
AuthorsMotz, C. / Witte, G. / Hopfner, K.P.
CitationJournal: Science / Year: 2013
Title: Paramyxovirus V proteins disrupt the fold of the RNA sensor MDA5 to inhibit antiviral signaling.
Authors: Motz, C. / Schuhmann, K.M. / Kirchhofer, A. / Moldt, M. / Witte, G. / Conzelmann, K.K. / Hopfner, K.P.
History
DepositionNov 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Jul 26, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Melanoma differentiation associated protein-5
B: Non-structural protein V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5624
Polymers34,4312
Non-polymers1312
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-9 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.070, 52.490, 120.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe complete biological assembly is present in the uploaded PDB: one chain A and one chain B in the unit cell (one heterodimer/ASU in P212121)

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Components

#1: Protein Melanoma differentiation associated protein-5


Mass: 28586.756 Da / Num. of mol.: 1
Fragment: helicase domain region 641-665 replaced by SGSGS, proteolysis by trypsin during crystallization
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: MDA5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: A7LCX1
#2: Protein Non-structural protein V


Mass: 5844.556 Da / Num. of mol.: 1
Fragment: region 55-79 replaced by SGSGSGSGSG, proteolysis by trypsin during crystallization
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 5 / Strain: W3 / Gene: P/V / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: P11207
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES pH7.5 18% (w/v) PEG1500 trace amounts of trypsin , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2012
RadiationMonochromator: Si 111 channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.293→50 Å / Num. all: 27871 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.17 % / Biso Wilson estimate: 39.03 Å2 / Rsym value: 0.137 / Net I/σ(I): 13.64
Reflection shellResolution: 2.29→2.35 Å / Redundancy: 6.77 % / Mean I/σ(I) obs: 2.58 / Num. unique all: 1874 / Rsym value: 0.838 / % possible all: 83.8

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Processing

Software
NameVersionClassification
DNAdata collection
SHARPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.293→48.141 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 21.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 1427 5.12 %RANDOM
Rwork0.1792 ---
all0.1817 27871 --
obs0.1817 27856 99.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.293→48.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 2 110 2471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092422
X-RAY DIFFRACTIONf_angle_d1.1733259
X-RAY DIFFRACTIONf_dihedral_angle_d16.027929
X-RAY DIFFRACTIONf_chiral_restr0.077355
X-RAY DIFFRACTIONf_plane_restr0.004421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2933-2.37530.24251160.22262467X-RAY DIFFRACTION93
2.3753-2.47040.31081370.22612673X-RAY DIFFRACTION100
2.4704-2.58280.29631720.21232624X-RAY DIFFRACTION100
2.5828-2.7190.28971770.21922662X-RAY DIFFRACTION100
2.719-2.88930.25811520.20742638X-RAY DIFFRACTION100
2.8893-3.11240.23831500.19172648X-RAY DIFFRACTION100
3.1124-3.42550.20351340.17062694X-RAY DIFFRACTION100
3.4255-3.9210.20261570.14772656X-RAY DIFFRACTION100
3.921-4.93930.1821320.13372668X-RAY DIFFRACTION100
4.9393-48.15160.22991000.19862699X-RAY DIFFRACTION99

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