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- PDB-3ts9: Crystal Structure of the MDA5 Helicase Insert Domain -

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Basic information

Entry
Database: PDB / ID: 3ts9
TitleCrystal Structure of the MDA5 Helicase Insert Domain
ComponentsInterferon-induced helicase C domain-containing protein 1
KeywordsANTIVIRAL PROTEIN / HYDROLASE / helix bundle / FANCM helicase / Super Family 2 helicase / SF2 helicase / DExD/H helicase / Rig-I-like helicase
Function / homology
Function and homology information


MDA-5 signaling pathway / Ub-specific processing proteases / positive regulation of response to cytokine stimulus / pattern recognition receptor activity / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / antiviral innate immune response / protein sumoylation / positive regulation of interferon-alpha production ...MDA-5 signaling pathway / Ub-specific processing proteases / positive regulation of response to cytokine stimulus / pattern recognition receptor activity / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / antiviral innate immune response / protein sumoylation / positive regulation of interferon-alpha production / ribonucleoprotein complex binding / positive regulation of interferon-beta production / response to virus / cellular response to virus / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / double-stranded RNA binding / protein complex oligomerization / defense response to virus / RNA helicase activity / single-stranded RNA binding / RNA helicase / protein domain specific binding / innate immune response / ATP hydrolysis activity / mitochondrion / DNA binding / zinc ion binding / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / 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 ...phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / 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 / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Death-like domain superfamily / Helicase conserved C-terminal domain / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Interferon-induced helicase C domain-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.003 Å
AuthorsBerke, I.C. / Modis, Y.
CitationJournal: Embo J. / Year: 2012
Title: MDA5 cooperatively forms dimers and ATP-sensitive filaments upon binding double-stranded RNA.
Authors: Berke, I.C. / Modis, Y.
History
DepositionSep 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon-induced helicase C domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7424
Polymers16,4541
Non-polymers2883
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)23.878, 57.618, 90.332
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Interferon-induced helicase C domain-containing protein 1 / MDA-5 / Melanoma differentiation-associated protein 5 / Helicase with 2 CARD domains / Helicard / ...MDA-5 / Melanoma differentiation-associated protein 5 / Helicase with 2 CARD domains / Helicard / Interferon induced with helicase C domain protein


Mass: 16453.766 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ifih1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8R5F7, RNA helicase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN FRAGMENT COMPRISES THE MDA5 HELICASE INSERT (UNP RESIDUES 545-697) WITH RESIDUES 646-663 DELETED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.8934.86
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop9Crystal #1: 1.9 M ammonium sulfate, 49 mM sodium phosphate, 49 mM glycine, 14 mM succinic acid, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop9Crystal #2: 2.0 M ammonium sulfate, 49 mM sodium phosphate, 49 mM glycine, 14 mM succinic acid, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.075
SYNCHROTRONNSLS X29A20.9791, 0.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJun 22, 2010
ADSC QUANTUM 3152CCDApr 29, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Cryogenically cooled double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirrorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0751
20.97911
30.97931
ReflectionRedundancy: 12.6 % / Av σ(I) over netI: 17.84 / Number: 99334 / Rmerge(I) obs: 0.13 / Χ2: 1.71 / D res high: 2.05 Å / D res low: 50 Å / Num. obs: 7880 / % possible obs: 92
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.425099.510.0923.38812.2
3.514.4280.310.1012.28112.3
3.063.5110010.1212.30213.4
2.783.0610010.1531.92913.2
2.582.7899.610.1821.53713.1
2.432.5898.110.2161.29213.3
2.312.4397.610.2751.08213.2
2.212.3148.210.4481.00110.5
2.122.219710.4790.86612.4
2.052.1297.410.4920.67811.2
ReflectionResolution: 2.003→50 Å / Num. all: 8917 / Num. obs: 8873 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.87 / Redundancy: 6.7 % / Rmerge(I) obs: 0.122 / Χ2: 1.573 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
2.003-2.096.88481.2671,2100
2.09-2.186.88821.3311,21000.683
2.18-2.276.98361.3861,21000.552
2.27-2.396.98961.5711,21000.4
2.39-2.546.88471.6651,21000.322
2.54-2.746.88871.7371,21000.24
2.74-3.026.88921.8751,21000.174
3.02-3.456.88891.7021,21000.127
3.45-4.356.69001.7741,21000.095
4.35-506.19961.4011,299.70.07

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
Phasing MADD res high: 2.05 Å / D res low: 1000 Å / FOM : 0.51 / Reflection: 7735
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
2 wavelength110.97911.58-7.05
2 wavelength120.97931.25-9.38
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se11.4850.7640.9520.2742.091
2Se29.3470.8680.1180.152.069
3Se600.8510.1420.9052.486
4Se17.0560.8590.3230.7831.135
5Se54.5680.9490.1340.4172.289
Phasing MAD shell
Resolution (Å)FOM Reflection
7.49-10000.69432
4.69-7.490.76732
3.65-4.690.65784
3.09-3.650.691069
2.73-3.090.591197
2.47-2.730.471271
2.27-2.470.31847
2.12-2.270.211403
Phasing dmFOM : 0.65 / FOM acentric: 0.66 / FOM centric: 0.65 / Reflection: 7681 / Reflection acentric: 6264 / Reflection centric: 1417
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.9-500.910.930.88413232181
3.7-5.90.930.940.911120834286
2.9-3.70.850.860.8113441078266
2.6-2.90.730.740.6514041179225
2.2-2.60.520.540.4219151646269
2.1-2.20.30.320.1414851295190

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.15phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
RefinementMethod to determine structure: MAD / Resolution: 2.003→35.546 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8031 / SU ML: 0.56 / σ(F): 0 / σ(I): 1.87 / Phase error: 25.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 442 5.01 %RANDOM
Rwork0.1927 ---
all0.1943 8917 --
obs0.1943 8829 99.04 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.692 Å2 / ksol: 0.392 e/Å3
Displacement parametersBiso max: 126.59 Å2 / Biso mean: 41.0735 Å2 / Biso min: 15.31 Å2
Baniso -1Baniso -2Baniso -3
1--2.6168 Å20 Å20 Å2
2--13.6007 Å2-0 Å2
3---1.8683 Å2
Refinement stepCycle: LAST / Resolution: 2.003→35.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 15 40 1102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021078
X-RAY DIFFRACTIONf_angle_d0.5781447
X-RAY DIFFRACTIONf_chiral_restr0.047150
X-RAY DIFFRACTIONf_plane_restr0.002186
X-RAY DIFFRACTIONf_dihedral_angle_d14.204406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.003-2.29310.32231400.24752660280097
2.2931-2.88890.2531470.198127972944100
2.8889-35.5520.19131550.180129303085100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.4402-1.4151-0.46844.7821-1.21083.1987-0.061-0.10790.46810.24980.0051-0.0185-0.32840.11010.10860.1347-0.0341-0.02110.1825-0.06040.19136.68234.917960.7585
24.58130.13640.1085.6789-1.13646.68830.11340.0721-0.1333-0.0285-0.05850.2567-0.1243-0.2043-0.06240.07250.02310.0010.1022-0.03870.13822.250128.653256.6718
37.59640.91960.42914.13264.23214.322-0.29850.9048-0.5264-0.0176-0.22930.25660.8505-0.10910.37020.4452-0.02040.01120.3239-0.07580.23156.337116.528850.8499
44.0341-0.22270.3914.8991-3.33327.9891-0.1984-0.4578-0.17420.2804-0.0049-0.36361.00780.90670.12680.24130.1294-0.05950.3587-0.04390.209713.37121.809461.3425
56.09882.5839-5.08566.1348-3.68934.7064-0.37610.3958-1.45750.6211-0.0389-0.50120.6834-1.01640.3890.74-0.1582-0.01521.0414-0.12420.70059.436316.791838.578
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1resid 7:43 and chain AA7 - 43
2X-RAY DIFFRACTION2resid 44:86 and chain AA44 - 86
3X-RAY DIFFRACTION3chain A and resid 87:99A87 - 99
4X-RAY DIFFRACTION4resid 111:138 and chain AA111 - 138
5X-RAY DIFFRACTION5chain A and resid 100:110A100 - 110

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