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- PDB-3b6e: Crystal structure of human DECH-box RNA Helicase MDA5 (Melanoma d... -

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Basic information

Entry
Database: PDB / ID: 3b6e
TitleCrystal structure of human DECH-box RNA Helicase MDA5 (Melanoma differentiation-associated protein 5), DECH-domain
ComponentsInterferon-induced helicase C domain-containing protein 1
KeywordsHYDROLASE / DECH / DExD/H RNA-binding helicase / innate immunity / IFIH1 / Structural Genomics / Structural Genomics Consortium / SGC / Antiviral defense / ATP-binding / Diabetes mellitus / Host-virus interaction / Immune response / Nucleotide-binding / Nucleus / Phosphorylation
Function / homology
Function and homology information


MDA-5 signaling pathway / regulation of type III interferon production / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / pattern recognition receptor activity / TRAF6 mediated IRF7 activation / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA ...MDA-5 signaling pathway / regulation of type III interferon production / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / pattern recognition receptor activity / TRAF6 mediated IRF7 activation / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of interferon-alpha production / antiviral innate immune response / TRAF6 mediated NF-kB activation / protein sumoylation / ribonucleoprotein complex binding / positive regulation of interferon-beta production / Negative regulators of DDX58/IFIH1 signaling / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / cellular response to virus / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / Ovarian tumor domain proteases / positive regulation of tumor necrosis factor production / double-stranded RNA binding / protein complex oligomerization / TRAF3-dependent IRF activation pathway / defense response to virus / RNA helicase activity / single-stranded RNA binding / Ub-specific processing proteases / RNA helicase / innate immune response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Interferon-induced helicase C domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsKarlberg, T. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Karlberg, T. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kallas, A. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Holmberg-Schiavone, L. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human DECH-box RNA Helicase MDA5 (Melanoma differentiation-associated protein 5), DECH-domain.
Authors: Karlberg, T. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / ...Authors: Karlberg, T. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kallas, A. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Holmberg-Schiavone, L.
History
DepositionOct 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)24,1282
Polymers24,1051
Non-polymers231
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.830, 72.830, 182.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Interferon-induced helicase C domain-containing protein 1 / Interferon-induced with helicase C domain protein 1 / Helicase with 2 CARD domains / Helicard / ...Interferon-induced with helicase C domain protein 1 / Helicase with 2 CARD domains / Helicard / Melanoma differentiation-associated protein 5 / MDA-5 / RNA helicase-DEAD box protein 116 / Murabutide down-regulated protein


Mass: 24104.863 Da / Num. of mol.: 1 / Fragment: DECH domain: Residues 277-490
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFIH1, MDA5, RH116 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold pRARE2
References: UniProt: Q9BYX4, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.2M Sodium citrate, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 12, 2007 / Details: Mirrors
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 38652 / Num. obs: 38652 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16 % / Rmerge(I) obs: 0.047 / Rsym value: 0.033 / Net I/σ(I): 37.7
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 10 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 7.4 / Num. unique all: 6278 / Rsym value: 0.196 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MAR345CCDdata collection
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→19.97 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.203 / SU ML: 0.04 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.069 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20371 1933 5 %RANDOM
Rwork0.17936 ---
all0.18057 36717 --
obs0.18057 36717 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.086 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 1 174 1616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221519
X-RAY DIFFRACTIONr_bond_other_d0.0010.021080
X-RAY DIFFRACTIONr_angle_refined_deg1.5362.0072060
X-RAY DIFFRACTIONr_angle_other_deg0.90832680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7365195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5725.08559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76615309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.808158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02263
X-RAY DIFFRACTIONr_nbd_refined0.220.2291
X-RAY DIFFRACTIONr_nbd_other0.1850.21084
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2727
X-RAY DIFFRACTIONr_nbtor_other0.0860.2802
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2104
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9881.5940
X-RAY DIFFRACTIONr_mcbond_other0.2631.5370
X-RAY DIFFRACTIONr_mcangle_it1.84721541
X-RAY DIFFRACTIONr_scbond_it2.7813588
X-RAY DIFFRACTIONr_scangle_it4.6724.5511
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 139 -
Rwork0.179 2641 -
obs--100 %
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)
10.9012-0.41351.15025.42414.97797.25910.04150.0418-0.0173-0.3343-0.48730.37770.3413-0.99630.4459-0.027-0.13480.06230.2916-0.16780.0417.05932.83823.131
20.40180.3130.26053.351-0.67691.52260.0623-0.09860.01910.1945-0.1687-0.0997-0.16630.06950.1064-0.0123-0.0528-0.0197-0.04350.0141-0.056624.98811.9217.677
31.20561.46380.76322.9971.25721.2067-0.09780.1123-0.1341-0.1290.1242-0.38580.03710.1139-0.02640.0271-0.02860.0275-0.03140.0123-0.009823.98-2.0337.675
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA292 - 30918 - 35
2X-RAY DIFFRACTION2AA310 - 41936 - 145
3X-RAY DIFFRACTION3AA420 - 490146 - 216

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