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- PDB-6up2: Crystal structure of the murine DHX36 helicase -

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Basic information

Entry
Database: PDB / ID: 6up2
TitleCrystal structure of the murine DHX36 helicase
ComponentsDhx36 protein
KeywordsRNA BINDING PROTEIN / helicase / ATP-dependent / RNA-binding / DNA-binding / G4 resolvase
Function / homology
Function and homology information


positive regulation of intracellular mRNA localization / positive regulation of hematopoietic progenitor cell differentiation / positive regulation of cardioblast differentiation / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / positive regulation of mRNA 3'-end processing / telomerase RNA stabilization / positive regulation of telomere maintenance via telomere lengthening / pre-miRNA binding / G-quadruplex DNA unwinding / positive regulation of myeloid dendritic cell cytokine production ...positive regulation of intracellular mRNA localization / positive regulation of hematopoietic progenitor cell differentiation / positive regulation of cardioblast differentiation / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / positive regulation of mRNA 3'-end processing / telomerase RNA stabilization / positive regulation of telomere maintenance via telomere lengthening / pre-miRNA binding / G-quadruplex DNA unwinding / positive regulation of myeloid dendritic cell cytokine production / RNA secondary structure unwinding / G-quadruplex DNA binding / positive regulation of dendritic spine morphogenesis / regulation of transcription by RNA polymerase III / 3'-UTR-mediated mRNA destabilization / mRNA 3'-UTR AU-rich region binding / positive regulation of telomere maintenance / positive regulation of cytoplasmic translation / cellular response to arsenite ion / telomerase RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / response to exogenous dsRNA / positive regulation of interferon-alpha production / regulation of embryonic development / positive regulation of transcription initiation by RNA polymerase II / ATP-dependent activity, acting on DNA / regulation of mRNA stability / DNA helicase activity / ossification / mRNA 3'-UTR binding / response to virus / mRNA 5'-UTR binding / cytoplasmic stress granule / histone deacetylase binding / cellular response to UV / single-stranded DNA binding / double-stranded RNA binding / cellular response to heat / perikaryon / G-quadruplex RNA binding / spermatogenesis / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / negative regulation of translation / RNA helicase activity / chromosome, telomeric region / cell differentiation / nucleic acid binding / transcription cis-regulatory region binding / hydrolase activity / RNA helicase / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / axon / innate immune response / dendrite / positive regulation of gene expression / magnesium ion binding / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase ...: / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA helicase / ATP-dependent DNA/RNA helicase DHX36
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / molecular replacement / Resolution: 1.97 Å
AuthorsChuenchor, W. / Jiang, J. / Xiao, T.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Z01AI000960 United States
CitationJournal: To be published
Title: Crystal structure of the murine DHX36 helicase
Authors: Chuenchor, W. / Jiang, J. / Xiao, T.S.
History
DepositionOct 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dhx36 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2173
Polymers95,0901
Non-polymers1282
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-10 kcal/mol
Surface area34930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.246, 67.691, 103.683
Angle α, β, γ (deg.)90.000, 92.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dhx36 protein /


Mass: 95089.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dhx36 / Plasmid: pSMT3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B2RQS6, UniProt: Q8VHK9*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5 / Details: 10% PEG3350, 200 mM proline, 100 mM HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 8, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.97→45.392 Å / Num. obs: 59446 / % possible obs: 99 % / Redundancy: 3.4 % / Biso Wilson estimate: 38.16 Å2 / CC1/2: 1 / Rrim(I) all: 0.057 / Net I/σ(I): 20.5
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5706 / CC1/2: 0.52 / Rrim(I) all: 0.643 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.97→45.392 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / Phase error: 26.95
RfactorNum. reflection% reflection
Rfree0.2291 3000 5.06 %
Rwork0.1798 --
obs0.1822 59264 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 163.68 Å2 / Biso mean: 48.86 Å2 / Biso min: 19.7 Å2
Refinement stepCycle: final / Resolution: 1.97→45.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6493 0 7 272 6772
Biso mean--61.18 48.68 -
Num. residues----809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096633
X-RAY DIFFRACTIONf_angle_d1.2858966
X-RAY DIFFRACTIONf_chiral_restr0.0521019
X-RAY DIFFRACTIONf_plane_restr0.0081141
X-RAY DIFFRACTIONf_dihedral_angle_d15.0082529
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.97-2.00230.42221480.3753247892
2.0023-2.03680.35741590.3067265098
2.0368-2.07390.33521340.2901255295
2.0739-2.11380.36921500.2711264397
2.1138-2.15690.32221320.25072680100
2.1569-2.20380.29771150.2422689100
2.2038-2.25510.31111420.2372271398
2.2551-2.31150.30671470.2371264599
2.3115-2.37390.27911300.21422723100
2.3739-2.44380.28241580.21092693100
2.4438-2.52270.26981420.19692714100
2.5227-2.61280.23461470.19012711100
2.6128-2.71740.23771440.1967266499
2.7174-2.84110.22591300.19022733100
2.8411-2.99080.25391480.19252692100
2.9908-3.17820.23491350.1948272199
3.1782-3.42350.23021570.1828270899
3.4235-3.76790.2181370.1611270299
3.7679-4.31270.20041400.1421271299
4.3127-5.43210.16621640.1344271199
5.4321-45.390.18791410.1532273097
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)
10.89840.7433-0.17560.66930.55321.0461-0.02120.1630.0756-0.04920.02220.05150.0095-0.0517-0.00010.2915-0.0008-0.02110.37010.02710.3026-0.55218.5742-44.0998
20.9472-0.32430.01631.2050.050.9969-0.06830.0953-0.06810.15540.04490.15630.0469-0.1191-0.00020.2455-0.0132-0.00410.3570.07640.3379-34.312333.4095-35.6495
30.3662-0.07140.02070.4833-0.26260.2773-0.02220.1295-0.0086-0.0612-0.0225-0.02940.05220.013-0.00010.2562-0.01030.0020.27230.00680.2455-23.883114.5879-25.9007
40.90520.08720.13891.495-0.35280.8321-0.01410.0191-0.08370.1751-0.09390.00340.1529-0.0862-0.00010.3207-0.00010.01910.2082-0.01160.2438-23.5729-1.992-8.0625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 158:378)A158 - 378
2X-RAY DIFFRACTION2(chain A and resid 379:519)A379 - 519
3X-RAY DIFFRACTION3(chain A and resid 520:789)A520 - 789
4X-RAY DIFFRACTION4(chain A and resid 790:981)A790 - 981

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