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- PDB-5vha: DHX36 with an N-terminal truncation -

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Basic information

Entry
Database: PDB / ID: 5vha
TitleDHX36 with an N-terminal truncation
ComponentsDEAH (Asp-Glu-Ala-His) box polypeptide 36
KeywordsHYDROLASE
Function / homology
Function and homology information


DEx/H-box helicases activate type I IFN and inflammatory cytokines production / positive regulation of intracellular mRNA localization / positive regulation of hematopoietic progenitor cell differentiation / positive regulation of cardioblast differentiation / positive regulation of mRNA 3'-end processing / positive regulation of telomere maintenance via telomere lengthening / pre-miRNA binding / G-quadruplex DNA unwinding / RNA secondary structure unwinding / G-quadruplex DNA binding ...DEx/H-box helicases activate type I IFN and inflammatory cytokines production / positive regulation of intracellular mRNA localization / positive regulation of hematopoietic progenitor cell differentiation / positive regulation of cardioblast differentiation / positive regulation of mRNA 3'-end processing / positive regulation of telomere maintenance via telomere lengthening / pre-miRNA binding / G-quadruplex DNA unwinding / 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 cytoplasmic translation / cellular response to arsenite ion / telomerase RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / regulation of embryonic development / positive regulation of transcription initiation by RNA polymerase II / regulation of mRNA stability / DNA helicase activity / mRNA 3'-UTR binding / mRNA 5'-UTR binding / cytoplasmic stress granule / cellular response to UV / cellular response to heat / perikaryon / G-quadruplex RNA binding / spermatogenesis / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / DNA helicase / negative regulation of translation / RNA helicase activity / chromosome, telomeric region / cell differentiation / 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 / 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
ATP-dependent DNA/RNA helicase DHX36
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.227 Å
AuthorsChen, M. / Ferre-D'Amare, A.
CitationJournal: Nature / Year: 2018
Title: Structural basis of G-quadruplex unfolding by the DEAH/RHA helicase DHX36.
Authors: Chen, M.C. / Tippana, R. / Demeshkina, N.A. / Murat, P. / Balasubramanian, S. / Myong, S. / Ferre-D'Amare, A.R.
History
DepositionApr 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.4Mar 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DEAH (Asp-Glu-Ala-His) box polypeptide 36


Theoretical massNumber of molelcules
Total (without water)100,2111
Polymers100,2111
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.324, 109.191, 62.406
Angle α, β, γ (deg.)90.00, 112.71, 90.00
Int Tables number4
Space group name H-MP1211
DetailsMonomer as determined by gel filtration

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Components

#1: Protein DEAH (Asp-Glu-Ala-His) box polypeptide 36 / DEAH-box helicase 36


Mass: 100211.336 Da / Num. of mol.: 1 / Fragment: residues 150-1010
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: DHX36 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05B79
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 1.92 Å3/Da / Density % sol: 36.05 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M ammonium citrate tribasic pH 7.0 and 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 18, 2016
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.227→39.614 Å / Num. obs: 37011 / % possible obs: 99.75 % / Redundancy: 6.5 % / Biso Wilson estimate: 40.32 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08661 / Rpim(I) all: 0.03684 / Net I/σ(I): 18.28

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet labeled protein

Resolution: 2.227→39.614 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2174 1995 5.39 %
Rwork0.1767 --
obs0.1789 37004 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.227→39.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6286 0 0 191 6477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046413
X-RAY DIFFRACTIONf_angle_d0.7448720
X-RAY DIFFRACTIONf_dihedral_angle_d15.0513884
X-RAY DIFFRACTIONf_chiral_restr0.0491017
X-RAY DIFFRACTIONf_plane_restr0.0051114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2272-2.28290.28611440.23162438X-RAY DIFFRACTION97
2.2829-2.34460.26631460.21742470X-RAY DIFFRACTION100
2.3446-2.41360.27221360.20332505X-RAY DIFFRACTION100
2.4136-2.49150.23821400.21022495X-RAY DIFFRACTION100
2.4915-2.58050.26571460.20882506X-RAY DIFFRACTION100
2.5805-2.68380.3031370.20912490X-RAY DIFFRACTION100
2.6838-2.80590.25421400.20552498X-RAY DIFFRACTION100
2.8059-2.95380.23781510.20412497X-RAY DIFFRACTION100
2.9538-3.13880.2451340.21132526X-RAY DIFFRACTION100
3.1388-3.3810.24741430.19992495X-RAY DIFFRACTION100
3.381-3.72110.22981440.17492493X-RAY DIFFRACTION100
3.7211-4.2590.20241450.15192515X-RAY DIFFRACTION100
4.259-5.36370.16591370.14312526X-RAY DIFFRACTION100
5.3637-39.62020.17551520.15212555X-RAY DIFFRACTION100
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)
11.0356-0.0806-0.37480.851-0.12281.24840.0758-0.08530.083-0.025-0.078-0.0375-0.12770.05350.01460.26560.0140.05420.2297-0.00320.309937.38710.165765.3918
22.27230.4047-2.26890.3357-0.34672.6532-0.0590.0072-0.0779-0.0347-0.02740.06780.1366-0.05840.09460.27920.0120.00840.2561-0.00710.310729.9913-4.628253.1964
32.5421-0.2045-0.85791.54150.47562.58970.11030.2495-0.1411-0.3227-0.05220.2213-0.0716-0.2593-0.07520.3323-0.0122-0.070.2201-0.00110.375211.2264-27.962152.641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 167 through 487 )
2X-RAY DIFFRACTION2chain 'A' and (resid 488 through 678 )
3X-RAY DIFFRACTION3chain 'A' and (resid 679 through 994 )

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