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- PDB-5vhd: DHX36 with an N-terminal truncation bound to ADP-AlF4 -

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Basic information

Entry
Database: PDB / ID: 5vhd
TitleDHX36 with an N-terminal truncation bound to ADP-AlF4
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 / 3'-UTR-mediated mRNA destabilization / mRNA 3'-UTR AU-rich region binding / positive regulation of cytoplasmic translation / regulation of transcription by RNA polymerase III / 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 / DNA helicase activity / regulation of mRNA stability / mRNA 3'-UTR binding / mRNA 5'-UTR binding / cytoplasmic stress granule / cellular response to UV / cellular response to heat / G-quadruplex RNA binding / spermatogenesis / perikaryon / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / DNA helicase / chromosome, telomeric region / RNA helicase activity / cell differentiation / negative regulation of translation / 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 / cytoplasm / cytosol
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
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / ATP-dependent DNA/RNA helicase DHX36
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 13, 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 1.3Mar 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 1.4Apr 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
D: DEAH (Asp-Glu-Ala-His) box polypeptide 36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7423
Polymers100,2111
Non-polymers5302
Water1,946108
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)62.030, 112.500, 63.180
Angle α, β, γ (deg.)90.00, 110.33, 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: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M potassium sodium tartrate and 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 28, 2016
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→46.734 Å / Num. obs: 26260 / % possible obs: 98.84 % / Redundancy: 5.1 % / Biso Wilson estimate: 42.18 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1495 / Rpim(I) all: 0.0709 / Net I/σ(I): 9.89

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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: 2.55→46.734 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 1004 3.82 %
Rwork0.1728 --
obs0.1744 26260 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→46.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6126 0 32 108 6266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026281
X-RAY DIFFRACTIONf_angle_d0.5628548
X-RAY DIFFRACTIONf_dihedral_angle_d14.1443793
X-RAY DIFFRACTIONf_chiral_restr0.0411004
X-RAY DIFFRACTIONf_plane_restr0.0031080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5501-2.68450.24991410.2053584X-RAY DIFFRACTION98
2.6845-2.85270.24841480.20563581X-RAY DIFFRACTION99
2.8527-3.07290.2691370.20993573X-RAY DIFFRACTION99
3.0729-3.3820.23621490.19913595X-RAY DIFFRACTION99
3.382-3.87120.22181410.1693624X-RAY DIFFRACTION99
3.8712-4.87650.18611460.14633617X-RAY DIFFRACTION99
4.8765-46.74230.1831420.15873682X-RAY DIFFRACTION99
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)
14.43990.3605-0.7851.8578-0.261.27390.01370.3153-0.1014-0.0684-0.00320.0866-0.0629-0.15760.00180.2949-0.00440.03010.3144-0.01870.2056-2.3194-3.8791-17.6446
20.8593-0.0743-0.66010.8085-0.67432.8541-0.0451-0.1734-0.0250.09910.005-0.1239-0.08040.16870.01410.2788-0.02030.04890.2937-0.02380.33793.3130.743210.7091
31.0398-0.6983-0.62770.74960.28390.61860.05850.00220.0632-0.1665-0.047-0.1312-0.07660.0688-0.04320.2673-0.03060.03340.2920.01510.278720.5888-7.8596-4.539
42.7660.1549-1.24471.63930.36763.22990.1683-0.2672-0.03080.2504-0.1119-0.099-0.10770.0731-0.02160.3566-0.00910.01120.20730.00990.363924.8336-30.27635.6236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 167 through 358 )
2X-RAY DIFFRACTION2chain 'D' and (resid 359 through 604 )
3X-RAY DIFFRACTION3chain 'D' and (resid 605 through 713 )
4X-RAY DIFFRACTION4chain 'D' and (resid 714 through 990 )

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