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- PDB-6up4: Crystal structure of the murine DHX36 helicase in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 6up4
TitleCrystal structure of the murine DHX36 helicase in complex with ADP
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
ADENOSINE-5'-DIPHOSPHATE / RNA helicase / ATP-dependent DNA/RNA helicase DHX36
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / molecular replacement / Resolution: 2.4 Å
AuthorsLiu, Z. / Xiao, T.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R21AR069908 United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Function of Auxiliary Domains of the DEAH/RHA Helicase DHX36 in RNA Remodeling.
Authors: Srinivasan, S. / Liu, Z. / Chuenchor, W. / Xiao, T.S. / Jankowsky, E.
History
DepositionOct 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)95,5413
Polymers95,0901
Non-polymers4522
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-19 kcal/mol
Surface area35710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.160, 115.930, 132.570
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 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-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7
Details: 10% PEG 5000 MME, 0.1 M HEPES pH 7.0, 5% v/v Tacsimate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.98 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 4, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→46.826 Å / Num. obs: 77042 / % possible obs: 100 % / Redundancy: 3.9 % / CC1/2: 1 / Rrim(I) all: 0.12 / Net I/σ(I): 10.8
Reflection shellResolution: 2.4→2.46 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2698 / CC1/2: 0.47 / Rrim(I) all: 1.52

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXdev_3374refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.4→46.826 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / Phase error: 26.71
RfactorNum. reflection% reflection
Rfree0.2357 2084 5.13 %
Rwork0.1861 --
obs0.1887 40658 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.06 Å2 / Biso mean: 60.1748 Å2 / Biso min: 19.82 Å2
Refinement stepCycle: final / Resolution: 2.4→46.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6546 0 28 145 6719
Biso mean--66.55 54.26 -
Num. residues----814
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4-2.45580.4181290.32222569
2.4558-2.51720.35181280.29472529
2.5172-2.58530.3051420.2782528
2.5853-2.66140.31151320.2382539
2.6614-2.74720.30961250.23412559
2.7472-2.84540.29751370.23482541
2.8454-2.95930.29511290.24072530
2.9593-3.0940.33661400.22892561
3.094-3.25710.24991320.21292570
3.2571-3.46110.27751630.20562525
3.4611-3.72820.23891510.17892560
3.7282-4.10320.22851430.16422586
4.1032-4.69650.1911410.14142599
4.6965-5.91520.19741480.15242622
5.9152-46.80.15831440.1462756
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)
11.4110.8549-0.59681.2757-0.640.9162-0.29690.2064-0.1029-0.65690.1948-0.10280.19580.15250.05450.6052-0.01640.03380.4232-0.03110.30679.644131.146711.9379
21.60240.8565-0.06973.2912-0.10491.6208-0.0476-0.11610.004-0.0659-0.0115-0.46660.0380.20040.04810.20030.0160.0020.23670.01520.3172-3.28069.803434.6876
32.1784-0.1810.42191.113-0.30591.44220.00420.0058-0.3888-0.008-0.0295-0.00220.19050.27850.03960.24770.03680.02680.2976-0.04430.333123.709927.30350.0368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 153 through 390 )A153 - 390
2X-RAY DIFFRACTION2chain 'A' and (resid 391 through 614 )A391 - 614
3X-RAY DIFFRACTION3chain 'A' and (resid 615 through 982 )A615 - 982

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