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- PDB-5xdr: Crystal structure of human DEAH-box RNA helicase DHX15 in complex... -

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Basic information

Entry
Database: PDB / ID: 5xdr
TitleCrystal structure of human DEAH-box RNA helicase DHX15 in complex with ADP
ComponentsPre-mRNA-splicing factor ATP-dependent RNA helicase DHX15
KeywordsHYDROLASE / RNA helicase / DEAH-box / DHX15 / Prp43
Function / homology
Function and homology information


U12-type spliceosomal complex / response to alkaloid / ATP-dependent activity, acting on RNA / mRNA Polyadenylation / mRNA Splicing - Major Pathway / RNA splicing / helicase activity / antiviral innate immune response / spliceosomal complex / mRNA splicing, via spliceosome ...U12-type spliceosomal complex / response to alkaloid / ATP-dependent activity, acting on RNA / mRNA Polyadenylation / mRNA Splicing - Major Pathway / RNA splicing / helicase activity / antiviral innate immune response / spliceosomal complex / mRNA splicing, via spliceosome / Dengue Virus-Host Interactions / response to toxic substance / mRNA processing / double-stranded RNA binding / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / RNA helicase activity / nuclear speck / RNA helicase / nucleolus / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
DHX15, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. ...DHX15, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / 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 domain / DEAD/DEAH box helicase / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent RNA helicase DHX15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsMurakami, K. / Nakano, K. / Shimizu, T. / Ohto, U.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: The crystal structure of human DEAH-box RNA helicase 15 reveals a domain organization of the mammalian DEAH/RHA family
Authors: Murakami, K. / Nakano, K. / Shimizu, T. / Ohto, U.
History
DepositionMar 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7555
Polymers79,1121
Non-polymers6444
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area30970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.919, 89.377, 211.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 / ATP-dependent RNA helicase #46 / DEAH box protein 15


Mass: 79111.758 Da / Num. of mol.: 1 / Fragment: UNP residues 110-795 / Mutation: T678S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHX15, DBP1, DDX15 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43143, RNA helicase
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG4000, lithium sulfate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→105.9 Å / Num. obs: 31906 / % possible obs: 99.98 % / Redundancy: 13.5 % / Net I/σ(I): 18.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 2→105.54 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.907 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26911 2649 5 %RANDOM
Rwork0.22282 ---
obs0.22523 50047 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.787 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å2-0 Å2
2--0.17 Å20 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 2→105.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5458 0 38 90 5586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195610
X-RAY DIFFRACTIONr_bond_other_d0.0020.025249
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.9817610
X-RAY DIFFRACTIONr_angle_other_deg1.028312190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2795678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67623.893262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.007151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6921545
X-RAY DIFFRACTIONr_chiral_restr0.0980.2853
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216136
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021115
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.164.8262715
X-RAY DIFFRACTIONr_mcbond_other2.164.8262714
X-RAY DIFFRACTIONr_mcangle_it3.4157.233392
X-RAY DIFFRACTIONr_mcangle_other3.4157.2313393
X-RAY DIFFRACTIONr_scbond_it2.135.112895
X-RAY DIFFRACTIONr_scbond_other2.1195.12888
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4087.5594207
X-RAY DIFFRACTIONr_long_range_B_refined5.67756.2186217
X-RAY DIFFRACTIONr_long_range_B_other5.66956.1866204
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 204 -
Rwork0.328 3661 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 19.8432 Å / Origin y: -21.7664 Å / Origin z: 27.9568 Å
111213212223313233
T0.0719 Å2-0.0719 Å2-0.0067 Å2-0.0774 Å20.0247 Å2--0.1643 Å2
L0.3595 °20.2125 °2-0.1859 °2-0.214 °2-0.3574 °2--0.8496 °2
S-0.1312 Å °0.1538 Å °0.0565 Å °-0.1095 Å °0.1116 Å °-0.0088 Å °0.1796 Å °-0.1602 Å °0.0196 Å °

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