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- PDB-8ejm: Crystal structure of human DEAH-box helicase DHX15 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8ejm
TitleCrystal structure of human DEAH-box helicase DHX15 in complex with SUGP1 G-patch
Components
  • ATP-dependent RNA helicase DHX15
  • SURP and G-patch domain-containing protein 1
KeywordsRNA BINDING PROTEIN / HYDROLASE / Complex / helicase / splicing factor
Function / homology
Function and homology information


response to alkaloid / U12-type spliceosomal complex / ATP-dependent activity, acting on RNA / antiviral innate immune response / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / helicase activity / mRNA splicing, via spliceosome / response to toxic substance ...response to alkaloid / U12-type spliceosomal complex / ATP-dependent activity, acting on RNA / antiviral innate immune response / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / helicase activity / mRNA splicing, via spliceosome / response to toxic substance / mRNA processing / double-stranded RNA binding / defense response to virus / RNA helicase activity / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / nuclear speck / RNA helicase / mRNA binding / nucleolus / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
SURP and G-patch domain-containing protein 1/2 / DHX15, DEXH-box helicase domain / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. ...SURP and G-patch domain-containing protein 1/2 / DHX15, DEXH-box helicase domain / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / : / 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 / SURP and G-patch domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHuang, J. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118093 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: DHX15 is involved in SUGP1-mediated RNA missplicing by mutant SF3B1 in cancer.
Authors: Zhang, J. / Huang, J. / Xu, K. / Xing, P. / Huang, Y. / Liu, Z. / Tong, L. / Manley, J.L.
History
DepositionSep 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DHX15
B: SURP and G-patch domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,72310
Polymers86,8242
Non-polymers8998
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-88 kcal/mol
Surface area31400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.300, 90.956, 213.187
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-802-

GOL

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein ATP-dependent RNA helicase DHX15 / ATP-dependent RNA helicase #46 / DEAH box protein 15 / Splicing factor Prp43 / hPrp43


Mass: 78730.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHX15, DBP1, DDX15 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O43143, RNA helicase
#2: Protein SURP and G-patch domain-containing protein 1 / RNA-binding protein RBP / Splicing factor 4


Mass: 8094.042 Da / Num. of mol.: 1 / Fragment: residues 543-614
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUGP1, SF4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8IWZ8

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Non-polymers , 6 types, 281 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, ammonium sulfate, HEPES buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→58.7 Å / Num. obs: 74658 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 36.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.2
Reflection shellResolution: 1.8→1.91 Å / Rmerge(I) obs: 1.324 / Num. unique obs: 11895 / CC1/2: 0.696

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SH6

6sh6


Resolution: 1.8→58.67 Å / SU ML: 0.299 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.5971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2244 3731 5 %
Rwork0.1887 70866 -
obs0.1905 74597 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.55 Å2
Refinement stepCycle: LAST / Resolution: 1.8→58.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5787 0 52 273 6112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135976
X-RAY DIFFRACTIONf_angle_d1.15368101
X-RAY DIFFRACTIONf_chiral_restr0.0721905
X-RAY DIFFRACTIONf_plane_restr0.00991058
X-RAY DIFFRACTIONf_dihedral_angle_d14.26822296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.42953680.40816966X-RAY DIFFRACTION99.11
1.86-1.940.34373690.31077010X-RAY DIFFRACTION99.96
1.94-2.020.28493690.24457005X-RAY DIFFRACTION99.92
2.02-2.130.26613700.20887054X-RAY DIFFRACTION99.85
2.13-2.260.25343720.21037073X-RAY DIFFRACTION99.87
2.26-2.440.27713710.21167039X-RAY DIFFRACTION99.87
2.44-2.680.26793720.20287080X-RAY DIFFRACTION99.95
2.68-3.070.24423750.19697124X-RAY DIFFRACTION99.95
3.07-3.870.21323770.17637146X-RAY DIFFRACTION99.89
3.87-58.670.17433880.15747369X-RAY DIFFRACTION99.74

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