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- PDB-6sh7: Crystal structure of the human DEAH-helicase DHX15 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6sh7
TitleCrystal structure of the human DEAH-helicase DHX15 in complex with the NKRF G-patch
Components
  • NF-kappa-B-repressing factor
  • Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15
KeywordsHYDROLASE / G-patch / DEAH helicase / DExH helicase
Function / homology
Function and homology information


U12-type spliceosomal complex / response to alkaloid / ATP-dependent activity, acting on RNA / ATPase activator activity / antiviral innate immune response / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / helicase activity / mRNA splicing, via spliceosome ...U12-type spliceosomal complex / response to alkaloid / ATP-dependent activity, acting on RNA / ATPase activator activity / 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 / DNA-binding transcription activator activity, RNA polymerase II-specific / defense response to virus / RNA helicase activity / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / nuclear speck / RNA helicase / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
NF-kappaB-repression factor, R3H domain / Putative single-stranded nucleic acids-binding domain / R3H domain / R3H domain / R3H domain superfamily / R3H domain profile. / DHX15, DEXH-box helicase domain / G-patch domain / G-patch domain profile. / G-patch domain ...NF-kappaB-repression factor, R3H domain / Putative single-stranded nucleic acids-binding domain / R3H domain / R3H domain / R3H domain superfamily / R3H domain profile. / DHX15, DEXH-box helicase domain / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding 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 / Double-stranded RNA binding motif / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Double-stranded RNA-binding domain / 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
NF-kappa-B-repressing factor / ATP-dependent RNA helicase DHX15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsJonas, S. / Studer, M.K. / Ivanovic, L.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179498 Switzerland
Swiss National Science Foundation182880 Switzerland
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural basis for DEAH-helicase activation by G-patch proteins.
Authors: Studer, M.K. / Ivanovic, L. / Weber, M.E. / Marti, S. / Jonas, S.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionAug 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: NF-kappa-B-repressing factor


Theoretical massNumber of molelcules
Total (without water)86,4892
Polymers86,4892
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-29 kcal/mol
Surface area31650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.243, 90.024, 213.885
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-834-

HOH

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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: 79063.750 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: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: O43143, RNA helicase
#2: Protein NF-kappa-B-repressing factor / NFkB-repressing factor / Protein ITBA4 / Transcription factor NRF


Mass: 7425.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NKRF, ITBA4, NRF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: O15226
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M carboxylic acids, 0.1 M BICINE/Tris pH 8.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000041 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000041 Å / Relative weight: 1
ReflectionResolution: 2.21→46.23 Å / Num. obs: 39975 / % possible obs: 99.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 61.95 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.052 / Rrim(I) all: 0.187 / Net I/σ(I): 8.2
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 13.5 % / Num. unique obs: 3912 / CC1/2: 0.38 / Rpim(I) all: 0.763 / % possible all: 98.7

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XDR

5xdr


Resolution: 2.21→46.23 Å / SU ML: 0.3908 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.7663
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2508 1983 4.96 %
Rwork0.209 37975 -
obs0.2111 39958 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.88 Å2
Refinement stepCycle: LAST / Resolution: 2.21→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5711 0 0 34 5745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00185824
X-RAY DIFFRACTIONf_angle_d0.47167880
X-RAY DIFFRACTIONf_chiral_restr0.0391883
X-RAY DIFFRACTIONf_plane_restr0.00361020
X-RAY DIFFRACTIONf_dihedral_angle_d15.76153578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.270.36491370.35282668X-RAY DIFFRACTION98.15
2.27-2.330.33371360.31452661X-RAY DIFFRACTION99.96
2.33-2.40.33811330.30542674X-RAY DIFFRACTION99.93
2.4-2.480.37861420.30172694X-RAY DIFFRACTION99.89
2.48-2.560.34411430.27972704X-RAY DIFFRACTION99.82
2.56-2.670.2771420.26542686X-RAY DIFFRACTION99.82
2.67-2.790.28681410.25632682X-RAY DIFFRACTION99.89
2.79-2.940.33311420.26352689X-RAY DIFFRACTION100
2.94-3.120.3191410.27222692X-RAY DIFFRACTION100
3.12-3.360.27141440.23452735X-RAY DIFFRACTION99.86
3.36-3.70.24651430.20582705X-RAY DIFFRACTION99.89
3.7-4.230.2061440.17282736X-RAY DIFFRACTION100
4.23-5.330.20041460.16442759X-RAY DIFFRACTION99.97
5.33-46.230.24061490.18622890X-RAY DIFFRACTION99.93
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)
12.20235662497-0.404890519916-0.1110112244622.67705165755-0.4930903043154.0407555015-0.2004877476860.128408531653-0.21130423297-0.2022116271380.0176834684262-0.1605262499570.4132052766950.1856787674910.1398565260850.583775077908-0.03357989450690.05361960802170.6060971727150.06347244087950.54914100685127.1800297032-15.19136575499.51694345003
23.008335879820.9088846782130.9374957975692.824742567591.059291805132.22076653264-0.2988555447680.694014961683-0.46105683904-0.4911374077220.312623291454-0.04566290221960.2035913146890.212329290506-0.02700226893860.882215412116-0.17578024890.03045590149830.797617464727-0.09746354067370.6811693400238.63617435735-34.833631801921.1585882122
31.36689719549-0.1665587012690.06623762683811.60981735062-0.3865143766061.470437429710.00218408445554-0.00216647813150.0682928609479-0.00409557049459-0.02004525123790.0638452710688-0.0416536325807-0.003012133431720.00269018638820.439773764016-0.0306164453808-0.02869033121360.5027138173210.003031748839220.4977530569621.3678419529-15.356909814646.0846385556
48.07883333407-1.27534444925.481248774789.30051990242.188535087034.74749683986-0.120007626623-1.02783673705-0.3614510799071.23922435455-0.02243112528091.359929485570.436673792798-1.33112695649-0.3416072756161.276371314960.1136798813080.1011794467690.944968283937-0.01344455661211.087261819728.561193161255.8087035299138.6768198513
50.2128222882250.1890375549580.1238583675430.182523254490.1184179174710.08659179182530.005779527780540.24334012580.38748820425-0.973522018209-0.5166558780810.4984076973980.234187030013-1.13222456771-0.02418043556930.8840513937920.0513394056915-0.03680637164991.173886489150.1398963199510.7595683246692.65286219292-0.71817743575826.8513791256
60.0171361869999-0.0177677968904-0.001361376939820.03381417010310.007153662166660.00709876766067-0.349919523755-0.185775998420.148373278573-0.2030474150760.1149098199030.311765106656-0.2279024596280.0995048275537-0.0001019928125571.268099527890.0243259589646-0.110959626461.02202114142-0.0845787928181.11531710616-4.13910403954-29.460640152931.6672556523
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 109 through 314 )
2X-RAY DIFFRACTION2chain 'A' and (resid 315 through 499 )
3X-RAY DIFFRACTION3chain 'A' and (resid 500 through 789 )
4X-RAY DIFFRACTION4chain 'B' and (resid 551 through 562 )
5X-RAY DIFFRACTION5chain 'B' and (resid 563 through 582 )
6X-RAY DIFFRACTION6chain 'B' and (resid 583 through 596 )

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