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- PDB-6hyt: Crystal structure of DHX8 helicase domain bound to ADP at 2.3 Angstrom -

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Basic information

Entry
Database: PDB / ID: 6hyt
TitleCrystal structure of DHX8 helicase domain bound to ADP at 2.3 Angstrom
ComponentsATP-dependent RNA helicase DHX8
KeywordsRNA BINDING PROTEIN / helicase / splicing / RNA
Function / homology
Function and homology information


spliceosomal complex disassembly / ATP-dependent activity, acting on RNA / U2-type catalytic step 2 spliceosome / RNA processing / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / RNA helicase activity ...spliceosomal complex disassembly / ATP-dependent activity, acting on RNA / U2-type catalytic step 2 spliceosome / RNA processing / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / RNA helicase activity / nuclear body / RNA helicase / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
DHX8/ Prp22, DEXH-box helicase domain / : / : / : / 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 ...DHX8/ Prp22, DEXH-box helicase domain / : / : / : / 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. / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / 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 / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / ATP-dependent RNA helicase DHX8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsFelisberto-Rodrigues, C. / Thomas, J.C. / McAndrew, P.C. / Le Bihan, Y.V. / Burke, R. / Workman, P. / van Montfort, R.L.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC309/A11566 United Kingdom
Cancer Research UKC2739/A22897 United Kingdom
CitationJournal: Biochem.J. / Year: 2019
Title: Structural and functional characterisation of human RNA helicase DHX8 provides insights into the mechanism of RNA-stimulated ADP release.
Authors: Felisberto-Rodrigues, C. / Thomas, J.C. / McAndrew, C. / Le Bihan, Y.V. / Burke, R. / Workman, P. / van Montfort, R.L.M.
History
DepositionOct 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DHX8
B: ATP-dependent RNA helicase DHX8
C: ATP-dependent RNA helicase DHX8
D: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,38346
Polymers307,2904
Non-polymers4,09342
Water10,917606
1
A: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,78911
Polymers76,8231
Non-polymers96710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,10215
Polymers76,8231
Non-polymers1,27914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,74610
Polymers76,8231
Non-polymers9249
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,74610
Polymers76,8231
Non-polymers9249
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.947, 167.576, 137.231
Angle α, β, γ (deg.)90.00, 92.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
ATP-dependent RNA helicase DHX8 / DEAH box protein 8 / RNA helicase HRH1


Mass: 76822.562 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHX8, DDX8 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q14562, RNA helicase

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Non-polymers , 7 types, 648 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 606 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% 2-Methyl-2,4-pentanediol, 100 mM Sodium Acetate, 6%DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.33→48.25 Å / Num. obs: 127918 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 53.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.9
Reflection shellResolution: 2.33→2.37 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.554 / Mean I/σ(I) obs: 0.9 / CC1/2: 0.293 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→33.8 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.274 / SU Rfree Blow DPI: 0.2 / SU Rfree Cruickshank DPI: 0.205
RfactorNum. reflection% reflectionSelection details
Rfree0.222 6422 5.02 %RANDOM
Rwork0.187 ---
obs0.189 127850 99.4 %-
Displacement parametersBiso mean: 66.55 Å2
Baniso -1Baniso -2Baniso -3
1--6.6244 Å20 Å23.428 Å2
2---1.5811 Å20 Å2
3---8.2055 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: 1 / Resolution: 2.33→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19267 0 236 606 20109
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0119992HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1527197HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6750SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3389HARMONIC5
X-RAY DIFFRACTIONt_it19992HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion18.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2741SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies11HARMONIC1
X-RAY DIFFRACTIONt_utility_distance24HARMONIC1
X-RAY DIFFRACTIONt_utility_angle32HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact23017SEMIHARMONIC4
LS refinement shellResolution: 2.33→2.35 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.229 109 4.26 %
Rwork0.2108 2448 -
all0.2116 2557 -
obs--99.46 %
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)
13.17571.0623-0.07312.5859-0.23231.209-0.1267-0.05130.1466-0.14210.0331-0.0963-0.00440.13340.0936-0.1724-0.0045-0.0104-0.0334-0.0179-0.06424.984510.7918135.3653
21.7473-0.04610.29931.1173-0.48072.2496-0.05210.05780.3298-0.01660.0220.0221-0.1781-0.20690.0301-0.09150.0345-0.0037-0.15470.0058-0.03148.073825.4579123.5597
31.072-0.12820.19840.5891-0.242.911-0.0387-0.22480.31940.08260.0851-0.0701-0.3050.354-0.0464-0.1005-0.0298-0.0345-0.0794-0.1034-0.031514.913529.8614136.7098
41.2787-0.09090.08851.69820.45422.6515-0.1829-0.0818-0.04960.26360.17830.1169-0.13810.01820.0045-0.09750.0962-0.0029-0.08110.0172-0.1296-2.829821.4702157.0364
52.15840.6450.87152.44180.98581.86640.0444-0.1996-0.1269-0.1564-0.06310.15090.0556-0.55420.0187-0.2231-0.064-0.01870.08590.0242-0.1052-4.2161-9.5839134.1756
61.09190.1250.0881.47150.78423.1780.0575-0.0561-0.26870.03850.0087-0.12760.4860.1269-0.0662-0.0255-0.06-0.0163-0.22880.0739-0.088913.772-24.3532123.7693
70.8224-0.2170.07860.55680.40872.80560.0982-0.1623-0.14480.04570.060.03760.5571-0.4952-0.1582-0.0217-0.158-0.0351-0.08590.1259-0.10555.6869-28.9368136.4011
81.39070.27540.0382.6704-0.7613.835-0.25580.1419-0.12830.2560.1629-0.45830.18740.17320.0929-0.22380.07180.0024-0.126-0.015-0.075421.3103-20.1721158.5739
92.6946-0.9210.84692.4106-0.69212.49710.06070.0728-0.1923-0.1074-0.0746-0.1135-0.07350.24330.0139-0.12020.00760.0373-0.02650.0362-0.137829.1673-6.757580.8975
100.7218-0.0287-0.85661.1604-0.93163.23570.05750.0285-0.3291-0.23-0.117-0.09310.5446-0.09770.05960.01730.00690.0101-0.1906-0.0497-0.126116.5932-26.843591.2714
110.2960.3925-0.25320.0549-0.05053.9332-0.03820.1402-0.1517-0.1008-0.0298-0.11350.45920.41950.0680.02520.08760.0445-0.0834-0.05-0.129419.9231-25.518580.7854
120.7911-0.2054-0.09872.01560.81212.244-0.0945-0.02860.001-0.1981-0.0450.1663-0.0048-0.12410.1395-0.0046-0.06970.0056-0.1005-0.0354-0.17237.0251-22.721556.3435
133.1201-0.818-0.38681.89690.51513.0734-0.05230.06990.05650.0026-0.01050.09750.0557-0.3980.0628-0.12090.0229-0.01780.00650.0089-0.1777-3.10227.738279.1849
140.90430.28310.10680.46640.38783.0906-0.08430.26710.1482-0.2001-0.0619-0.0289-0.5559-0.07080.14620.00110.0614-0.0018-0.1470.136-0.15466.628527.046783.5081
151.28020.05460.00181.7669-0.79632.7897-0.1403-0.10720.0111-0.13730.1002-0.1622-0.09320.12730.0401-0.0107-0.0737-0.0044-0.058-0.0405-0.228621.490223.382557.0372
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|555 - 718}
2X-RAY DIFFRACTION2{A|719 - 825}
3X-RAY DIFFRACTION3{A|826 - 964}
4X-RAY DIFFRACTION4{A|965 - 1186}
5X-RAY DIFFRACTION5{B|556 - 717}
6X-RAY DIFFRACTION6{B|718 - 825}
7X-RAY DIFFRACTION7{B|826 - 964}
8X-RAY DIFFRACTION8{B|965 - 1189}
9X-RAY DIFFRACTION9{C|556 - 717}
10X-RAY DIFFRACTION10{C|718 - 800}
11X-RAY DIFFRACTION11{C|801 - 964}
12X-RAY DIFFRACTION12{C|965 - 1188}
13X-RAY DIFFRACTION13{D|556 - 717}
14X-RAY DIFFRACTION14{D|718 - 964}
15X-RAY DIFFRACTION15{D|965 - 1187}

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