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- PDB-6hyu: Crystal structure of DHX8 helicase bound to single stranded poly-... -

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Basic information

Entry
Database: PDB / ID: 6hyu
TitleCrystal structure of DHX8 helicase bound to single stranded poly-adenine RNA
Components
  • ATP-dependent RNA helicase DHX8
  • RNA (5'-R(*A*AP*A)-3')
  • RNA (5'-R(*AP*AP*AP*AP*AP*A)-3')
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
RNA / ATP-dependent RNA helicase DHX8
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 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
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: ATP-dependent RNA helicase DHX8
B: RNA (5'-R(*AP*AP*AP*AP*AP*A)-3')
C: ATP-dependent RNA helicase DHX8
D: RNA (5'-R(*A*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,5805
Polymers156,5184
Non-polymers621
Water48627
1
A: ATP-dependent RNA helicase DHX8
B: RNA (5'-R(*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8153
Polymers78,7532
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ATP-dependent RNA helicase DHX8
D: RNA (5'-R(*A*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)77,7652
Polymers77,7652
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.104, 138.601, 169.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

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


Mass: 76822.562 Da / Num. of mol.: 2
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
#2: RNA chain RNA (5'-R(*AP*AP*AP*AP*AP*A)-3')


Mass: 1930.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(*A*AP*A)-3')


Mass: 942.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
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: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.22→48.75 Å / Num. obs: 25940 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 80.94 Å2 / CC1/2: 0.79 / Rmerge(I) obs: 0.381 / Net I/σ(I): 4.7
Reflection shellResolution: 3.22→3.44 Å / Redundancy: 6.5 % / CC1/2: 0.768 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.22→48.75 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.83 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.537
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1292 4.99 %RANDOM
Rwork0.226 ---
obs0.229 25904 99.8 %-
Displacement parametersBiso mean: 117.02 Å2
Baniso -1Baniso -2Baniso -3
1--32.9407 Å20 Å20 Å2
2--25.4426 Å20 Å2
3---7.4981 Å2
Refine analyzeLuzzati coordinate error obs: 0.55 Å
Refinement stepCycle: 1 / Resolution: 3.22→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8729 161 4 27 8921
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019078HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2512407HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2902SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1512HARMONIC5
X-RAY DIFFRACTIONt_it9078HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion24.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1270SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10720SEMIHARMONIC4
LS refinement shellResolution: 3.22→3.35 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2394 149 5.18 %
Rwork0.2177 2729 -
all0.2188 2878 -
obs--99.55 %
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)
15.0795-1.30492.91041.4553-1.12475.8803-0.0568-0.16370.25870.1969-0.23510.04460.1696-0.24670.2919-0.304-0.00370.00610.2719-0.01750.038619.5515-65.9367-9.8192
21.63270.7961-1.44874.1972-1.37351.82430.11160.17350.1489-0.5338-0.0912-0.46120.1677-0.0374-0.0204-0.21250.0395-0.10550.1392-0.0057-0.293632.0796-55.8687-27.0947
30.6131-1.007-0.41013.0814-0.50242.6805-0.1074-0.10060.0047-0.3191-0.1527-0.2525-0.23710.12440.2601-0.23680.0249-0.08820.16460.0102-0.057236.8375-57.1958-25.8824
41.4099-0.9857-0.46212.6616-0.42762.8269-0.3067-0.3369-0.2965-0.54270.08510.09650.54390.25850.2217-0.1060.03750.0851-0.04040.0159-0.277841.5814-86.0765-22.4451
57.0083-1.5962-2.91040.05582.83190.36740.0161-0.3536-0.30670.1978-0.150.1664-0.11660.28520.1340.25630.0338-0.152-0.1660.1071-0.136249.697-10.2378-7.2677
600.975-0.48882.71571.12970.62140.0888-0.08310.1145-0.0864-0.11230.351-0.3351-0.24960.0235-0.14330.034-0.152-0.17670.15130.252934.6063-22.5579-23.9526
72.3660.2742-0.98891.24990.0210-0.02170.367-0.2825-0.1212-0.14490.0403-0.32460.02750.16660.1392-0.11650.1516-0.30080.1520.174344.282-7.2889-29.7561
83.03751.213-1.02723.8607-0.28240.58820.2601-0.06640.25440.1267-0.05160.5307-0.2272-0.3761-0.20840.30330.0380.152-0.304-0.09260.113426.673112.7894-22.6509
900.86220.11410-0.35352.6408-0.0034-0.1054-0.2166-0.01410.073-0.07340.0758-0.1079-0.06970.2867-0.010.00860.18310.057-0.30438.0786-73.3742-21.5891
100-0.02250.106600.00610.0394-0.0004-0.0016-0.00360-0.0070.0015-0.00460.0070.00750.03290.0734-0.0571-0.01990.01050.009433.0351-6.2777-25.5951
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|568 - 707}
2X-RAY DIFFRACTION2{A|708 - 800}
3X-RAY DIFFRACTION3{A|801 - 904}
4X-RAY DIFFRACTION4{A|905 - 1181}
5X-RAY DIFFRACTION5{C|568 - 716}
6X-RAY DIFFRACTION6{C|717 - 850}
7X-RAY DIFFRACTION7{C|851 - 964}
8X-RAY DIFFRACTION8{C|965 - 1187}
9X-RAY DIFFRACTION9{B|1 - 6}
10X-RAY DIFFRACTION10{D|2 - 3}

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