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- PDB-6hys: Crystal structure of DHX8 helicase domain bound to ADP at 2.6 angstrom -

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Basic information

Entry
Database: PDB / ID: 6hys
TitleCrystal structure of DHX8 helicase domain bound to ADP at 2.6 angstrom
ComponentsATP-dependent RNA helicase DHX8
KeywordsRNA BINDING PROTEIN / Helicase / Splicing / RNA
Function / homology
Function and homology information


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 ...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 (HA2), winged-helix / Helicase-associated domain / 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 (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. / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 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 / Nucleic acid-binding, OB-fold / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
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: 2.6 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 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)312,14653
Polymers307,2904
Non-polymers4,85649
Water8,053447
1
A: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,08214
Polymers76,8231
Non-polymers1,26013
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)78,02013
Polymers76,8231
Non-polymers1,19812
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)78,03913
Polymers76,8231
Non-polymers1,21712
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)78,00413
Polymers76,8231
Non-polymers1,18212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.960, 167.940, 137.110
Angle α, β, γ (deg.)90.00, 92.71, 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 / Plasmid: baculovirus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q14562, RNA helicase

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Non-polymers , 6 types, 496 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% 2-Methyl-2,4-pentanediol, 100mM 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: 0.92044 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92044 Å / Relative weight: 1
ReflectionResolution: 2.6→49.49 Å / Num. obs: 92707 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 55.4 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.8
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.319 / % 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
Starting model: 2XAU and 3I4U

2xau

3i4u


Resolution: 2.6→37.59 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.579 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.524 / SU Rfree Blow DPI: 0.249 / SU Rfree Cruickshank DPI: 0.257
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4414 4.76 %RANDOM
Rwork0.182 ---
obs0.183 92658 99.8 %-
Displacement parametersBiso mean: 67.41 Å2
Baniso -1Baniso -2Baniso -3
1--5.8782 Å20 Å22.5246 Å2
2--5.1599 Å20 Å2
3---0.7182 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.6→37.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19040 0 276 447 19763
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0119801HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1426913HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6588SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3365HARMONIC5
X-RAY DIFFRACTIONt_it19801HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion19.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2710SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies9HARMONIC1
X-RAY DIFFRACTIONt_utility_distance24HARMONIC1
X-RAY DIFFRACTIONt_utility_angle64HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact22388SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.62 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2348 -4.15 %
Rwork0.2307 1777 -
all0.2309 1854 -
obs--99.48 %
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)
12.07010.516-0.0012.56290.00441.7234-0.07610.02510.0203-0.05840.0832-0.1327-0.08950.1766-0.0071-0.06270.0063-0.0115-0.0488-0.0022-0.077524.77811.2032135.2688
21.1549-0.65690.37931.5243-0.44152.4617-0.0058-0.05730.17710.08810.018-0.0672-0.3239-0.1851-0.01220.06810.00790.0249-0.21690.0363-0.10349.849728.3915123.5058
30.9239-0.0452-0.19010.6539-0.172.4269-0.0706-0.21780.17030.12730.1288-0.088-0.2960.2999-0.05830.07230.0025-0.0279-0.181-0.0601-0.108712.904227.0956137.7722
41.3894-0.20210.31232.0440.14152.6362-0.2088-0.0814-0.05390.27850.16550.1915-0.3534-0.150.04330.02580.1165-0.0002-0.10360.0116-0.1679-4.623321.859156.2391
50.9928-0.1931-0.30131.36160.05721.2863-0.0047-0.0084-0.1152-0.19680.05660.15760.2083-0.3457-0.0519-0.0239-0.0743-0.0199-0.02870.0565-0.0706-3.789-13.1892132.2468
62.1023-0.66231.88375.139-0.24122.2230.00710.0915-0.0720.20410.1121-0.10270.04850.4212-0.11920.122-0.01310.0128-0.1473-0.0019-0.149223.5963-22.2992123.0903
70.5776-0.0477-0.7530.12850.29353.74840.0045-0.0628-0.073-0.0640.11190.08210.4082-0.3597-0.11640.1968-0.10210.005-0.16670.0865-0.12028.7779-28.7049131.0125
81.23810.18620.55172.0913-0.95332.4291-0.18560.0127-0.02210.13250.147-0.24220.1904-0.05240.0387-0.02710.04790.0415-0.16690.0009-0.153218.7565-20.5884157.512
9-0.01210.50610.1280.258-0.2340.0121-0.00160.0035-0.001-0.00560.00420.0182-0.0004-0.0028-0.00270.0623-0.0128-0.0413-0.0706-0.020.086614.5653-38.9721176.5972
103.0497-0.75260.56132.6293-0.11311.99250.01290.1166-0.25260.0816-0.0203-0.17430.00630.25760.0074-0.019-0.00360.0232-0.0583-0.0058-0.145429.3436-6.793680.8421
111.41830.5591-0.16341.927-0.84423.57190.0148-0.0554-0.1133-0.14110.0509-0.0650.5392-0.3177-0.06570.1915-0.01250.0017-0.2707-0.0573-0.267113.6311-24.674190.8314
120.06420.5771-0.75150-0.40883.11660.020.07370.04180.00140.0028-0.16280.43140.3985-0.02270.27240.14630.0236-0.1006-0.0511-0.209520.0006-27.530883.8838
131.2326-0.04330.1032.00571.12621.8094-0.1008-0.00280.0589-0.20870.07710.10410.06760.03280.02380.1071-0.0480.064-0.1544-0.0346-0.24539.953-22.642256.8991
142.5303-0.7437-0.6091.8370.49662.69590.0035-0.00490.07140.0404-0.06640.04920.0782-0.31570.0629-0.0218-0.0159-0.0004-0.0187-0.0328-0.1618-3.11888.229778.9702
150.9473-0.36330.2970.91370.32623.52020.04210.12630.0283-0.174-0.0863-0.0708-0.5430.03910.04420.15270.03750.0261-0.21490.077-0.18068.628427.727487.9845
161.2111-0.26630.05091.817-0.69682.0548-0.1316-0.01020.0031-0.17610.0941-0.1492-0.21270.00710.03750.1248-0.04730.0002-0.115-0.024-0.30417.808623.838157.1027
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|555 - 719}
2X-RAY DIFFRACTION2{A|720 - 800}
3X-RAY DIFFRACTION3{A|801 - 986}
4X-RAY DIFFRACTION4{A|987 - 1186}
5X-RAY DIFFRACTION5{B|555 - 755}
6X-RAY DIFFRACTION6{B|756 - 823}
7X-RAY DIFFRACTION7{B|824 - 934}
8X-RAY DIFFRACTION8{B|935 - 1181}
9X-RAY DIFFRACTION9{B|1182 - 1187}
10X-RAY DIFFRACTION10{C|556 - 720}
11X-RAY DIFFRACTION11{C|721 - 823}
12X-RAY DIFFRACTION12{C|824 - 934}
13X-RAY DIFFRACTION13{C|935 - 1186}
14X-RAY DIFFRACTION14{D|556 - 720}
15X-RAY DIFFRACTION15{D|721 - 925}
16X-RAY DIFFRACTION16{D|926 - 1187}

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