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- PDB-8ark: Crystal structure of DEAD-box protein Dbp2 in apo form -

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Basic information

Entry
Database: PDB / ID: 8ark
TitleCrystal structure of DEAD-box protein Dbp2 in apo form
ComponentsATP-dependent RNA helicase DBP2
KeywordsHYDROLASE / helicase
Function / homology
Function and homology information


: / nuclear polyadenylation-dependent mRNA catabolic process / SUMOylation of transcription cofactors / ATP-dependent activity, acting on RNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / snoRNA binding / termination of RNA polymerase II transcription / Estrogen-dependent gene expression / rRNA processing / RNA helicase activity ...: / nuclear polyadenylation-dependent mRNA catabolic process / SUMOylation of transcription cofactors / ATP-dependent activity, acting on RNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / snoRNA binding / termination of RNA polymerase II transcription / Estrogen-dependent gene expression / rRNA processing / RNA helicase activity / RNA helicase / ribonucleoprotein complex / mRNA binding / ATP hydrolysis activity / mitochondrion / RNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / 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-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent RNA helicase DBP2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsRety, S. / Xi, X.G.
Funding support China, France, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870788 and 32071291) China
Centre National de la Recherche Scientifique (CNRS)LIA Helicase-mediated G-quadruplex DNA unwinding and genome stability France
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Nonstructural N- and C-tails of Dbp2 confer the protein full helicase activities.
Authors: Song, Q.X. / Liu, N.N. / Liu, Z.X. / Zhang, Y.Z. / Rety, S. / Hou, X.M. / Xi, X.G.
History
DepositionAug 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Refinement description / Category: citation / struct_ncs_dom_lim
Item: _citation.journal_volume / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DBP2
B: ATP-dependent RNA helicase DBP2
C: ATP-dependent RNA helicase DBP2


Theoretical massNumber of molelcules
Total (without water)183,2473
Polymers183,2473
Non-polymers00
Water00
1
A: ATP-dependent RNA helicase DBP2


Theoretical massNumber of molelcules
Total (without water)61,0821
Polymers61,0821
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent RNA helicase DBP2


Theoretical massNumber of molelcules
Total (without water)61,0821
Polymers61,0821
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ATP-dependent RNA helicase DBP2


Theoretical massNumber of molelcules
Total (without water)61,0821
Polymers61,0821
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)204.103, 115.124, 81.411
Angle α, β, γ (deg.)90.000, 101.920, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 57 or resid 59 through 63...
d_2ens_1(chain "B" and (resid 57 or resid 59 through 63...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLUGLUGLUAA5757
d_12ILEILETRPTRPAA59 - 6359 - 63
d_13LEULEULYSLYSAA67 - 6967 - 69
d_14PHEPHETYRTYRAA73 - 7873 - 78
d_15GLUGLUVALVALAA80 - 8480 - 84
d_16ASPASPARGARGAA86 - 9686 - 96
d_17ASNASNGLYGLYAA99 - 10599 - 105
d_18ASPASPASPASPAA107 - 134107 - 134
d_19PROPROARGARGAA136 - 196136 - 196
d_110LEULEUGLYGLYAA198 - 210198 - 210
d_111SERSERSERSERAA212 - 213212 - 213
d_112ILEILEILEILEAA215215
d_113ASNASNILEILEAA217 - 230217 - 230
d_114ASPASPSERSERAA232 - 234232 - 234
d_115GLYGLYGLYGLYAA236 - 245236 - 245
d_116LEULEUPROPROAA247 - 302247 - 302
d_117GLUGLUPHEPHEAA304 - 342304 - 342
d_118LYSLYSLYSLYSAA344344
d_119ASPASPASPASPAA346 - 358346 - 358
d_120THRTHRTHRTHRAA363 - 377363 - 377
d_121LEULEUASPASPAA380 - 393380 - 393
d_122ASPASPASPASPAA395395
d_123ASPASPASPASPAA400400
d_124VALVALVALVALAA402402
d_125PHEPHEPHEPHEAA406406
d_126ASNASNGLYGLYAA408 - 409408 - 409
d_127SERSERALAALAAA411 - 421411 - 421
d_128GLYGLYVALVALAA423 - 426423 - 426
d_129GLYGLYGLYGLYAA428 - 452428 - 452
d_130ALAALAASNASNAA456 - 468456 - 468
d_131GLYGLYALAALAAA470 - 473470 - 473
d_132LEULEUPROPROAA475 - 488475 - 488
d_133LEULEULEULEUAA490 - 491490 - 491
d_134TYRTYRASPASPAA493 - 494493 - 494
d_135ARGARGARGARGAA496496
d_21GLUGLUGLUGLUBB5757
d_22ILEILETRPTRPBB59 - 6359 - 63
d_23LEULEULYSLYSBB67 - 6967 - 69
d_24PHEPHETYRTYRBB73 - 7873 - 78
d_25GLUGLUVALVALBB80 - 8480 - 84
d_26ASPASPARGARGBB86 - 9686 - 96
d_27ASNASNGLYGLYBB99 - 10599 - 105
d_28ASPASPASPASPBB107 - 134107 - 134
d_29PROPROARGARGBB136 - 196136 - 196
d_210LEULEUGLYGLYBB198 - 210198 - 210
d_211SERSERSERSERBB212 - 213212 - 213
d_212ILEILEILEILEBB215215
d_213ASNASNILEILEBB217 - 230217 - 230
d_214ASPASPSERSERBB232 - 234232 - 234
d_215GLYGLYGLYGLYBB236 - 245236 - 245
d_216LEULEUPROPROBB247 - 302247 - 302
d_217GLUGLUPHEPHEBB304 - 342304 - 342
d_218LYSLYSLYSLYSBB344344
d_219ASPASPASPASPBB346 - 358346 - 358
d_220THRTHRTHRTHRBB363 - 377363 - 377
d_221LEULEUASPASPBB380 - 393380 - 393
d_222ASPASPASPASPBB395395
d_223ASPASPASPASPBB400400
d_224VALVALVALVALBB402402
d_225PHEPHEPHEPHEBB406406
d_226ASNASNGLYGLYBB408 - 409408 - 409
d_227SERSERALAALABB411 - 421411 - 421
d_228GLYGLYVALVALBB423 - 426423 - 426
d_229GLYGLYGLYGLYBB428 - 452428 - 452
d_230ALAALAASNASNBB456 - 468456 - 468
d_231GLYGLYALAALABB470 - 473470 - 473
d_232LEULEUPROPROBB475 - 488475 - 488
d_233LEULEULEULEUBB490 - 491490 - 491
d_234TYRTYRASPASPBB493 - 494493 - 494
d_235ARGARGARGARGBB496496

NCS oper: (Code: givenMatrix: (0.556899916385, -0.766154837454, 0.320732362222), (-0.763999839775, -0.6240113078, -0.164055272889), (0.325832361737, -0.153677105594, -0.932854018194)Vector: -17. ...NCS oper: (Code: given
Matrix: (0.556899916385, -0.766154837454, 0.320732362222), (-0.763999839775, -0.6240113078, -0.164055272889), (0.325832361737, -0.153677105594, -0.932854018194)
Vector: -17.4619980162, 6.87678261265, 90.4954740825)

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Components

#1: Protein ATP-dependent RNA helicase DBP2 / DEAD box protein 2 / p68-like protein


Mass: 61082.387 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: DBP2, YNL112W, N1945 / Plasmid: pET21a HMT / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): C2566H / References: UniProt: P24783, RNA helicase

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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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.12 M Monosaccharides 1 M Sodium HEPES; MOPS (acid) pH 7.5 19% w/v PEG 500MME PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97777 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97777 Å / Relative weight: 1
ReflectionResolution: 3.22→38.85 Å / Num. obs: 28601 / % possible obs: 94.47 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 101.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06332 / Net I/σ(I): 15.1
Reflection shellResolution: 3.22→3.33 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.5775 / Mean I/σ(I) obs: 2.63 / Num. unique obs: 2971 / CC1/2: 0.812 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2i4i

2i4i


Resolution: 3.22→38.85 Å / SU ML: 0.4376 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.6957
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2528 1438 5.06 %
Rwork0.2236 26959 -
obs0.2251 28397 94.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 134.7 Å2
Refinement stepCycle: LAST / Resolution: 3.22→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9085 0 0 0 9085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00489265
X-RAY DIFFRACTIONf_angle_d1.033112548
X-RAY DIFFRACTIONf_chiral_restr0.05471388
X-RAY DIFFRACTIONf_plane_restr0.01151651
X-RAY DIFFRACTIONf_dihedral_angle_d9.47821254
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.2201760444 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.22-3.330.40551470.38222791X-RAY DIFFRACTION98.46
3.33-3.470.35841280.33022201X-RAY DIFFRACTION78.29
3.47-3.620.32911390.2872804X-RAY DIFFRACTION98.33
3.62-3.810.31781290.25852361X-RAY DIFFRACTION82.94
3.81-4.050.25021420.23192607X-RAY DIFFRACTION91.88
4.05-4.370.21331600.20372802X-RAY DIFFRACTION99.33
4.37-4.80.24181490.18412855X-RAY DIFFRACTION99.5
4.8-5.50.28121270.21742861X-RAY DIFFRACTION99.8
5.5-6.920.24961740.23142825X-RAY DIFFRACTION99.11
6.92-38.850.20431430.19362852X-RAY DIFFRACTION97.4
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)
15.050470680222.52067975249-1.142053012414.49672396899-0.4852007857924.97287201885-0.05112290604730.144884084133-0.0415995064453-0.3627590794530.07275802191940.0941601152781-0.342899684304-0.0790471233041-6.66910715244E-50.9158296616770.0657663330164-0.03594761870630.891652994975-0.01536038265750.97761937245118.59159273124.478355308734.3084482458
20.4733507351890.5380178052290.2678916403980.9718469345121.157935865261.95584455583-0.0882699948387-0.6813160369440.04028325250670.372764233562-0.298847476809-0.7872888931670.2784703452690.02091150025984.96657080594E-51.161430893240.0007661867920610.02390335440641.268365332080.1365099684551.2879741388321.395224000819.181455087950.7036413737
31.17632125041-0.3905289286350.8354780631732.89983499157-0.6450356258211.31564752102-0.203076329548-0.2215065342260.4903282238930.5697714253650.5949056430030.0917057059762-0.0062731352673-0.1267982123138.57254609157E-51.454731804840.3256032616070.001525902210211.757083235260.1969368906731.5539570131931.1569495779-2.5412865003861.3027797514
43.484844905361.09508392342-0.7013849465824.98095075934-0.8177265043555.83130409118-0.145443662521-0.5647454998140.003582403646930.163996171574-0.2686065170290.1320009743820.7677399695810.3649667312013.1646219474E-51.30851825352-0.01005946150520.06829750008981.2672893346-0.05137705267971.10509019466-14.909228208-28.152369766460.7399802612
52.114012534930.8739315847990.9335463120460.7074621855750.9255277039781.301971818630.2247040529290.200022014873-0.164827777612-0.0905361920346-0.0320462807211-0.3449329629390.4720593099730.609744276317-2.93707925985E-61.389267448250.191929433681-0.0004291944128941.787021004860.1808179158731.5026229075216.7093064447-26.396969797244.4754141651
61.97837334122-0.51678387779-2.328043043173.98005206353-0.2563387976523.52388248242-0.0973454850462-0.19067080413-0.4991865287580.195145336337-0.01879278461430.1930331455880.351839206172-0.635839333207-0.0001063467986071.2453764809-0.07284808778710.006423486112141.258454046-0.02606033836251.191462702736.8283039177413.213583988472.8730810935
74.165759012380.7193820364360.905026299142.48697468999-0.2458951758132.76078370102-0.088342469627-0.5931757775690.2041575619310.374418830691-0.1162361150830.0253241299925-0.549991880480.566046063802-0.0001568047847491.10149330812-0.0695083983803-0.03655082297081.145542608980.03661152647180.98073927819616.482022104926.273884102778.48595948
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 57 through 302 )AA57 - 3021 - 246
22chain 'A' and (resid 303 through 341 )AA303 - 341247 - 285
33chain 'A' and (resid 342 through 496 )AA342 - 496286 - 440
44chain 'B' and (resid 57 through 302 )BB57 - 3021 - 246
55chain 'B' and (resid 303 through 496 )BB303 - 496247 - 440
66chain 'C' and (resid 57 through 163 )CC57 - 1631 - 107
77chain 'C' and (resid 164 through 326 )CC164 - 326108 - 270

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