[English] 日本語
Yorodumi
- PDB-8ark: Crystal structure of DEAD-box protein Dbp2 in apo form -

+
Open data


ID or keywords:

Loading...

-
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 / G-quadruplex DNA binding / alternative mRNA splicing, via spliceosome / 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 ...nuclear polyadenylation-dependent mRNA catabolic process / SUMOylation of transcription cofactors / G-quadruplex DNA binding / alternative mRNA splicing, via spliceosome / 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 / G-quadruplex RNA binding / RNA helicase activity / RNA helicase / ribonucleoprotein complex / mRNA binding / ATP hydrolysis activity / mitochondrion / 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 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-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 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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more