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- PDB-2xgj: Structure of Mtr4, a DExH helicase involved in nuclear RNA proces... -

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Basic information

Entry
Database: PDB / ID: 2xgj
TitleStructure of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance
Components
  • ATP-DEPENDENT RNA HELICASE DOB1
  • RNA (5'-(*AP*AP*AP*AP*A)-3')
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / HYDROLASE / TRAMP / EXOSOME / DEAD / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


TRAMP complex / nuclear polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / U5 snRNA 3'-end processing / RNA fragment catabolic process / TRAMP-dependent tRNA surveillance pathway / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...TRAMP complex / nuclear polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / U5 snRNA 3'-end processing / RNA fragment catabolic process / TRAMP-dependent tRNA surveillance pathway / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA catabolic process / 3'-5' RNA helicase activity / nuclear mRNA surveillance / poly(A) binding / RNA catabolic process / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA processing / RNA helicase activity / oxidoreductase activity / RNA helicase / mRNA binding / nucleolus / ATP hydrolysis activity / DNA binding / ATP binding / nucleus
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #300 / YheA-like fold - #20 / YheA-like fold / Sec63 N-terminal domain-like fold - #30 / Sec63 N-terminal domain-like fold / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : ...Elongation Factor Tu (Ef-tu); domain 3 - #300 / YheA-like fold - #20 / YheA-like fold / Sec63 N-terminal domain-like fold - #30 / Sec63 N-terminal domain-like fold / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / : / Prismane-like superfamily / Elongation Factor Tu (Ef-tu); domain 3 / 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 / Up-down Bundle / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / RNA / ATP-dependent RNA helicase DOB1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWeir, J.R. / Bonneau, F. / Hentschel, J. / Conti, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural Analysis Reveals the Characteristic Features of Mtr4, a Dexh Helicase Involved in Nuclear RNA Processing and Surveillance.
Authors: Weir, J.R. / Bonneau, F. / Hentschel, J. / Conti, E.
History
DepositionJun 4, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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 DOB1
B: ATP-DEPENDENT RNA HELICASE DOB1
C: RNA (5'-(*AP*AP*AP*AP*A)-3')
D: RNA (5'-(*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,4646
Polymers233,6094
Non-polymers8542
Water1,45981
1
A: ATP-DEPENDENT RNA HELICASE DOB1
C: RNA (5'-(*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2323
Polymers116,8052
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-14.1 kcal/mol
Surface area43930 Å2
MethodPISA
2
B: ATP-DEPENDENT RNA HELICASE DOB1
D: RNA (5'-(*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2323
Polymers116,8052
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-12.7 kcal/mol
Surface area35500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.110, 126.019, 102.272
Angle α, β, γ (deg.)90.00, 99.21, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9412, -0.03596, -0.3359), (0.02998, -0.9993, 0.02298), (-0.3364, 0.01156, 0.9416)16.23, -64.53, 55.2
2given(-0.9467, 0.04752, -0.3186), (-0.01912, -0.9956, -0.09171), (-0.3215, -0.08073, 0.9435)18.42, -62.97, 52.48
3given(-0.9362, -0.009104, -0.3514), (0.02005, -0.9994, -0.02752), (-0.3509, -0.03281, 0.9358)17.57, -63.64, 53.83
4given(-0.9401, -0.04048, -0.3386), (0.03436, -0.9991, 0.02406), (-0.3393, 0.01098, 0.9406)15.93, -64.57, 55.22
5given(-0.9458, -0.03107, -0.3233), (0.03545, -0.9993, -0.007659), (-0.3228, -0.0187, 0.9463)15.97, -64.07, 54.04

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Components

#1: Protein ATP-DEPENDENT RNA HELICASE DOB1 / MTR4P / MRNA TRANSPORT REGULATOR MTR4


Mass: 115203.617 Da / Num. of mol.: 2 / Fragment: RESIDUES 81-1073 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P47047, RNA helicase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: RNA chain RNA (5'-(*AP*AP*AP*AP*A)-3')


Mass: 1601.072 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-80 REMOVED FROM THIS CONSTRUCT. N-TERMINAL METHIONINE IS REMNANT FROM TAG CLEVAGE.

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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: 3.2 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growpH: 6
Details: PROTEIN WAS CRYSTALLISED IN 50 MM MES PH 6.0, 200 MM AMMONIUM ACETATE, 20 % (W/V) PEG3350. 15% ETHYLENE GLYCOL WAS USED AS A CRYOPROTECTANT.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2009 / Details: DYNAMICALLY BENDABLE MIRROR, MERIDIONAL - VERTICAL
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→53.4 Å / Num. obs: 55417 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 53.84 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.3
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN HOUSE SE-MET MAD STRUCTURE

Resolution: 2.9→53.453 Å / SU ML: 0.38 / σ(F): 1.35 / Phase error: 25.32 / Stereochemistry target values: ML
Details: RESIDUES 363-391 IN CHAIN A ARE DISORDERED. RESIDUES 81-116, 363-391 509-511, 522-531 AND 672-809 IN CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2474 2806 5.1 %
Rwork0.2005 --
obs0.203 55391 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.11 Å2 / ksol: 0.282 e/Å3
Displacement parametersBiso mean: 51.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.2091 Å20 Å22.288 Å2
2--2.5094 Å20 Å2
3----2.3003 Å2
Refinement stepCycle: LAST / Resolution: 2.9→53.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13537 217 54 81 13889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214102
X-RAY DIFFRACTIONf_angle_d0.62319139
X-RAY DIFFRACTIONf_dihedral_angle_d15.7045179
X-RAY DIFFRACTIONf_chiral_restr0.0412203
X-RAY DIFFRACTIONf_plane_restr0.0022403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.950.29831360.23512654X-RAY DIFFRACTION100
2.95-3.00360.31641400.24772609X-RAY DIFFRACTION100
3.0036-3.06140.31911420.24632647X-RAY DIFFRACTION100
3.0614-3.12390.2891440.24842622X-RAY DIFFRACTION100
3.1239-3.19180.32781360.24312625X-RAY DIFFRACTION100
3.1918-3.2660.30871400.23462604X-RAY DIFFRACTION100
3.266-3.34770.28381330.23952631X-RAY DIFFRACTION100
3.3477-3.43820.31441400.2252658X-RAY DIFFRACTION100
3.4382-3.53940.26291440.21322606X-RAY DIFFRACTION100
3.5394-3.65360.28041430.19932625X-RAY DIFFRACTION100
3.6536-3.78410.23131400.18462617X-RAY DIFFRACTION100
3.7841-3.93560.22161350.1882658X-RAY DIFFRACTION100
3.9356-4.11460.24531280.1772607X-RAY DIFFRACTION100
4.1146-4.33150.22781540.1652633X-RAY DIFFRACTION100
4.3315-4.60270.1981470.15422610X-RAY DIFFRACTION99
4.6027-4.95790.17841440.14812618X-RAY DIFFRACTION99
4.9579-5.45640.22941500.18412625X-RAY DIFFRACTION99
5.4564-6.24490.28521270.19442653X-RAY DIFFRACTION99
6.2449-7.86390.21331460.19812630X-RAY DIFFRACTION99
7.8639-53.46160.1941370.19372653X-RAY DIFFRACTION98

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