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- PDB-5ooq: Structure of the Mtr4 Nop53 Complex -

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Basic information

Entry
Database: PDB / ID: 5ooq
TitleStructure of the Mtr4 Nop53 Complex
Components
  • ATP-dependent RNA helicase DOB1
  • Ribosome biogenesis protein NOP53
KeywordsRNA BINDING PROTEIN / Helicase / RNA / exosome / ribosome biogenesis
Function / homology
Function and homology information


TRAMP complex / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / nuclear exosome (RNase complex) ...TRAMP complex / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / nuclear exosome (RNase complex) / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 3'-5' RNA helicase activity / nuclear mRNA surveillance / rRNA catabolic process / poly(A) binding / RNA catabolic process / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / ribosomal large subunit export from nucleus / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA processing / rRNA processing / 5S rRNA binding / ribosomal large subunit assembly / oxidoreductase activity / RNA helicase activity / rRNA binding / RNA helicase / mRNA binding / nucleolus / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus
Similarity search - Function
rRNA-processing arch domain / Mtr4-like, beta-barrel domain / Ribosome biogenesis protein Nop53/GLTSCR2 / Nop53 (60S ribosomal biogenesis) / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT ...rRNA-processing arch domain / Mtr4-like, beta-barrel domain / Ribosome biogenesis protein Nop53/GLTSCR2 / Nop53 (60S ribosomal biogenesis) / 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 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase DOB1 / Ribosome biogenesis protein NOP53
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsFalk, S. / Basquin, J. / Conti, E.
Funding support Germany, 6items
OrganizationGrant numberCountry
German Research FoundationSFB646 Germany
German Research FoundationSFB1035 Germany
German Research FoundationGRK1721 Germany
German Research FoundationFOR1680 Germany
German Research FoundationEXC114 Germany
CitationJournal: RNA / Year: 2017
Title: Structural insights into the interaction of the nuclear exosome helicase Mtr4 with the preribosomal protein Nop53.
Authors: Falk, S. / Tants, J.N. / Basquin, J. / Thoms, M. / Hurt, E. / Sattler, M. / Conti, E.
History
DepositionAug 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DOB1
B: ATP-dependent RNA helicase DOB1
C: Ribosome biogenesis protein NOP53
D: Ribosome biogenesis protein NOP53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,5259
Polymers236,0444
Non-polymers4805
Water1,24369
1
A: ATP-dependent RNA helicase DOB1
C: Ribosome biogenesis protein NOP53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3105
Polymers118,0222
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-40 kcal/mol
Surface area43350 Å2
MethodPISA
2
B: ATP-dependent RNA helicase DOB1
D: Ribosome biogenesis protein NOP53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2144
Polymers118,0222
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-27 kcal/mol
Surface area44700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.231, 151.370, 133.043
Angle α, β, γ (deg.)90.00, 92.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP-dependent RNA helicase DOB1 / mRNA transport regulator MTR4


Mass: 113649.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MTR4, DOB1, YJL050W, J1158 / Production host: Escherichia coli (E. coli) / References: UniProt: P47047, RNA helicase
#2: Protein/peptide Ribosome biogenesis protein NOP53 / Nucleolar protein 53


Mass: 4372.265 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: NOP53, YPL146C, LPI2C, P2610 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12080
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.42 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 6000 200 mM Lithium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→66.5 Å / Num. obs: 55220 / % possible obs: 99.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 109.9 Å2 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.0048 / Net I/σ(I): 14
Reflection shellResolution: 3.2→3.3 Å / Num. unique obs: 4762 / CC1/2: 0.316 / Rpim(I) all: 0.9083 / % possible all: 94.54

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XGJ

2xgj


Resolution: 3.2→66.5 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.267 --
Rwork0.211 --
obs-50186 99.3 %
Refinement stepCycle: LAST / Resolution: 3.2→66.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13955 0 25 69 14049

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