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- PDB-2vgm: Structure of S. cerevisiae Dom34, a translation termination-like ... -

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Basic information

Entry
Database: PDB / ID: 2vgm
TitleStructure of S. cerevisiae Dom34, a translation termination-like factor involved in RNA quality control pathways and interacting with Hbs1 (Unlabeled protein)
ComponentsDOM34
KeywordsCELL CYCLE / TRANSLATION TERMINATION FACTOR / PROTEIN BIOSYNTHESIS / TRANSLATION REGULATION / CELL DIVISION / MRNA DEGRADATION / NUCLEOTIDE BINDING / MITOSIS / MEIOSIS / CYTOPLASM / NO-GO DECAY
Function / homology
Function and homology information


RNA surveillance / Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / ribosome disassembly / nonfunctional rRNA decay / positive regulation of translational initiation / rescue of stalled ribosome / RNA endonuclease activity / positive regulation of translation ...RNA surveillance / Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / ribosome disassembly / nonfunctional rRNA decay / positive regulation of translational initiation / rescue of stalled ribosome / RNA endonuclease activity / positive regulation of translation / meiotic cell cycle / cell division / metal ion binding / cytoplasm
Similarity search - Function
Pelota, domain A / eRF1 domain 2 / Translation release factor pelota / Pelota/DOM34, N-terminal domain / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 ...Pelota, domain A / eRF1 domain 2 / Translation release factor pelota / Pelota/DOM34, N-terminal domain / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 / eRF1 domain 3 / eRF1_1 / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / 50S ribosomal protein L30e-like / SH3 type barrels. / Nucleotidyltransferase; domain 5 / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsGraille, M. / Chaillet, M. / Van Tilbeurgh, H.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure of Yeast Dom34: A Protein Related to Translation Termination Factor Erf1 and Involved in No-Go Decay.
Authors: Graille, M. / Chaillet, M. / Van Tilbeurgh, H.
History
DepositionNov 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Mar 17, 2021Group: Other / Structure summary / Category: pdbx_database_status / struct / Item: _pdbx_database_status.status_code_sf / _struct.title
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DOM34


Theoretical massNumber of molelcules
Total (without water)44,1201
Polymers44,1201
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.500, 75.500, 163.981
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein DOM34


Mass: 44119.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Plasmid: PET9 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLySS / References: UniProt: P33309
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.2 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 6.7
Details: 7.5% POLYETHYLENE GLYCOL 4000, 50MM NAH2PO4 PH 6.7, 3% XYLITOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.6→35 Å / Num. obs: 16966 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.3
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.4 / % possible all: 99.9

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Processing

Software
NameClassification
CNSrefinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.6→35 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1452 5 %RANDOM
Rwork0.226 ---
obs0.226 29045 0.23 %-
Displacement parametersBiso mean: 65 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 0 0 26 2866
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.079
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.66 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.401 122 5 %
Rwork0.335 1841 -
obs--98 %

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