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

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Basic information

Entry
Database: PDB / ID: 2vgn
TitleStructure of S. cerevisiae Dom34, a translation termination-like factor involved in RNA quality control pathways and interacting with Hbs1 (SelenoMet-labeled 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 / RNA endonuclease activity / rescue of stalled ribosome / meiotic cell cycle ...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 / RNA endonuclease activity / rescue of stalled ribosome / meiotic cell cycle / positive regulation of translation / 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
PHOSPHATE ION / Protein DOM34
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.505 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: Derived calculations / Other / Structure summary / Category: pdbx_database_status / struct / struct_conn
Item: _pdbx_database_status.status_code_sf / _struct.title / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
B: DOM34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4575
Polymers89,1772
Non-polymers2793
Water4,107228
1
A: DOM34


Theoretical massNumber of molelcules
Total (without water)44,5891
Polymers44,5891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: DOM34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8684
Polymers44,5891
Non-polymers2793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.640, 75.640, 324.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2006-

HOH

21B-2018-

HOH

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Components

#1: Protein DOM34


Mass: 44588.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SEMET SUBSTITUTED PROTEIN
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.1 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: 2.5→14 Å / Num. obs: 69296 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.3
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.75 / % possible all: 91.1

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Processing

Software
NameClassification
CNSrefinement
SHELXDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.505→13.976 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 3498 5.1 %RANDOM
Rwork0.2097 ---
obs0.2097 69285 96.4 %-
Displacement parametersBiso mean: 36 Å2
Refinement stepCycle: LAST / Resolution: 2.505→13.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5760 0 17 228 6005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.1
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_deg1.33
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: 2.5→2.54 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.3284 150 5 %
Rwork0.304 2516 -
obs--94 %

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