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- PDB-4ogp: Structure of C-terminal domain from S. cerevisiae Pat1 decapping ... -

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Basic information

Entry
Database: PDB / ID: 4ogp
TitleStructure of C-terminal domain from S. cerevisiae Pat1 decapping activator (Space group : P21)
ComponentsDNA topoisomerase 2-associated protein PAT1
KeywordsRNA BINDING PROTEIN / ARM-repeat fold / Dcp2 / Lsm1-7
Function / homology
Function and homology information


mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / deadenylation-dependent decapping of nuclear-transcribed mRNA / formation of translation preinitiation complex / P-body assembly / regulation of translational initiation / negative regulation of translational initiation / P-body / kinetochore / mRNA processing ...mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / deadenylation-dependent decapping of nuclear-transcribed mRNA / formation of translation preinitiation complex / P-body assembly / regulation of translational initiation / negative regulation of translational initiation / P-body / kinetochore / mRNA processing / cytoplasmic stress granule / cytosolic small ribosomal subunit / cell cycle / cell division / mRNA binding / chromatin binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
mRNA decay factor PAT1 domain / Pat1-like / Topoisomerase II-associated protein PAT1
Similarity search - Domain/homology
DNA topoisomerase 2-associated protein PAT1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsFourati-Kammoun, Z. / Kolesnikova, O. / Back, R. / Keller, J. / Lazar, N. / Gaudon-Plesse, C. / Seraphin, B. / Graille, M.
CitationJournal: Plos One / Year: 2014
Title: The C-terminal domain from S. cerevisiae Pat1 displays two conserved regions involved in decapping factor recruitment.
Authors: Fourati, Z. / Kolesnikova, O. / Back, R. / Keller, J. / Charenton, C. / Taverniti, V. / Plesse, C.G. / Lazar, N. / Durand, D. / van Tilbeurgh, H. / Seraphin, B. / Graille, M.
History
DepositionJan 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: DNA topoisomerase 2-associated protein PAT1
B: DNA topoisomerase 2-associated protein PAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5467
Polymers76,9692
Non-polymers5775
Water2,540141
1
A: DNA topoisomerase 2-associated protein PAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8044
Polymers38,4841
Non-polymers3193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA topoisomerase 2-associated protein PAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7423
Polymers38,4841
Non-polymers2572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.120, 88.460, 67.910
Angle α, β, γ (deg.)90.00, 96.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA topoisomerase 2-associated protein PAT1 / Decapping activator and translational repressor PAT1 / Topoisomerase II-associated protein PAT1 / ...Decapping activator and translational repressor PAT1 / Topoisomerase II-associated protein PAT1 / mRNA turnover protein 1


Mass: 38484.418 Da / Num. of mol.: 2 / Fragment: unp residues 473-796
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PAT1, MRT1, YCR077C, YCR77C / Production host: Escherichia coli (E. coli) / References: UniProt: P25644
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 15% PEG6000, 7.5% MPD, 100 mM MES, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2012
RadiationMonochromator: Channel-cut monochromator Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 142169 / Num. obs: 35407 / % possible obs: 98 %
Reflection shellResolution: 2.14→2.27 Å / % possible all: 95.8

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→46.591 Å / SU ML: 0.28 / σ(F): 1.99 / Phase error: 29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2606 1767 4.99 %
Rwork0.204 --
obs0.2068 35382 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→46.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5184 0 36 141 5361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075299
X-RAY DIFFRACTIONf_angle_d0.9917139
X-RAY DIFFRACTIONf_dihedral_angle_d18.5122038
X-RAY DIFFRACTIONf_chiral_restr0.068836
X-RAY DIFFRACTIONf_plane_restr0.004887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1401-2.1980.30631270.26862405X-RAY DIFFRACTION93
2.198-2.26270.31941340.24852561X-RAY DIFFRACTION99
2.2627-2.33570.29631350.2242557X-RAY DIFFRACTION99
2.3357-2.41920.2721380.20962625X-RAY DIFFRACTION99
2.4192-2.5160.29511350.20732573X-RAY DIFFRACTION99
2.516-2.63050.2731350.21232582X-RAY DIFFRACTION99
2.6305-2.76920.25731370.21152602X-RAY DIFFRACTION99
2.7692-2.94270.27321360.21052598X-RAY DIFFRACTION100
2.9427-3.16980.28831370.2252597X-RAY DIFFRACTION100
3.1698-3.48870.2951370.21832602X-RAY DIFFRACTION100
3.4887-3.99330.26651390.18782641X-RAY DIFFRACTION100
3.9933-5.03020.2191370.17572610X-RAY DIFFRACTION100
5.0302-46.60250.22271400.19332662X-RAY DIFFRACTION99

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