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- PDB-5lmg: Structure of C-terminal domain from S. cerevisiae Pat1 decapping ... -

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Basic information

Entry
Database: PDB / ID: 5lmg
TitleStructure of C-terminal domain from S. cerevisiae Pat1 decapping activator bound to Dcp2 HLM10 peptide (region 954-970)
Components
  • DNA topoisomerase 2-associated protein PAT1
  • mRNA decapping protein 2
KeywordsRNA BINDING PROTEIN / Protein peptide complex / ISOMERASE
Function / homology
Function and homology information


Dcp1-Dcp2 complex / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / Lsm1-7-Pat1 complex / cytoplasmic side of membrane / m7G(5')pppN diphosphatase activity / deadenylation-dependent decapping of nuclear-transcribed mRNA ...Dcp1-Dcp2 complex / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / Lsm1-7-Pat1 complex / cytoplasmic side of membrane / m7G(5')pppN diphosphatase activity / deadenylation-dependent decapping of nuclear-transcribed mRNA / P-body assembly / formation of translation preinitiation complex / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of transcription initiation by RNA polymerase II / stress granule assembly / negative regulation of translational initiation / P-body / kinetochore / cytoplasmic stress granule / mRNA processing / cytosolic small ribosomal subunit / manganese ion binding / hydrolase activity / cell cycle / cell division / mRNA binding / chromatin binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
mRNA decay factor PAT1 domain / Topoisomerase II-associated protein PAT1 / Pat1-like / Dcp2, box A domain / Dcp2, box A domain / mRNA decapping enzyme 2 , NUDIX hydrolase domain / mRNA decapping protein 2, Box A domain / mRNA decapping protein 2, Box A domain superfamily / NUDIX hydrolase, conserved site / Nudix box signature. ...mRNA decay factor PAT1 domain / Topoisomerase II-associated protein PAT1 / Pat1-like / Dcp2, box A domain / Dcp2, box A domain / mRNA decapping enzyme 2 , NUDIX hydrolase domain / mRNA decapping protein 2, Box A domain / mRNA decapping protein 2, Box A domain superfamily / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
mRNA decapping protein 2 / DNA topoisomerase 2-associated protein PAT1 / m7GpppN-mRNA hydrolase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsCharenton, C. / Gaudon-Plesse, C. / Fourati, Z. / Taverniti, V. / Back, R. / Kolesnikova, O. / Seraphin, B. / Graille, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: A unique surface on Pat1 C-terminal domain directly interacts with Dcp2 decapping enzyme and Xrn1 5'-3' mRNA exonuclease in yeast.
Authors: Charenton, C. / Gaudon-Plesse, C. / Fourati, Z. / Taverniti, V. / Back, R. / Kolesnikova, O. / Seraphin, B. / Graille, M.
History
DepositionJul 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.3Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Sep 26, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 2-associated protein PAT1
B: DNA topoisomerase 2-associated protein PAT1
C: mRNA decapping protein 2
D: mRNA decapping protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,63419
Polymers87,6804
Non-polymers95315
Water3,531196
1
A: DNA topoisomerase 2-associated protein PAT1
D: mRNA decapping protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,54513
Polymers43,8402
Non-polymers70511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint11 kcal/mol
Surface area17110 Å2
MethodPISA
2
B: DNA topoisomerase 2-associated protein PAT1
C: mRNA decapping protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0886
Polymers43,8402
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-1 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.686, 123.029, 126.562
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-810-

MG

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#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: 42282.438 Da / Num. of mol.: 2 / Fragment: UNP residues 437-796 / Mutation: Q706A/L713A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: PAT1, MRT1, YCR077C, YCR77C / Production host: Escherichia coli (E. coli) / References: UniProt: P25644
#2: Protein/peptide mRNA decapping protein 2 / DCP2 decapping factor


Mass: 1557.772 Da / Num. of mol.: 2 / Fragment: UNP residues 956-969 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: B3LNX5, UniProt: P53550*PLUS

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Non-polymers , 4 types, 211 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M MgCl2 ; 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.28361 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28361 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 59110 / % possible obs: 97.2 % / Redundancy: 4.2 % / Rsym value: 0.06 / Net I/σ(I): 12.15
Reflection shellResolution: 1.89→2 Å / Mean I/σ(I) obs: 0.6 / CC1/2: 0.459 / % possible all: 88.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.2data extraction
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OGP
Resolution: 1.89→21.82 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.937 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.151 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.139
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2953 5 %RANDOM
Rwork0.204 ---
obs0.206 59059 96.6 %-
Displacement parametersBiso max: 168.62 Å2 / Biso mean: 57.51 Å2 / Biso min: 34.56 Å2
Baniso -1Baniso -2Baniso -3
1-16.1599 Å20 Å20 Å2
2---3.629 Å20 Å2
3----12.5309 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 1.89→21.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5398 0 61 196 5655
Biso mean--68.45 54.05 -
Num. residues----663
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2050SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes161HARMONIC2
X-RAY DIFFRACTIONt_gen_planes745HARMONIC5
X-RAY DIFFRACTIONt_it5524HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion754SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6592SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5524HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7413HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.3
X-RAY DIFFRACTIONt_other_torsion18.89
LS refinement shellResolution: 1.89→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 165 5.01 %
Rwork0.36 3129 -
all-3294 -
obs--73.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.5499-0.27010.04120.61220.0130.17860.0036-0.0660.01620.02510.0160.0607-0.0231-0.0408-0.0196-0.0771-0.0068-0.0227-0.06290.0106-0.004612.755823.036737.0044
20.5286-0.30110.10821.4997-0.04750.4201-0.03130.003-0.0145-0.1235-0.05410.08950.0210.01480.0854-0.111-0.0095-0.0271-0.1182-0.0126-0.018426.1937.328232.8533
30.2127-0.1644-0.20440.2715-0.15810.38190.00490.03810.011-0.02850.0150.00250.00150.0074-0.0199-0.07930.0479-0.00090.04970.10190.02811.309540.883516.4436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A468 - 796
2X-RAY DIFFRACTION2{ B|* }B473 - 796
3X-RAY DIFFRACTION3{ D|* }D958 - 970

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