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- PDB-5lm5: Structure of C-terminal domain from S. cerevisiae Pat1 decapping ... -

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Basic information

Entry
Database: PDB / ID: 5lm5
TitleStructure of C-terminal domain from S. cerevisiae Pat1 decapping activator bound to Dcp2 HLM2 peptide (region 435-451)
Components
  • DNA topoisomerase 2-associated protein PAT1
  • mRNA decapping protein 2
KeywordsRNA BINDING PROTEIN / Protein peptide complex / ISOMERASE
Function / homology
Function and homology information


RNA decapping complex / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA 5'-diphosphatase activity / mRNA decay by 5' to 3' exoribonuclease / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / Lsm1-7-Pat1 complex / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / cytoplasmic side of membrane ...RNA decapping complex / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA 5'-diphosphatase activity / mRNA decay by 5' to 3' exoribonuclease / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / Lsm1-7-Pat1 complex / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / cytoplasmic side of membrane / deadenylation-dependent decapping of nuclear-transcribed mRNA / formation of translation preinitiation complex / P-body assembly / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of transcription initiation by RNA polymerase II / cellular response to glucose starvation / stress granule assembly / negative regulation of translational initiation / P-body / kinetochore / cytoplasmic stress granule / mRNA processing / manganese ion binding / cytosolic small ribosomal subunit / hydrolase activity / 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 / mRNA decapping protein 2, Box A domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping enzyme 2 , NUDIX hydrolase domain / Dcp2, box A domain / Dcp2, box A domain / NUDIX hydrolase, conserved site / Nudix box signature. ...mRNA decay factor PAT1 domain / Pat1-like / Topoisomerase II-associated protein PAT1 / mRNA decapping protein 2, Box A domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping enzyme 2 , NUDIX hydrolase domain / Dcp2, box A domain / Dcp2, box A domain / 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 / Deadenylation-dependent mRNA-decapping factor PAT1 / m7GpppN-mRNA hydrolase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 29, 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
Revision 1.5Jan 10, 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

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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
C: mRNA decapping protein 2
D: mRNA decapping protein 2


Theoretical massNumber of molelcules
Total (without water)87,4844
Polymers87,4844
Non-polymers00
Water00
1
A: DNA topoisomerase 2-associated protein PAT1
C: mRNA decapping protein 2


Theoretical massNumber of molelcules
Total (without water)43,7422
Polymers43,7422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-10 kcal/mol
Surface area16490 Å2
MethodPISA
2
B: DNA topoisomerase 2-associated protein PAT1
D: mRNA decapping protein 2


Theoretical massNumber of molelcules
Total (without water)43,7422
Polymers43,7422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-9 kcal/mol
Surface area16730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.280, 115.960, 122.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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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: 42282.438 Da / Num. of mol.: 2 / Mutation: Q706A/L713A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer'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: 1459.623 Da / Num. of mol.: 2 / Fragment: UNP residues 436-449 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: B3LNX5, UniProt: P53550*PLUS

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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: 2.29 Å3/Da / Density % sol: 46.35 %
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: 0.97533 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97533 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 21634 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 83.16 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.134 / Net I/σ(I): 6.52
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.6-2.751.3911.010.542198.9
2.75-2.850.971.480.667199.1
2.85-30.6442.070.826199
3-3.50.3213.820.959199.3
3.5-40.1398.170.989199.2
4-50.08212.570.995199.6
5-60.08130.995199.5
6-100.05716.480.998198.4
100.04721.730.996196.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.2data extraction
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OGP

4ogp


Resolution: 2.6→49.14 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.916 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 2.926 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.725 / SU Rfree Blow DPI: 0.336 / SU Rfree Cruickshank DPI: 0.347
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1126 5.21 %RANDOM
Rwork0.256 ---
obs0.256 21633 99.2 %-
Displacement parametersBiso max: 199.74 Å2 / Biso mean: 108.91 Å2 / Biso min: 62.13 Å2
Baniso -1Baniso -2Baniso -3
1-19.4434 Å20 Å20 Å2
2---39.5537 Å20 Å2
3---20.1103 Å2
Refine analyzeLuzzati coordinate error obs: 1.03 Å
Refinement stepCycle: final / Resolution: 2.6→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5339 0 0 0 5339
Num. residues----656
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2003SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes163HARMONIC2
X-RAY DIFFRACTIONt_gen_planes733HARMONIC5
X-RAY DIFFRACTIONt_it5418HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion744SEMIHARMONIC5
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_contact6366SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5418HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7301HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion2.2
X-RAY DIFFRACTIONt_other_torsion20.57
LS refinement shellResolution: 2.6→2.73 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.381 140 4.96 %
Rwork0.34 2685 -
all-2825 -
obs--98.81 %
Refinement TLS params.

T22: 0.6079 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0084-0.0108-0.02010.83780.65631.9834-0.07990.2861-0.167-0.03750.01250.11030.0015-0.01210.0675-0.42750.03850.00340.0107-0.428112.666524.69123.101
24.0032-0.3944-0.19450.53030.39732.6736-0.00251.0420.0855-0.16170.0218-0.0919-0.28190.1873-0.0192-0.4998-0.0168-0.02820.0508-0.602426.535730.63798.6834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A468 - 795
2X-RAY DIFFRACTION2{ B|* }B468 - 796

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