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- PDB-7q73: Structure of Pla1 apo -

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Basic information

Entry
Database: PDB / ID: 7q73
TitleStructure of Pla1 apo
ComponentsPoly(A) polymerase pla1
KeywordsTRANSFERASE / PolyA polymerase
Function / homology
Function and homology information


cleavage body / nuclear exosome focus / nuclear mRNA surveillance of meiosis-specific transcripts / Mei2 nuclear dot complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / mRNA cleavage and polyadenylation specificity factor complex / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / RNA binding / nucleoplasm ...cleavage body / nuclear exosome focus / nuclear mRNA surveillance of meiosis-specific transcripts / Mei2 nuclear dot complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / mRNA cleavage and polyadenylation specificity factor complex / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / RNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Poly(A) polymerase / Poly(A) polymerase, RNA-binding domain / Poly(A) polymerase, central domain / : / Poly(A) polymerase predicted RNA binding domain / Poly(A) polymerase central domain / Poly(A) polymerase nucleotidyltransferase domain / Nucleotidyltransferase, class I-like, C-terminal / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Poly(A) polymerase pla1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSoni, K. / Wild, K. / Sinning, I.
CitationJournal: Nat Commun / Year: 2023
Title: Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex.
Authors: Soni, K. / Sivadas, A. / Horvath, A. / Dobrev, N. / Hayashi, R. / Kiss, L. / Simon, B. / Wild, K. / Sinning, I. / Fischer, T.
History
DepositionNov 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly(A) polymerase pla1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4732
Polymers65,3811
Non-polymers921
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-0 kcal/mol
Surface area24880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.060, 66.750, 88.120
Angle α, β, γ (deg.)90.000, 118.170, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Poly(A) polymerase pla1 / PAP / Polynucleotide adenylyltransferase


Mass: 65380.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: pla1, SPBC646.04 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q10295, polynucleotide adenylyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M lithium citrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 25, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9→77.679 Å / Num. obs: 49224 / % possible obs: 99.5 % / Redundancy: 6.772 % / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Rrim(I) all: 0.122 / Χ2: 1.047 / Net I/σ(I): 11.64 / Num. measured all: 333356 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.956.6971.2321.5823976363235800.6521.33698.6
1.95-27.0170.9952.0824840355435400.7611.07599.6
2-2.066.9650.8432.4823842343834230.8170.91299.6
2.06-2.126.8790.6643.1122860334233230.8790.71999.4
2.12-2.196.7460.4934.1121761324032260.9260.53599.6
2.19-2.276.4460.4164.7420138313531240.9420.45399.6
2.27-2.366.5450.3216.0219949305730480.9660.34999.7
2.36-2.457.0720.2757.2420558291829070.9780.29899.6
2.45-2.567.0350.2338.3619706280728010.980.25299.8
2.56-2.697.0060.1999.5918726268226730.9850.21599.7
2.69-2.836.8480.1512.1617354253825340.9910.16299.8
2.83-36.3530.11614.815412243424260.9940.12799.7
3-3.217.0550.09219.2316014227722700.9950.09999.7
3.21-3.476.9670.07423.3814825213421280.9970.0899.7
3.47-3.86.7920.06227.3713190195119420.9970.06799.5
3.8-4.256.2580.0530.9310946176117490.9980.05499.3
4.25-4.916.4150.04433.910084157815720.9980.04899.6
4.91-6.016.7970.04533.359020133413270.9990.04899.5
6.01-8.56.1860.04233.616458105410440.9980.04699.1
8.5-77.6796.2980.03141.9236975975870.9990.03498.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.12refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HHP

2hhp


Resolution: 1.9→77.679 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1923 2462 5 %
Rwork0.169 46761 -
obs0.1702 49223 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.74 Å2 / Biso mean: 32.6838 Å2 / Biso min: 13.79 Å2
Refinement stepCycle: final / Resolution: 1.9→77.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4117 0 14 527 4658
Biso mean--42.07 39.69 -
Num. residues----513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034300
X-RAY DIFFRACTIONf_angle_d0.555858
X-RAY DIFFRACTIONf_chiral_restr0.044659
X-RAY DIFFRACTIONf_plane_restr0.004752
X-RAY DIFFRACTIONf_dihedral_angle_d13.4582635
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.93660.37281350.3397255498
1.9366-1.97610.30861360.2742585100
1.9761-2.01910.25051350.25012577100
2.0191-2.0660.27641370.22822587100
2.066-2.11770.24081340.20952558100
2.1177-2.1750.24131370.19992607100
2.175-2.2390.24091360.18982578100
2.239-2.31120.23031360.17922586100
2.3112-2.39390.18941370.17222602100
2.3939-2.48970.23171360.17222585100
2.4897-2.6030.21711370.17162590100
2.603-2.74030.2041360.17612584100
2.7403-2.9120.21071380.17462635100
2.912-3.13680.20431370.16332594100
3.1368-3.45250.19141370.15842616100
3.4525-3.9520.15121380.14532610100
3.952-4.9790.13441380.13052629100
4.979-77.6790.15991420.15812684100

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