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- PDB-7q72: Structure of Pla1 in complex with Red1 -

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Basic information

Entry
Database: PDB / ID: 7q72
TitleStructure of Pla1 in complex with Red1
Components
  • NURS complex subunit red1
  • Poly(A) polymerase pla1
KeywordsTRANSFERASE / PolyA polymerase
Function / homology
Function and homology information


MTREC complex / nucleolar peripheral inclusion body / cleavage body / sno(s)RNA processing / regulation of siRNA-mediated facultative heterochromatin formation / siRNA-independent facultative heterochromatin formation / regulation of siRNA-independent facultative heterochromatin formation / nuclear exosome focus / nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts / Mei2 nuclear dot complex ...MTREC complex / nucleolar peripheral inclusion body / cleavage body / sno(s)RNA processing / regulation of siRNA-mediated facultative heterochromatin formation / siRNA-independent facultative heterochromatin formation / regulation of siRNA-independent facultative heterochromatin formation / nuclear exosome focus / nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts / Mei2 nuclear dot complex / heterochromatin island / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / exosome (RNase complex) / mRNA cleavage and polyadenylation specificity factor complex / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / : / protein-macromolecule adaptor activity / nuclear body / chromatin / RNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Putative zinc-finger domain / NURS complex subunit red1 / Putative zinc-finger domain / Poly(A) polymerase / : / Poly(A) polymerase nucleotidyltransferase domain / Poly(A) polymerase, RNA-binding domain / Poly(A) polymerase, central domain / Poly(A) polymerase predicted RNA binding domain / Poly(A) polymerase central domain ...Putative zinc-finger domain / NURS complex subunit red1 / Putative zinc-finger domain / Poly(A) polymerase / : / Poly(A) polymerase nucleotidyltransferase domain / Poly(A) polymerase, RNA-binding domain / Poly(A) polymerase, central domain / Poly(A) polymerase predicted RNA binding domain / Poly(A) polymerase central domain / Nucleotidyltransferase, class I-like, C-terminal / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Poly(A) polymerase pla1 / NURS complex subunit red1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsSoni, K. / Wild, K. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
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 1.2May 1, 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
C: NURS complex subunit red1
B: Poly(A) polymerase pla1
D: NURS complex subunit red1


Theoretical massNumber of molelcules
Total (without water)146,0064
Polymers146,0064
Non-polymers00
Water543
1
A: Poly(A) polymerase pla1
C: NURS complex subunit red1


Theoretical massNumber of molelcules
Total (without water)73,0032
Polymers73,0032
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-12 kcal/mol
Surface area27020 Å2
MethodPISA
2
B: Poly(A) polymerase pla1
D: NURS complex subunit red1


Theoretical massNumber of molelcules
Total (without water)73,0032
Polymers73,0032
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-8 kcal/mol
Surface area24910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.644, 151.337, 65.408
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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Components

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


Mass: 65380.855 Da / Num. of mol.: 2
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: Protein NURS complex subunit red1


Mass: 7622.071 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: red1, iss3, SPAC1006.03c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UTR8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium formate, 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: P14 (MX2) / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 6, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.8→98.017 Å / Num. obs: 20986 / % possible obs: 97.3 % / Redundancy: 13.164 % / Biso Wilson estimate: 51.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.1031 / Net I/σ(I): 9.91
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
2.89-2.9713.3654.3710.5827037212820230.4064.54695.1
2.97-3.0513.8393.7210.7627429203819820.513.86497.3
3.05-3.1413.8033.2070.8926585199519260.6143.3396.5
3.14-3.2313.6482.211.3425972196319030.7492.29796.9
3.23-3.3413.5971.8551.6524720189118180.7881.92896.1
3.34-3.4613.3861.4842.123265183417380.8811.54394.8
3.46-3.5913.431.1422.7622791178316970.9281.18895.2
3.59-3.7313.5780.6834.3722092168916270.9760.71196.3
3.73-3.913.5920.4246.5321883165616100.9880.44197.2
3.9-4.0913.3010.3088.7320550158015450.9940.32197.8
4.09-4.3113.1920.22511.1219353149114670.9940.23598.4
4.31-4.5713.0250.17713.3618313142414060.9970.18498.7
4.57-4.8912.7590.14615.7516868133213220.9970.15399.2
4.89-5.2812.5180.13916.5315623125812480.9970.14599.2
5.28-5.7812.5450.1317.2814552116811600.9950.13699.3
5.78-6.4712.8130.11619.5613620106710630.9970.12199.6
6.47-7.4712.1520.0923.25113389389330.9980.09499.5
7.47-9.1411.6770.06628.2694008128050.9980.06999.1
9.14-12.9311.5220.05932.0574436466460.9980.062100
12.93-98.0179.770.05929.237423893830.9920.06398.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.89 Å97.7 Å
Translation2.89 Å97.7 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158+SVNrefinement
STARANISOdata scaling
XDSdata scaling
XDSdata reduction
PHASER2.8.0phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: deposition ID D_1292115151

Resolution: 2.8→98.017 Å / SU ML: 0.3699 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8469
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2835 1999 9.74 %
Rwork0.2407 18528 -
obs0.2448 20527 63.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.93 Å2
Refinement stepCycle: LAST / Resolution: 2.8→98.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8528 0 0 3 8531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00188732
X-RAY DIFFRACTIONf_angle_d0.466911865
X-RAY DIFFRACTIONf_chiral_restr0.04121339
X-RAY DIFFRACTIONf_plane_restr0.00371514
X-RAY DIFFRACTIONf_dihedral_angle_d20.0993240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.5038440.3284410X-RAY DIFFRACTION20.17
2.88-2.950.3618510.3279464X-RAY DIFFRACTION22.82
2.95-3.040.4425550.3393518X-RAY DIFFRACTION25.7
3.04-3.140.3223630.3362579X-RAY DIFFRACTION28.03
3.14-3.250.3235750.326694X-RAY DIFFRACTION34.32
3.25-3.380.2866930.3043860X-RAY DIFFRACTION42.34
3.38-3.530.36561400.29851293X-RAY DIFFRACTION63.16
3.53-3.720.34591710.29181597X-RAY DIFFRACTION77.44
3.72-3.950.32181860.25251711X-RAY DIFFRACTION83.79
3.95-4.260.2962110.23141961X-RAY DIFFRACTION94.07
4.26-4.690.25212230.21572063X-RAY DIFFRACTION99.39
4.69-5.360.28562240.21412077X-RAY DIFFRACTION99.22
5.37-6.760.26752260.23612097X-RAY DIFFRACTION99.44
6.76-98.020.20712370.20152204X-RAY DIFFRACTION98.51

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