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- PDB-7qy5: Crystal structure of the S.pombe Ars2-Red1 complex. -

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Basic information

Entry
Database: PDB / ID: 7qy5
TitleCrystal structure of the S.pombe Ars2-Red1 complex.
Components
  • (NURS complex subunit pir2) x 2
  • RNA elimination defective protein Red1
KeywordsRNA / RNA degradation / RNA targeting complex
Function / homology
Function and homology information


MTREC complex / regulatory ncRNA-mediated heterochromatin formation / mRNA processing / nuclear body / chromatin / nucleus / metal ion binding
Similarity search - Function
SERRATE/Ars2 , C-terminal / SERRATE/Ars2, N-terminal / SERRATE/Ars2 / Arsenite-resistance protein 2 / SERRATE/Ars2, N-terminal domain / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
NURS complex subunit pir2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsFoucher, A.E. / Kadlec, J.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE11-0021-01 France
CitationJournal: Nat Commun / Year: 2022
Title: Structural analysis of Red1 as a conserved scaffold of the RNA-targeting MTREC/PAXT complex.
Authors: Foucher, A.E. / Touat-Todeschini, L. / Juarez-Martinez, A.B. / Rakitch, A. / Laroussi, H. / Karczewski, C. / Acajjaoui, S. / Soler-Lopez, M. / Cusack, S. / Mackereth, C.D. / Verdel, A. / Kadlec, J.
History
DepositionJan 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1May 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

Downloads & links

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Assembly

Deposited unit
A: NURS complex subunit pir2
C: NURS complex subunit pir2
F: RNA elimination defective protein Red1
G: RNA elimination defective protein Red1
B: NURS complex subunit pir2
D: NURS complex subunit pir2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,1968
Polymers111,0656
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19240 Å2
ΔGint-106 kcal/mol
Surface area43850 Å2
Unit cell
Length a, b, c (Å)64.670, 128.281, 89.261
Angle α, β, γ (deg.)90.000, 108.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NURS complex subunit pir2


Mass: 14315.451 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: pir2, ars2, SPBC725.08 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: O94326
#2: Protein/peptide RNA elimination defective protein Red1


Mass: 2401.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#3: Protein NURS complex subunit pir2


Mass: 38815.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: pir2, ars2, SPBC725.08 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: O94326
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
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: 3.46 Å3/Da / Density % sol: 64.41 %
Crystal growTemperature: 278.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 200mM Ammonium Formate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Nov 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.77→84.85 Å / Num. obs: 26786 / % possible obs: 76 % / Redundancy: 5.56 % / CC1/2: 0.98 / Rmerge(I) obs: 0.29 / Net I/σ(I): 5.3
Reflection shellResolution: 2.771→2.994 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1339 / CC1/2: 0.55 / % possible all: 18.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alpafold

Resolution: 2.77→84.85 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.865 / SU B: 21.803 / SU ML: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.488 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2977 1313 4.9 %RANDOM
Rwork0.228 ---
obs0.2314 25473 76.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 160.83 Å2 / Biso mean: 52.291 Å2 / Biso min: 24 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å2-0.42 Å2
2--0.54 Å2-0 Å2
3---0.17 Å2
Refinement stepCycle: final / Resolution: 2.77→84.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7172 0 2 0 7174
Biso mean--67.44 --
Num. residues----878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0137334
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156721
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.6419923
X-RAY DIFFRACTIONr_angle_other_deg1.1631.58815521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5135868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29123.395430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.709151281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.2671540
X-RAY DIFFRACTIONr_chiral_restr0.050.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028306
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021710
LS refinement shellResolution: 2.771→2.843 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.551 6 -
Rwork0.362 82 -
all-88 -
obs--3.39 %

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