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- PDB-3g10: Structure of S. pombe Pop2p - Mg2+ and Mn2+ bound form -

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Basic information

Entry
Database: PDB / ID: 3g10
TitleStructure of S. pombe Pop2p - Mg2+ and Mn2+ bound form
ComponentsCCR4-Not complex subunit Caf1
KeywordsHydrolase / Gene Regulation / mRNA turnover / deadenylation / Ccr4-Not / Pop2p / Caf1p / DEDD exonuclease
Function / homology
Function and homology information


poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT core complex / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / regulatory ncRNA-mediated gene silencing / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA nuclease activity / P-body / manganese ion binding ...poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT core complex / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / regulatory ncRNA-mediated gene silencing / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA nuclease activity / P-body / manganese ion binding / mRNA binding / chromatin binding / zinc ion binding / nucleus / metal ion binding / cytosol
Similarity search - Function
CCR4-NOT transcription complex subunit 7/8/Pop2 / Ribonuclease CAF1 / CAF1 family ribonuclease / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Poly(A) ribonuclease pop2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.597 Å
AuthorsAndersen, K.R. / Jonstrup, A.T. / Van, L.B. / Brodersen, D.E.
CitationJournal: Rna / Year: 2009
Title: The activity and selectivity of fission yeast Pop2p are affected by a high affinity for Zn2+ and Mn2+ in the active site
Authors: Andersen, K.R. / Jonstrup, A.T. / Van, L.B. / Brodersen, D.E.
History
DepositionJan 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CCR4-Not complex subunit Caf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3963
Polymers37,3171
Non-polymers792
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.124, 53.991, 95.646
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CCR4-Not complex subunit Caf1 / Caf1p / Pop2p


Mass: 37316.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: caf1, SPCC18.06c / Plasmid: pET30 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta DE3 / References: UniProt: O74856
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.84 Å3/Da / Density % sol: 33.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: 18% PEG 8000, 200mM magnesium acetate, 100mM MES, pH 6.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.271 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 9, 2008
RadiationMonochromator: Si(111) double crystal monochromator, water-cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.271 Å / Relative weight: 1
ReflectionResolution: 2.597→47.823 Å / Num. obs: 8371 / % possible obs: 93.2 % / Redundancy: 6.1 % / Biso Wilson estimate: 51.69 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 20.168
Reflection shellResolution: 2.597→2.69 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.6 / Num. unique all: 500 / % possible all: 57.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.82 Å
Translation2.5 Å47.82 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
ProDCdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P51

2p51


Resolution: 2.597→47.823 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.75 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 25.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 253 3.04 %
Rwork0.187 --
obs0.1884 8326 93.11 %
all-8371 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.845 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso mean: 62.684 Å2
Baniso -1Baniso -2Baniso -3
1-4.728 Å2-0 Å2-0 Å2
2---12.738 Å20 Å2
3----7.972 Å2
Refinement stepCycle: LAST / Resolution: 2.597→47.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 0 2 47 2082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062081
X-RAY DIFFRACTIONf_angle_d1.0282822
X-RAY DIFFRACTIONf_dihedral_angle_d18.041753
X-RAY DIFFRACTIONf_chiral_restr0.07309
X-RAY DIFFRACTIONf_plane_restr0.003365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5971-3.2720.31011070.23853672X-RAY DIFFRACTION86
3.272-47.83110.20791460.17114401X-RAY DIFFRACTION100

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