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- PDB-2cl3: Crystal structure of human Cleavage and Polyadenylation Specifici... -

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Basic information

Entry
Database: PDB / ID: 2cl3
TitleCrystal structure of human Cleavage and Polyadenylation Specificity Factor 5 (CPSF5)
ComponentsCLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 5
KeywordsNUCLEAR PROTEIN / PRECURSOR MRNA CLEAVAGE FACTOR IM / MRNA / CPSF5 / CFIM25 / RNA-BINDING / MRNA PROCESSING / PHOSPHORYLATION
Function / homology
Function and homology information


positive regulation of pro-B cell differentiation / mRNA cleavage factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / positive regulation of stem cell differentiation / mRNA 3'-UTR AU-rich region binding / mRNA 3'-end processing / mRNA 3'-end processing ...positive regulation of pro-B cell differentiation / mRNA cleavage factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / positive regulation of stem cell differentiation / mRNA 3'-UTR AU-rich region binding / mRNA 3'-end processing / mRNA 3'-end processing / paraspeckles / RNA Polymerase II Transcription Termination / post-transcriptional regulation of gene expression / protein heterotetramerization / Processing of Capped Intron-Containing Pre-mRNA / protein tetramerization / centriolar satellite / histone deacetylase binding / mRNA processing / cell differentiation / nuclear body / mRNA binding / centrosome / chromatin binding / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Cleavage/polyadenylation specificity factor subunit 5 / Nucleotide hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Cleavage and polyadenylation specificity factor subunit 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsStenmark, P. / Hogbom, M. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. ...Stenmark, P. / Hogbom, M. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg Schiavone, L. / Kotenyova, T. / Magnusdottir, A. / Nilsson-Ehle, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Thorsell, A.G. / Van Den Berg, S. / Wallden, K. / Weigelt, J. / Nordlund, P.
CitationJournal: Proteins / Year: 2008
Title: The Crystal Structure of Human Cleavage and Polyadenylation Specific Factor-5 Reveals a Dimeric Nudix Protein with a Conserved Catalytic Site.
Authors: Tresaugues, L. / Stenmark, P. / Schuler, H. / Flodin, S. / Welin, M. / Nyman, T. / Hammarstrom, M. / Moche, M. / Graslund, S. / Nordlund, P.
History
DepositionApr 25, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 5


Theoretical massNumber of molelcules
Total (without water)26,7211
Polymers26,7211
Non-polymers00
Water3,891216
1
A: CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 5

A: CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 5


Theoretical massNumber of molelcules
Total (without water)53,4412
Polymers53,4412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)79.920, 79.920, 72.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2039-

HOH

21A-2060-

HOH

31A-2210-

HOH

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Components

#1: Protein CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 5 / CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 25 KDA SUBUNIT / CPSF 25 KDA SUBUNIT / PRE-MRNA ...CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 25 KDA SUBUNIT / CPSF 25 KDA SUBUNIT / PRE-MRNA CLEAVAGE FACTOR IM 25-KDA SUBUNIT / NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 21 / NUDIX MOTIF 21


Mass: 26720.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43809
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.8 Å3/Da / Density % sol: 57 %
Description: THE NATIVE DATA WAS COLLECTED AT BESSY, THE ADDITIONAL DATASET IS THE SE-MET SAD DATA FROM ESRF.
Crystal growDetails: 0.2M CALCIUM CHLORIDE, 0.1M MES PH 6, 20% W/V PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98401
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98401 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 21406 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.22
Reflection shellResolution: 1.9→2 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→19.98 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.805 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1070 5 %RANDOM
Rwork0.17 ---
obs0.171 20321 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0.17 Å20 Å2
2---0.33 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 0 216 1880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221722
X-RAY DIFFRACTIONr_bond_other_d0.0010.021215
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.9812340
X-RAY DIFFRACTIONr_angle_other_deg0.97332961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7635204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5823.7882
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8515301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7661511
X-RAY DIFFRACTIONr_chiral_restr0.10.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021875
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02349
X-RAY DIFFRACTIONr_nbd_refined0.2060.2242
X-RAY DIFFRACTIONr_nbd_other0.1990.21167
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2782
X-RAY DIFFRACTIONr_nbtor_other0.0850.2897
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2132
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2040.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3761.51328
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5621662
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4723829
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3894.5676
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 77
Rwork0.222 1479

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