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- PDB-2j8q: Crystal structure of human cleavage and polyadenylation specifici... -

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Basic information

Entry
Database: PDB / ID: 2j8q
TitleCrystal structure of human cleavage and polyadenylation specificity factor 5 (CPSF5) in complex with a sulphate ion.
ComponentsCLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 5
KeywordsNUCLEAR PROTEIN / RNA-BINDING / MRNA PROCESSING / PHOSPHORYLATION / 3'MRNA CLEAVAGE AND POLYADENYLATION FACTOR
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMoche, M. / Stenmark, P. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. ...Moche, M. / Stenmark, P. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg, S.L. / Hogbom, M. / Johansson, I. / Karlberg, T. / Kosinska, U. / Kotenyova, T. / Magnusdottir, A. / Nilsson, M.E. / Nilsson-Ehle, P. / Nyman, T. / Persson, C. / Sagemark, J. / Sundstrom, M. / Uppenberg, J. / Upsten, M. / Thorsell, A.G. / Van Den Berg, S. / Wallden, K. / Weigelt, J. / Welin, M. / 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
DepositionOct 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

Downloads & links

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Assembly

Deposited unit
A: CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 5
B: CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0334
Polymers52,8412
Non-polymers1922
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.400, 86.400, 139.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9945, 0.02949, -0.1006), (0.007481, -0.9372, -0.3487), (-0.1045, -0.3476, 0.9318)
Vector: -6.493, 105.2, 18.43)

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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: 26420.318 Da / Num. of mol.: 2 / Fragment: RESIDUES 24-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43809
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT HAS AN N-TERMINAL HIS TAG

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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: 2.72 Å3/Da / Density % sol: 54.48 %
Crystal growDetails: 17%(W/V)PEG3350, 0.2M AMSO4, 0.1M BIS TRIS PH 5.2.MIX 1:1UL DROPS OF 9MG/ML PROTEIN WITH WELL SOLUTION IN RT THEN MOVE TO CR.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 24012 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.5 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.94 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CL3

2cl3


Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.897 / SU B: 15.452 / SU ML: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1201 5 %RANDOM
Rwork0.218 ---
obs0.22 22810 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å20 Å2
2--1.41 Å20 Å2
3----2.83 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 10 129 3419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223381
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9844591
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9155394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10623.765162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6415584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3051522
X-RAY DIFFRACTIONr_chiral_restr0.1040.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022588
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.21240
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22190
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2151
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4631.52071
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8123254
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.08131509
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6984.51337
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: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.334 84
Rwork0.28 1587
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.33770.4020.19261.89140.02382.8825-0.02210.1326-0.251-0.08550.02970.11160.3611-0.0948-0.0076-0.104-0.0230.0362-0.1727-0.0155-0.1573-4.226239.04679.2662
24.22590.2518-0.97782.82130.24172.81690.07970.02030.5212-0.08530.0841-0.0563-0.5270.0327-0.1638-0.0427-0.00390.0501-0.1778-0.0074-0.1064-0.995666.105213.5176
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 227
2X-RAY DIFFRACTION2B28 - 227

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