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- PDB-6m8q: Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3)... -

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Basic information

Entry
Database: PDB / ID: 6m8q
TitleCleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in complex with NVP-LTM531
ComponentsCleavage and polyadenylation specificity factor subunit 3
KeywordsHYDROLASE / POLYADENYLATION / METALLO-B-LACTAMASE / PRE-MRNA PROCESSING / ARTEMIS / V(D)J RECOMBINATION / DOUBLE-STRAND BREAK REPAIR / RNA BINDING PROTEIN / HYDROXYLASE
Function / homology
Function and homology information


co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / mRNA 3'-end processing by stem-loop binding and cleavage / 5'-3' RNA exonuclease activity / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA Polymerase II Transcription Termination ...co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / mRNA 3'-end processing by stem-loop binding and cleavage / 5'-3' RNA exonuclease activity / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA Polymerase II Transcription Termination / : / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of G1/S transition of mitotic cell cycle / RNA endonuclease activity / ribonucleoprotein complex / RNA binding / nucleoplasm / metal ion binding
Similarity search - Function
Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / CPSF73-100_C / Rossmann fold - #10890 / Metallo-beta-lactamase superfamily domain / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain ...Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / CPSF73-100_C / Rossmann fold - #10890 / Metallo-beta-lactamase superfamily domain / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-JBG / PHOSPHATE ION / Cleavage and polyadenylation specificity factor subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsWeihofen, W.A. / Salcius, M. / Michaud, G.
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: CPSF3-dependent pre-mRNA processing as a druggable node in AML and Ewing's sarcoma.
Authors: Ross, N.T. / Lohmann, F. / Carbonneau, S. / Fazal, A. / Weihofen, W.A. / Gleim, S. / Salcius, M. / Sigoillot, F. / Henault, M. / Carl, S.H. / Rodriguez-Molina, J.B. / Miller, H.R. / ...Authors: Ross, N.T. / Lohmann, F. / Carbonneau, S. / Fazal, A. / Weihofen, W.A. / Gleim, S. / Salcius, M. / Sigoillot, F. / Henault, M. / Carl, S.H. / Rodriguez-Molina, J.B. / Miller, H.R. / Brittain, S.M. / Murphy, J. / Zambrowski, M. / Boynton, G. / Wang, Y. / Chen, A. / Molind, G.J. / Wilbertz, J.H. / Artus-Revel, C.G. / Jia, M. / Akinjiyan, F.A. / Turner, J. / Knehr, J. / Carbone, W. / Schuierer, S. / Reece-Hoyes, J.S. / Xie, K. / Saran, C. / Williams, E.T. / Roma, G. / Spencer, M. / Jenkins, J. / George, E.L. / Thomas, J.R. / Michaud, G. / Schirle, M. / Tallarico, J. / Passmore, L.A. / Chao, J.A. / Beckwith, R.E.J.
History
DepositionAug 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: 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 1.2Oct 11, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cleavage and polyadenylation specificity factor subunit 3
B: Cleavage and polyadenylation specificity factor subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,22511
Polymers108,6862
Non-polymers1,5399
Water8,719484
1
A: Cleavage and polyadenylation specificity factor subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1606
Polymers54,3431
Non-polymers8175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cleavage and polyadenylation specificity factor subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0655
Polymers54,3431
Non-polymers7224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.222, 106.222, 206.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cleavage and polyadenylation specificity factor subunit 3 / / Cleavage and polyadenylation specificity factor 73 kDa subunit / CPSF 73 kDa subunit / mRNA 3'-end- ...Cleavage and polyadenylation specificity factor 73 kDa subunit / CPSF 73 kDa subunit / mRNA 3'-end-processing endonuclease CPSF-73


Mass: 54343.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPSF3, CPSF73 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21(DE3)
References: UniProt: Q9UKF6, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-JBG / N-{3,5-dichloro-2-hydroxy-4-[2-(4-methylpiperazin-1-yl)ethoxy]benzene-1-carbonyl}-L-phenylalanine


Mass: 496.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27Cl2N3O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.67 Å3/Da / Density % sol: 54 % / Description: Tetragonal bipyrimidal
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Reservoir solution: 100 mM Tris HCl pH 7.0; 0.4 M NaH2PO4; 1.466 K2HPO; 0.2 M NaCl 10 mg/mL Protein solution: CPSF3 protein in; 20 mM Hepes pH 7.7; 150 mM NaCl; 5 % glycerol; 1 mM DTT; 0.5 ...Details: Reservoir solution: 100 mM Tris HCl pH 7.0; 0.4 M NaH2PO4; 1.466 K2HPO; 0.2 M NaCl 10 mg/mL Protein solution: CPSF3 protein in; 20 mM Hepes pH 7.7; 150 mM NaCl; 5 % glycerol; 1 mM DTT; 0.5 mM NVP-LTM531 Co-crystallization Protocol: 50 nL of protein mixed with 50 nL of reservoir solution. Crystals grew within 1 day with tetragonal bipyramidal habitus and reached a maximum size of 50 micrometers after 3 days. Cryo-protection Protocol: supplemented reservoir solution with 10 and 20% glycerol, respectively, and subsequently added both solution within 5 min. Crystals incubate for another 5 min before harvesting.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→94.41 Å / Num. obs: 42063 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 55.94 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 12.6
Reflection shellResolution: 2.49→2.5 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.272 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
BUSTER2.11.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I7T

2i7t


Resolution: 2.49→73.95 Å / Cor.coef. Fo:Fc: 0.9277 / Cor.coef. Fo:Fc free: 0.8951 / SU R Cruickshank DPI: 0.348 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.404 / SU Rfree Blow DPI: 0.242 / SU Rfree Cruickshank DPI: 0.237
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 2110 5.04 %RANDOM
Rwork0.1625 ---
obs0.1654 41862 99.41 %-
Displacement parametersBiso mean: 51.97 Å2
Baniso -1Baniso -2Baniso -3
1-9.2546 Å20 Å20 Å2
2--9.2546 Å20 Å2
3----18.5091 Å2
Refine analyzeLuzzati coordinate error obs: 0.239 Å
Refinement stepCycle: LAST / Resolution: 2.49→73.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7255 0 85 484 7824
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017507HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1810160HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2642SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes188HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1080HARMONIC5
X-RAY DIFFRACTIONt_it7507HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion21.45
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion976SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8861SEMIHARMONIC4
LS refinement shellResolution: 2.49→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2743 137 4.57 %
Rwork0.2112 2864 -
all0.214 3001 -
obs--99.41 %

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