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- PDB-8t1q: Crystal structure of human CPSF73 catalytic segment in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8t1q
TitleCrystal structure of human CPSF73 catalytic segment in complex with compound 1
ComponentsCleavage and polyadenylation specificity factor subunit 3
KeywordsHYDROLASE/INHIBITOR / nuclease / complex / HYDROLASE / HYDROLASE-INHIBITOR complex
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 / 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 ...Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / CPSF73-100_C / 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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
: / Chem-XYX / Cleavage and polyadenylation specificity factor subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHuang, J. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118093 United States
CitationJournal: Cell Chem Biol / Year: 2024
Title: Anticancer benzoxaboroles block pre-mRNA processing by directly inhibiting CPSF3.
Authors: Tao, Y. / Budhipramono, A. / Huang, J. / Fang, M. / Xie, S. / Kim, J. / Khivansara, V. / Dominski, Z. / Tong, L. / De Brabander, J.K. / Nijhawan, D.
History
DepositionJun 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year

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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 subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1697
Polymers54,4741
Non-polymers6956
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.074, 82.032, 102.835
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#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: 54474.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPSF3, CPSF73 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UKF6, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters

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Non-polymers , 5 types, 220 molecules

#2: Chemical ChemComp-XYX / 3-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-5-yl]-~{N}-[3-(4-ethanoylphenyl)phenyl]propanamide


Mass: 416.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23BNO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18-30% (w/v) PEG3350, 200-250 mM ammonium sulfate and 0.1 M Bis-Tris pH 6.3-6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→51.22 Å / Num. obs: 55262 / % possible obs: 99.2 % / Redundancy: 5.5 % / Biso Wilson estimate: 31.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Net I/σ(I): 19.3
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 5.1 % / Num. unique obs: 8739 / CC1/2: 0.577 / Χ2: 1.6 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→51.22 Å / SU ML: 0.2112 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7109
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2149 2764 5 %
Rwork0.1833 52496 -
obs0.1848 55260 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.08 Å2
Refinement stepCycle: LAST / Resolution: 1.7→51.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 40 214 3720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00753598
X-RAY DIFFRACTIONf_angle_d0.89764873
X-RAY DIFFRACTIONf_chiral_restr0.0678532
X-RAY DIFFRACTIONf_plane_restr0.0072645
X-RAY DIFFRACTIONf_dihedral_angle_d14.88511350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.31811310.29272486X-RAY DIFFRACTION94.99
1.73-1.760.31221360.26472572X-RAY DIFFRACTION99.6
1.76-1.80.26771370.25432612X-RAY DIFFRACTION99.35
1.8-1.830.29541370.28312602X-RAY DIFFRACTION99.96
1.83-1.870.3511380.28372621X-RAY DIFFRACTION100
1.87-1.920.27011380.22982624X-RAY DIFFRACTION100
1.92-1.960.22791380.19542610X-RAY DIFFRACTION100
1.96-2.020.23811370.1882603X-RAY DIFFRACTION100
2.02-2.080.22541370.18282605X-RAY DIFFRACTION100
2.08-2.140.21871380.18782633X-RAY DIFFRACTION99.89
2.14-2.220.22031390.19242629X-RAY DIFFRACTION99.68
2.22-2.310.22961370.19632611X-RAY DIFFRACTION99.82
2.31-2.410.21841400.18242652X-RAY DIFFRACTION99.68
2.41-2.540.24071360.17722593X-RAY DIFFRACTION99.09
2.54-2.70.23011390.18482647X-RAY DIFFRACTION99.43
2.7-2.910.21421400.19372644X-RAY DIFFRACTION99.54
2.91-3.20.2121380.17712635X-RAY DIFFRACTION98.97
3.2-3.660.19271400.16892651X-RAY DIFFRACTION98.87
3.66-4.610.18371400.15342654X-RAY DIFFRACTION97.39
4.62-51.220.20851480.18452812X-RAY DIFFRACTION98.83
Refinement TLS params.Method: refined / Origin x: -27.2919070651 Å / Origin y: -1.22979752928 Å / Origin z: 7.78220905275 Å
111213212223313233
T0.214592575779 Å2-0.0209606779596 Å2-0.00209939486434 Å2-0.209548173851 Å2-0.00612492998085 Å2--0.247309483201 Å2
L0.39233119918 °2-0.608744769309 °2-0.257446555505 °2-0.603742404568 °20.677685622687 °2--1.37814593104 °2
S0.00676730724203 Å °0.014451925735 Å °0.0728497293437 Å °-0.0660426300527 Å °0.0024144846105 Å °-0.0535500112217 Å °-0.120633203512 Å °0.00811377513343 Å °2.44622228529E-5 Å °
Refinement TLS groupSelection details: all

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