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- PDB-8ba1: CTD12-CTD12 heterodimer from CPSF73 and CPSF100 -

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Basic information

Entry
Database: PDB / ID: 8ba1
TitleCTD12-CTD12 heterodimer from CPSF73 and CPSF100
Components
  • Cleavage and polyadenylation specificity factor subunit 2
  • Cleavage and polyadenylation specificity factor subunit 3
KeywordsRNA BINDING PROTEIN / Cleavage and polyadenylation specificity factor
Function / homology
Function and homology information


mRNA 3'-end processing by stem-loop binding and cleavage / 5'-3' RNA exonuclease activity / mRNA cleavage and polyadenylation specificity factor complex / RNA endonuclease activity / RNA binding
Similarity search - Function
Cleavage and polyadenylation specificity factor subunit 2 / 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 ...Cleavage and polyadenylation specificity factor subunit 2 / 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
Cleavage and polyadenylation specificity factor subunit 2 / Endoribonuclease YSH1
Similarity search - Component
Biological speciesEncephalitozoon cuniculi (fungus)
MethodSOLUTION NMR / simulated annealing
AuthorsThore, S. / Mackereth, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Open Biology / Year: 2023
Title: Molecular details of the CPSF73-CPSF100 C-terminal heterodimer and interaction with Symplekin.
Authors: Thore, S. / Raoelijaona, F. / Talenton, V. / Fribourg, S. / Mackereth, C.D.
#1: Journal: Biorxiv / Year: 2023
Title: Molecular details of the CPSF73-CPSF100 C-terminal heterodimer and interaction with Symplekin
Authors: Thore, S. / Raoelijaona, F. / Talenton, V. / Fribourg, S. / Mackereth, C.
History
DepositionOct 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author

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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
B: Cleavage and polyadenylation specificity factor subunit 2


Theoretical massNumber of molelcules
Total (without water)26,3502
Polymers26,3502
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, heterodimer
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4130 Å2
ΔGint-21 kcal/mol
Surface area12920 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 250structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Cleavage and polyadenylation specificity factor subunit 3


Mass: 13521.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Strain: GB-M1 / Gene: ECU10_0900 / Plasmid: pET-MCN / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): lysY / References: UniProt: Q8SUE4
#2: Protein Cleavage and polyadenylation specificity factor subunit 2 / Cleavage and polyadenylation specificity factor 100 kDa subunit


Mass: 12828.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Gene: ECU05_0390 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): lysY / References: UniProt: M1JIZ1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-1H NOESY
122isotropic23D 1H-13C NOESY aliphatic
133isotropic13D 1H-13C NOESY aliphatic
144isotropic13D 1H-13C NOESY aliphatic
155isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1458 uM CPSF73, 458 uM CPSF100, 20 mM TRIS, 150 mM sodium chloride, 2 mM DTT, 100% D2Ounlabelled D2O100% D2O
solution2625 uM [13C-Ile; U-15N] CPSF73, 625 uM [13C-Ile; U-15N] CPSF100, 20 mM TRIS, 150 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O13C-Ile90% H2O/10% D2O
solution3694 uM [13C-Val/Leu, U-15N] CPSF73, 694 uM [13C-Val/Leu, U-15N] CPSF100, 20 mM TRIS, 150 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O13C-Val/Leu90% H2O/10% D2O
solution4230 uM [U-13C; U-15N] CPSF73, 230 uM [U-13C; U-15N] CPSF100, 20 mM TRIS, 150 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O13C,15N90% H2O/10% D2O
solution5880 uM [U-13C; U-15N] CPSF73, 880 uM [U-13C; U-15N] CPSF100, 20 mM TRIS, 150 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O15N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
458 uMCPSF73natural abundance1
458 uMCPSF100natural abundance1
20 mMTRISnatural abundance1
150 mMsodium chloridenatural abundance1
2 mMDTTnatural abundance1
625 uMCPSF73[13C-Ile; U-15N]2
625 uMCPSF100[13C-Ile; U-15N]2
20 mMTRISnatural abundance2
150 mMsodium chloridenatural abundance2
2 mMDTTnatural abundance2
694 uMCPSF73[13C-Val/Leu, U-15N]3
694 uMCPSF100[13C-Val/Leu, U-15N]3
20 mMTRISnatural abundance3
150 mMsodium chloridenatural abundance3
2 mMDTTnatural abundance3
230 uMCPSF73[U-13C; U-15N]4
230 uMCPSF100[U-13C; U-15N]4
20 mMTRISnatural abundance4
150 mMsodium chloridenatural abundance4
2 mMDTTnatural abundance4
880 uMCPSF73[U-13C; U-15N]5
880 uMCPSF100[U-13C; U-15N]5
20 mMTRISnatural abundance5
150 mMsodium chloridenatural abundance5
2 mMDTTnatural abundance5
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 7.5 pH* / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO8001
Bruker AVANCE NEOBrukerAVANCE NEO7002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin4Bruker Biospincollection
Refinement
MethodSoftware ordinal
simulated annealing1
simulated annealing2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 250 / Conformers submitted total number: 20

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