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- PDB-8b7t: CPSF73 CTD3 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8b7t
TitleCPSF73 CTD3
ComponentsCPSF73
KeywordsRNA BINDING PROTEIN / Cleavage and polyadenylation specifity 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
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 ...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
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 3, 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

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Assembly

Deposited unit
A: CPSF73


Theoretical massNumber of molelcules
Total (without water)8,4981
Polymers8,4981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, Final C-terminal domain of E. cuniculi CPSF73, as defined by limited proteolysis
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein CPSF73


Mass: 8497.995 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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
131isotropic22D 1H-13C HSQC methyl
141isotropic13D HNCO
151isotropic13D HN(CA)CO
161isotropic13D HNCA
171isotropic13D HN(CA)CB
181isotropic13D CBCA(CO)NH
191isotropic23D HNHA
1101isotropic23D HA(CACO)NH
1111isotropic23D (H)CCH-TOCSY
1121isotropic23D H(CCO)NH
1131isotropic23D H(CCO)NH
1141isotropic23D 1H-15N NOESY
1152isotropic23D 1H-13C NOESY
1163isotropic22D 1H-1H TOCSY
1173isotropic22D DQF-COSY
1183isotropic22D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1800 uM [U-13C; U-15N] CPSF73, 20 mM TRIS, 150 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O13C15N_H2O90% H2O/10% D2O
solution2800 uM [U-13C; U-15N] CPSF73, 20 mM TRIS, 150 mM sodium chloride, 2 mM DTT, 100% D2O13C15N_D2O100% D2O
solution3800 uM CPSF73, 20 mM TRIS, 150 mM sodium chloride, 2 mM DTT, 100% D2Ounlabelled_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
800 uMCPSF73[U-13C; U-15N]1
20 mMTRISnatural abundance1
150 mMsodium chloridenatural abundance1
2 mMDTTnatural abundance1
800 uMCPSF73[U-13C; U-15N]2
20 mMTRISnatural abundance2
150 mMsodium chloridenatural abundance2
2 mMDTTnatural abundance2
800 uMCPSF73natural abundance3
20 mMTRISnatural abundance3
150 mMsodium chloridenatural abundance3
2 mMDTTnatural abundance3
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 7.5 / 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
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TopSpinBruker 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: 100 / Conformers submitted total number: 20

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