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- PDB-5m9z: Second zinc-binding domain from yeast Pcf11 -

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Basic information

Entry
Database: PDB / ID: 5m9z
TitleSecond zinc-binding domain from yeast Pcf11
ComponentsProtein PCF11
KeywordsRNA BINDING PROTEIN / zinc-binding / mRNA / RNA processing
Function / homology
Function and homology information


termination of RNA polymerase II transcription, poly(A)-coupled / termination of RNA polymerase II transcription, exosome-dependent / mRNA cleavage factor complex / : / termination of RNA polymerase II transcription / RNA polymerase II complex binding / mRNA binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Subunit of cleavage factor IA Pcf11, C-terminal / Protein PCF11-like / : / Pcf11, Clp1-interaction domain / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsMackereth, C.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Distinct roles of Pcf11 zinc-binding domains in pre-mRNA 3'-end processing.
Authors: Guegueniat, J. / Dupin, A.F. / Stojko, J. / Beaurepaire, L. / Cianferani, S. / Mackereth, C.D. / Minvielle-Sebastia, L. / Fribourg, S.
History
DepositionNov 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2018Group: Data collection / Category: pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein PCF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9042
Polymers10,8391
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area100 Å2
ΔGint-39 kcal/mol
Surface area4230 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 40structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Protein PCF11 / protein 1 of CF I


Mass: 10838.987 Da / Num. of mol.: 1 / Fragment: UNP residues 530-626
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PCF11, YDR228C, YD9934.13C / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): LysY / References: UniProt: P39081
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic22D 1H-15N HSQC
123isotropic23D HNCO
133isotropic23D HN(CA)CO
143isotropic23D HNCA
153isotropic23D CBCA(CO)NH
163isotropic23D HN(CA)CB
172isotropic23D HNHA
184isotropic12D 1H-13C HSQC
193isotropic23D H(CCO)NH
1104isotropic13D (H)CCH-TOCSY
1114isotropic13D (H)CCH-TOCSY
1125isotropic12D 1H-13C HSQC CT
1132isotropic23D 1H-15N NOESY
1142isotropic22D 1H-15N HMBC
1154isotropic13D 1H-13C NOESY
1161isotropic22D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1360 uM Pcf11, 50 mM TRIS, 150 mM sodium chloride, 50 uM zinc acetate, 90% H2O/10% D2Ounlabeled90% H2O/10% D2O
solution2250 uM [U-99% 15N] Pcf11, 50 mM TRIS, 150 mM sodium chloride, 50 uM zinc acetate, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution3230 uM [U-99% 13C; U-99% 15N] Pcf11, 50 mM na TRIS, 150 mM na sodium chloride, 50 uM zinc acetate, 90% H2O/10% D2O13C_15N_sample90% H2O/10% D2O
solution4230 uM [U-99% 13C; U-99% 15N] Pcf11, 50 mM TRIS, 150 mM sodium chloride, 50 uM zinc acetate, 100% D2O13C_15N_D2O100% D2O
solution5100 uM [U-10% 13C; U-99% 15N] Pcf11, 50 mM TRIS, 150 mM sodium chloride, 50 uM zinc acetate, 90% H2O/10% D2O10_percent_13C90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
360 uMPcf11natural abundance1
50 mMTRISnatural abundance1
150 mMsodium chloridenatural abundance1
50 uMzinc acetatenatural abundance1
250 uMPcf11[U-99% 15N]2
50 mMTRISnatural abundance2
150 mMsodium chloridenatural abundance2
50 uMzinc acetatenatural abundance2
230 uMPcf11[U-99% 13C; U-99% 15N]3
50 mMTRISna3
150 mMsodium chloridena3
50 uMzinc acetatenatural abundance3
230 uMPcf11[U-99% 13C; U-99% 15N]4
50 mMTRISnatural abundance4
150 mMsodium chloridenatural abundance4
50 uMzinc acetatenatural abundance4
100 uMPcf11[U-10% 13C; U-99% 15N]5
50 mMTRISnatural abundance5
150 mMsodium chloridenatural abundance5
50 uMzinc acetatenatural abundance5
Sample conditionsIonic strength: 200 mM / Label: condition_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
ARIALinge, O'Donoghue and Nilgesstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 15

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