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- PDB-2nax: Structure of CCHC zinc finger domain of Pcf11 -

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Basic information

Entry
Database: PDB / ID: 2nax
TitleStructure of CCHC zinc finger domain of Pcf11
ComponentsProtein PCF11
KeywordsMETAL BINDING PROTEIN / zinc finger
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 / mRNA 3'-end processing / termination of RNA polymerase II transcription / RNA polymerase II complex binding / mRNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Pfc11 Rna14/15 interacting domain / Subunit of cleavage factor IA Pcf11, C-terminal / Protein PCF11-like / : / : / Pcf11, Clp1-interaction domain / Pcf11, C-terminal domain / CID domain / RPR ...: / Pfc11 Rna14/15 interacting domain / Subunit of cleavage factor IA Pcf11, C-terminal / Protein PCF11-like / : / : / Pcf11, Clp1-interaction domain / Pcf11, C-terminal domain / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsYang, F. / Varani, G.
CitationJournal: RNA / Year: 2017
Title: The C terminus of Pcf11 forms a novel zinc-finger structure that plays an essential role in mRNA 3'-end processing.
Authors: Yang, F. / Hsu, P. / Lee, S.D. / Yang, W. / Hoskinson, D. / Xu, W. / Moore, C. / Varani, G.
History
DepositionJan 12, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein PCF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7212
Polymers8,6551
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 8655.413 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: PCF11, YDR228C, YD9934.13C / Production host: Escherichia coli (E. coli) / 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-IDType
1122D 1H-15N HSQC
1232D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D HBHA(CO)NH
1833D (H)CCH-TOCSY
1923D 1H-15N NOESY-HSQC
11033D 1H-13C NOESY-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] protein_1, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 15N] protein_1, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-99% 13C; U-99% 15N] protein_1, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity_1-1[U-99% 13C; U-99% 15N]1
1 mMentity_1-2[U-99% 15N]2
1 mMentity_1-3[U-99% 13C; U-99% 15N]3
Sample conditionsIonic strength: 120 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CCPNMRCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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