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- PDB-2j8p: NMR structure of C-terminal domain of human CstF-64 -

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Basic information

Entry
Database: PDB / ID: 2j8p
TitleNMR structure of C-terminal domain of human CstF-64
ComponentsCLEAVAGE STIMULATION FACTOR 64 KDA SUBUNIT
KeywordsNUCLEAR PROTEIN / CLEAVAGE/POLYADENYLATION / ALTERNATIVE SPLICING RNA15 / PCF11 / CSTF-64 / RNA-BINDING / MRNA PROCESSING / PHOSPHORYLATION
Function / homology
Function and homology information


cleavage body / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / mRNA 3'-end processing / tRNA processing in the nucleus / RNA Polymerase II Transcription Termination / Processing of Capped Intron-Containing Pre-mRNA / cellular response to nerve growth factor stimulus / nuclear body ...cleavage body / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / mRNA 3'-end processing / tRNA processing in the nucleus / RNA Polymerase II Transcription Termination / Processing of Capped Intron-Containing Pre-mRNA / cellular response to nerve growth factor stimulus / nuclear body / mRNA binding / RNA binding / nucleoplasm
Similarity search - Function
Transcription termination and cleavage factor, C-terminal domain / Cleavage stimulation factor subunit 2, hinge domain / Hinge domain of cleavage stimulation factor subunit 2 / Transcription termination and cleavage factor, C-terminal domain / Transcription termination and cleavage factor, C-terminal domain superfamily / Transcription termination and cleavage factor C-terminal / Histone, subunit A / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...Transcription termination and cleavage factor, C-terminal domain / Cleavage stimulation factor subunit 2, hinge domain / Hinge domain of cleavage stimulation factor subunit 2 / Transcription termination and cleavage factor, C-terminal domain / Transcription termination and cleavage factor, C-terminal domain superfamily / Transcription termination and cleavage factor C-terminal / Histone, subunit A / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cleavage stimulation factor subunit 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsQu, X. / Perez-Canadillas, J.M. / Agrawal, S. / De Baecke, J. / Cheng, H. / Varani, G. / Moore, C.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The C-Terminal Domains of Vertebrate Cstf-64 and its Yeast Orthologue RNA15 Form a New Structure Critical for Mrna 3'-End Processing.
Authors: Qu, X. / Perez-Canadillas, J.M. / Agrawal, S. / De Baecke, J. / Cheng, H. / Varani, G. / Moore, C.
History
DepositionOct 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CLEAVAGE STIMULATION FACTOR 64 KDA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)5,4971
Polymers5,4971
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 35STRUCTURES HAVING NO DISTANCE RESTRAINT VIOLATION LARGER THAN 0.2 A OR NO VIOLATION OF DIHEDRAL ANGLE CONSTRAINTS LARGER THAN 5 DEGREES
RepresentativeModel #1

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Components

#1: Protein/peptide CLEAVAGE STIMULATION FACTOR 64 KDA SUBUNIT / CSTF 64 KDA SUBUNIT / CF-1 64 KDA SUBUNITCSTF-64 / CSTF-64


Mass: 5497.409 Da / Num. of mol.: 1 / Fragment: RESIDUES 531-577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33240
Sequence detailsSESIDUES 529 AND 530 ARE REMAINS OF THE FUSION TAG AFTER PROTEASE CLEAVAGE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1213D HN(CO)CA
1313D CBCA(CO)NH
1413D (H)CCH-COSY
1513D 13C-NOESY-HSQC
1613D 15N- NOESY-HSQC
1712D 15N-HSQC
1812D 13C-HSQC
1912D NOESY
11012D TOCSY
NMR detailsText: NONE

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Sample preparation

DetailsContents: 10% D2O/90% H2O
Sample conditionsIonic strength: 25 MM POTASSIUM PHOSPHATE / pH: 6.0 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAP.GUNTERT,C.MUMENTHALER,K.WUTHRICHrefinement
ANSIGstructure solution
TALOSstructure solution
CYANAstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: STRUCTURES HAVING NO DISTANCE RESTRAINT VIOLATION LARGER THAN 0.2 A OR NO VIOLATION OF DIHEDRAL ANGLE CONSTRAINTS LARGER THAN 5 DEGREES
Conformers calculated total number: 35 / Conformers submitted total number: 30

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