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- PDB-6tze: Human CstF-64 RRM mutant - D50A -

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Basic information

Entry
Database: PDB / ID: 6tze
TitleHuman CstF-64 RRM mutant - D50A
ComponentsCleavage stimulation factor subunit 2
KeywordsTRANSCRIPTION / RNA recognition motif / RNA cleavage and polyadenylation / RNA BINDING PROTEIN
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
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 / 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
Similarity search - Domain/homology
Cleavage stimulation factor subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLatham, M.P. / Masoumzadeh, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM128906-01 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: A missense mutation in the CSTF2 gene that impairs the function of the RNA recognition motif and causes defects in 3' end processing is associated with intellectual disability in humans.
Authors: Grozdanov, P.N. / Masoumzadeh, E. / Kalscheuer, V.M. / Bienvenu, T. / Billuart, P. / Delrue, M.A. / Latham, M.P. / MacDonald, C.C.
History
DepositionAug 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cleavage stimulation factor subunit 2


Theoretical massNumber of molelcules
Total (without water)12,0511
Polymers12,0511
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6550 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 3000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cleavage stimulation factor subunit 2 / / CF-1 64 kDa subunit / Cleavage stimulation factor 64 kDa subunit / CstF-64


Mass: 12051.438 Da / Num. of mol.: 1 / Mutation: D50A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSTF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P33240

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D CBCA(CO)NH
121isotropic13D HN(CA)CB
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 1.2 mM [U-100% 13C; U-100% 15N] CstF-64 RNA recognition motif mutant, 90% H2O/10% D2O
Label: 15N, 13C_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.2 mM / Component: CstF-64 RNA recognition motif mutant / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 10 mM / Label: conditions_1 / pH: 6 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Agilent DD2 / Manufacturer: Agilent / Model: DD2 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.4.2CCPNchemical shift assignment
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 3000 / Conformers submitted total number: 10

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