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- PDB-6pqt: N-terminal domain of dynein intermediate chain from Chaetomium th... -

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Basic information

Entry
Database: PDB / ID: 6pqt
TitleN-terminal domain of dynein intermediate chain from Chaetomium thermophilum
ComponentsDynein intermediate chain protein
KeywordsMOTOR PROTEIN / dynein / intermediate chain / intrinsically disordered protein / IDP
Function / homology: / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Putative dynein intermediate chain protein
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
MethodSOLUTION NMR / simulated annealing
AuthorsLoening, N.M. / Barbar, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1617019 United States
CitationJournal: Biophys.J. / Year: 2020
Title: Interplay of Disorder and Sequence Specificity in the Formation of Stable Dynein-Dynactin Complexes.
Authors: Loening, N.M. / Saravanan, S. / Jespersen, N.E. / Jara, K. / Barbar, E.
History
DepositionJul 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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

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Assembly

Deposited unit
A: Dynein intermediate chain protein


Theoretical massNumber of molelcules
Total (without water)10,0131
Polymers10,0131
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Dynein intermediate chain protein


Mass: 10013.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0056990 / Plasmid: pET-24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SCF1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY
121isotropic13D 1H-15N NOESY
131isotropic13D HNCO
151isotropic13D HN(CA)CB

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Sample preparation

DetailsType: solution
Contents: 200 uM [U-99% 13C; U-99% 15N] CT-IC 1-88, 95% H2O/5% D2O
Details: 50 mM sodium chloride, 50 mM phosphate, 1 mM sodium azide, 0.2 mM DSS
Label: 13C_15N_sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 200 uM / Component: CT-IC 1-88 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsDetails: 50 mM sodium chloride, 50 mM phosphate, 1 mM sodium azide, 0.2 mM DSS
Ionic strength: 100 mM / Label: Standard Conditions / pH: 6.5 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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