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- PDB-2xk0: Solution structure of the Tudor domain from Drosophila Polycombli... -

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Basic information

Entry
Database: PDB / ID: 2xk0
TitleSolution structure of the Tudor domain from Drosophila Polycomblike (Pcl)
ComponentsPOLYCOMB PROTEIN PCL
KeywordsTRANSCRIPTION / AROMATIC CAGE
Function / homology
Function and homology information


ventral cord development / polytene chromosome / anterior/posterior axis specification / defense response to fungus / chromatin organization / regulation of gene expression / microtubule binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding ...ventral cord development / polytene chromosome / anterior/posterior axis specification / defense response to fungus / chromatin organization / regulation of gene expression / microtubule binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Tudor domain / Tudor domain / SH3 type barrels. - #140 / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type ...Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Tudor domain / Tudor domain / SH3 type barrels. - #140 / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
Polycomb protein Pcl
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodSOLUTION NMR / CYANA
AuthorsFriberg, A. / Oddone, A. / Klymenko, T. / Mueller, J. / Sattler, M.
CitationJournal: Protein Sci. / Year: 2010
Title: Structure of an Atypical Tudor Domain in the Drosophila Polycomblike Protein
Authors: Friberg, A. / Oddone, A. / Klymenko, T. / Mueller, J. / Sattler, M.
History
DepositionJul 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Revision 1.4Jun 23, 2021Group: Data collection / Category: pdbx_nmr_spectrometer
Revision 1.5Jun 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 1.6Jun 19, 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: POLYCOMB PROTEIN PCL


Theoretical massNumber of molelcules
Total (without water)7,5881
Polymers7,5881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100ENERGY
Representative

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Components

#1: Protein POLYCOMB PROTEIN PCL / POLYCOMBLIKE PROTEIN


Mass: 7588.437 Da / Num. of mol.: 1 / Fragment: TUDOR DOMAIN, RESIDUES 339-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: Q24459
Sequence detailsTHE FIRST THREE RESIDUES (GAM) IS A CLONING ARTIFACT.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121HN(CA)CB
131CBCA(CO)NH
141(H)CC(CO)NH-TOCSY
151H(CC)(CO) NH-TOCSY
161H(C)CH-TOCSY
171(HB)CB(CG
181CD)HD
191(HB)CB(CG
1101CD
1111CE)HE
11211H-15N HSQC- NOESY
11311H-13C HMQC-NOESY
NMR detailsText: NONE

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 25 mM / pH: 6.3 / Pressure: 1.0 atm / Temperature: 298.5 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker6002
Bruker7503
Bruker9004

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
NMRViewstructure solution
RefinementMethod: CYANA / Software ordinal: 1 / Details: ADDITIONALLY WATER-REFINED
NMR ensembleConformer selection criteria: ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 10

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