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- PDB-2n1l: Solution structure of the BCOR PUFD -

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Basic information

Entry
Database: PDB / ID: 2n1l
TitleSolution structure of the BCOR PUFD
ComponentsBCL-6 corepressor
KeywordsTranscription Repressor / Polycomb / PcG / PRC1
Function / homology
Function and homology information


negative regulation of tooth mineralization / BCOR complex / specification of axis polarity / blastocyst hatching / negative regulation of bone mineralization / odontogenesis / roof of mouth development / heat shock protein binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / histone deacetylase binding ...negative regulation of tooth mineralization / BCOR complex / specification of axis polarity / blastocyst hatching / negative regulation of bone mineralization / odontogenesis / roof of mouth development / heat shock protein binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / histone deacetylase binding / transcription corepressor activity / heart development / DNA-binding transcription factor binding / transcription cis-regulatory region binding / chromatin remodeling / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
BCL-6 corepressor, non-ankyrin-repeat domain / BCL-6 co-repressor, non-ankyrin-repeat region / BCL-6 corepressor, PCGF1 binding domain / PCGF Ub-like fold discriminator superfamily / : / BCORL-PCGF1-binding domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats ...BCL-6 corepressor, non-ankyrin-repeat domain / BCL-6 co-repressor, non-ankyrin-repeat region / BCL-6 corepressor, PCGF1 binding domain / PCGF Ub-like fold discriminator superfamily / : / BCORL-PCGF1-binding domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
Model detailslowest energy, model1
AuthorsWong, S.J. / Gearhart, M.D. / Ha, D.J. / Corcoran, C.M. / Diaz, V. / Taylor, A.B. / Schirf, V. / Ilangovan, U. / Hinck, A.P. / Demeler, B. ...Wong, S.J. / Gearhart, M.D. / Ha, D.J. / Corcoran, C.M. / Diaz, V. / Taylor, A.B. / Schirf, V. / Ilangovan, U. / Hinck, A.P. / Demeler, B. / Hart, J. / Bardwell, V.J. / Kim, C.A.
CitationJournal: To be Published
Title: Structural basis for the hierarchical assembly of the core of PRC1.1
Authors: Wong, S.J. / Gearhart, M.D. / Ha, D.J. / Corcoran, C.M. / Diaz, V. / Taylor, A.B. / Schirf, V. / Ilangovan, U. / Hinck, A.P. / Demeler, B. / Hart, J. / Bardwell, V.J. / Kim, C.A.
History
DepositionApr 6, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
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

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Assembly

Deposited unit
A: BCL-6 corepressor


Theoretical massNumber of molelcules
Total (without water)13,1131
Polymers13,1131
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)1 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein BCL-6 corepressor / BCoR


Mass: 13112.706 Da / Num. of mol.: 1 / Fragment: residues 1634-1748
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCOR, KIAA1575 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6W2J9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D CBCA(CO)NH
1313D C(CO)NH
1413D (H)CCH-TOCSY
1513D HNCO
1613D HN(CO)CA
1713D 1H-15N NOESY
1813D 1H-13C NOESY

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Sample preparation

DetailsContents: 3 mM [U-13C; U-15N] BCOR PUFD, 10 mM TRIS, 50 mM sodium chloride, 1 mM TCEP, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3 mMBCOR PUFD-1[U-13C; U-15N]1
10 mMTRIS-21
50 mMsodium chloride-31
1 mMTCEP-41
Sample conditionsIonic strength: 30 / pH: 8 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificchemical shift calculation
NMRViewJohnson, One Moon Scientificdata analysis
TopSpinBruker Biospincollection
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 1

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