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- PDB-6b7g: Solution NMR structure of BCoR in complex with AF9 (BCoR-AF9) -

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Basic information

Entry
Database: PDB / ID: 6b7g
TitleSolution NMR structure of BCoR in complex with AF9 (BCoR-AF9)
Components
  • BCL-6 corepressor
  • Protein AF-9
KeywordsTRANSCRIPTION / Complex
Function / homology
Function and homology information


negative regulation of tooth mineralization / BCOR complex / specification of axis polarity / modification-dependent protein binding / regulation of stem cell division / segment specification / blastocyst hatching / regulation of chromatin organization / negative regulation of bone mineralization / positive regulation of Wnt signaling pathway, planar cell polarity pathway ...negative regulation of tooth mineralization / BCOR complex / specification of axis polarity / modification-dependent protein binding / regulation of stem cell division / segment specification / blastocyst hatching / regulation of chromatin organization / negative regulation of bone mineralization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / odontogenesis / anterior/posterior pattern specification / roof of mouth development / hematopoietic stem cell differentiation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / heat shock protein binding / transcription elongation factor complex / RNA polymerase II transcription regulatory region sequence-specific DNA binding / lysine-acetylated histone binding / negative regulation of canonical Wnt signaling pathway / histone deacetylase binding / transcription corepressor activity / chromosome / gene expression / heart development / histone binding / DNA-binding transcription factor binding / molecular adaptor activity / transcription cis-regulatory region binding / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol
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 / AF-9, ANC1 homology domain / ANC1 homology domain (AHD) / YEATS / YEATS superfamily ...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 / AF-9, ANC1 homology domain / ANC1 homology domain (AHD) / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / 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
Protein AF-9 / BCL-6 corepressor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSchmidt, C.R. / Kuntimaddi, A. / Leach, B.I. / Bushweller, J.H.
CitationJournal: Blood Cancer Discov / Year: 2020
Title: BCOR Binding to MLL-AF9 Is Essential for Leukemia via Altered EYA1, SIX, and MYC Activity.
Authors: Schmidt, C.R. / Achille, N.J. / Kuntimaddi, A. / Boulton, A.M. / Leach, B.I. / Zhang, S. / Zeleznik-Le, N.J. / Bushweller, J.H.
History
DepositionOct 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 / _entity.formula_weight / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 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 1.3May 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: Protein AF-9
B: BCL-6 corepressor


Theoretical massNumber of molelcules
Total (without water)11,9922
Polymers11,9922
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1440 Å2
ΔGint-12 kcal/mol
Surface area8700 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein AF-9 / ALL1-fused gene from chromosome 9 protein / Myeloid/lymphoid or mixed-lineage leukemia translocated ...ALL1-fused gene from chromosome 9 protein / Myeloid/lymphoid or mixed-lineage leukemia translocated to chromosome 3 protein / YEATS domain-containing protein 3


Mass: 8278.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT3, AF9, YEATS3 / Production host: Escherichia coli (E. coli) / References: UniProt: P42568
#2: Protein/peptide BCL-6 corepressor / / BCoR


Mass: 3713.134 Da / Num. of mol.: 1
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-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
131isotropic13D HNCO
141isotropic13D HNHA
151isotropic13D HN(CA)CB
1111isotropic13D CBCA(CO)NH
1101isotropic23D (H)CCH-TOCSY
191isotropic33D C(CO)NH
181isotropic23D 1H-13C NOESY aliphatic
171isotropic33D 1H-13C NOESY aromatic
161isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 750 uM [U-13C; U-15N] BCoR, 750 uM [U-13C; U-15N] AF9, 9.3 mM Bis-Tris, 15.8 mM MES, 100 mM NaCl, 1 mM DTT, 5 % [U-99% 2H] D2O, 95 % H2O, 95% H2O/5% D2O
Label: BCoR-AF9 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
750 uMBCoR[U-13C; U-15N]1
750 uMAF9[U-13C; U-15N]1
9.3 mMBis-Trisnatural abundance1
15.8 mMMESnatural abundance1
100 mMNaClnatural abundance1
1 mMDTTnatural abundance1
5 %D2O[U-99% 2H]1
95 %H2Onatural abundance1
Sample conditionsIonic strength: 100 mM / Label: BCoR-AF9 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AnalysisCCPNpeak picking
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
VNMRVariancollection
MOLMOLKoradi, Billeter and Wuthrichdata analysis
PyMOLSchroedingerdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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