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- PDB-2n4q: Solution NMR structure of CBX8 in complex with AF9 (CBX8-AF9) -

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Basic information

Entry
Database: PDB / ID: 2n4q
TitleSolution NMR structure of CBX8 in complex with AF9 (CBX8-AF9)
Components
  • Chromobox protein homolog 8
  • Protein AF-9
KeywordsTRANSCRIPTION / AF9 / MLLT3 / CBX8 / hPC3 / H3K27me3 / DOT1L / AF4 / Mixed Lineage Leukemia / MLL-AF9 / MLL / Intrinsically Disordered Protein / IDP / PRC1 / Polycomb / Polycomb Group Proteins / chromobox homolog 8 / Leukemia
Function / homology
Function and homology information


modification-dependent protein binding / regulation of stem cell division / PRC1 complex / segment specification / ubiquitin-protein transferase activator activity / regulation of chromatin organization / PcG protein complex / positive regulation of Wnt signaling pathway, planar cell polarity pathway / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins ...modification-dependent protein binding / regulation of stem cell division / PRC1 complex / segment specification / ubiquitin-protein transferase activator activity / regulation of chromatin organization / PcG protein complex / positive regulation of Wnt signaling pathway, planar cell polarity pathway / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / anterior/posterior pattern specification / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of collagen biosynthetic process / hematopoietic stem cell differentiation / heterochromatin / SUMOylation of DNA damage response and repair proteins / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / methylated histone binding / positive regulation of DNA repair / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / transcription elongation factor complex / Regulation of PTEN gene transcription / lysine-acetylated histone binding / negative regulation of canonical Wnt signaling pathway / cellular response to hydrogen peroxide / chromatin organization / chromosome / gene expression / histone binding / Oxidative Stress Induced Senescence / molecular adaptor activity / single-stranded RNA binding / chromatin binding / positive regulation of cell population proliferation / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
CBX family C-terminal motif / CBX family C-terminal motif / AF-9, ANC1 homology domain / ANC1 homology domain (AHD) / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Chromo domain, conserved site / Chromo domain signature. ...CBX family C-terminal motif / CBX family C-terminal motif / AF-9, ANC1 homology domain / ANC1 homology domain (AHD) / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily
Similarity search - Domain/homology
Protein AF-9 / Chromobox protein homolog 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsKuntimaddi, A. / Leach, B.I. / Bushweller, J.H.
CitationJournal: To be Published
Title: Solution NMR Structure of CBX8 in complex with AF9 (CBX8-AF9)
Authors: Kuntimaddi, A. / Leach, B.I. / Bushweller, J.H.
History
DepositionJun 30, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 20, 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: Chromobox protein homolog 8
B: Protein AF-9


Theoretical massNumber of molelcules
Total (without water)10,8562
Polymers10,8562
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1156 Å2
ΔGint-10.8 kcal/mol
Surface area7746.6 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/peptide Chromobox protein homolog 8 / Polycomb 3 homolog / Pc3 / hPc3 / Rectachrome 1


Mass: 2577.911 Da / Num. of mol.: 1 / Fragment: UNP residues 327-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX8, PC3, RC1 / Plasmid: PETDUET-1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 DE3 / References: UniProt: Q9HC52
#2: 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 / Fragment: UNP residues 500-568
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT3, AF9, YEATS3 / Plasmid: PETDUET-1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 DE3 / References: UniProt: P42568

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D (H)CCH-TOCSY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic
11013D H(CCO)NH

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Sample preparation

DetailsContents: 750 uM [U-100% 13C; U-100% 15N] Chromobox protein homolog 8, 750 uM [U-100% 13C; U-100% 15N] Protein AF, 9.5 mM BIS-TRIS, 15.8 mM MES, 100 mM sodium chloride, 1 mM DTT, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
750 uMChromobox protein homolog 8-1[U-100% 13C; U-100% 15N]1
750 uMProtein AF-9-2[U-100% 13C; U-100% 15N]1
9.5 mMBIS-TRIS-31
15.8 mMMES-41
100 mMsodium chloride-51
1 mMDTT-61
Sample conditionsIonic strength: 100 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
CcpNmr AnalysisCCPNpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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