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- PDB-2mj8: Solution structure of CDYL2 chromodomain -

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Basic information

Entry
Database: PDB / ID: 2mj8
TitleSolution structure of CDYL2 chromodomain
ComponentsChromodomain Y-like protein 2
KeywordsPROTEIN BINDING / chromodomain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H3K27me3 reader activity / histone H3K9me2/3 reader activity / : / transcription corepressor activity / nucleus
Similarity search - Function
: / Chromo domain, conserved site / Enoyl-CoA hydratase, C-terminal / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase ...: / Chromo domain, conserved site / Enoyl-CoA hydratase, C-terminal / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / ClpP/crotonase-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chromodomain Y-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsQin, S. / Houliston, S. / Arrowsmith, C.H. / Edwards, A.M. / Wu, H. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Cell Chem Biol / Year: 2020
Title: Structural Basis for the Binding Selectivity of Human CDY Chromodomains.
Authors: Dong, C. / Liu, Y. / Lyu, T.J. / Beldar, S. / Lamb, K.N. / Tempel, W. / Li, Y. / Li, Z. / James, L.I. / Qin, S. / Wang, Y. / Min, J.
History
DepositionDec 28, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _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: Chromodomain Y-like protein 2


Theoretical massNumber of molelcules
Total (without water)7,6961
Polymers7,6961
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Chromodomain Y-like protein 2 / CDY-like 2


Mass: 7695.596 Da / Num. of mol.: 1 / Fragment: UNP residues 2-64
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDYL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N8U2

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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 HNCO
1413D HNCA
1513D CBCA(CO)NH
1613D HBHA(CO)NH
1713D 1H-15N NOESY
1813D (H)CCH-TOCSY
1913D 1H-13C NOESY
11013D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 20 mM TRIS, 150 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMTRIS-11
150 mMsodium chloride-21
2 mMDTT-31
Sample conditionsIonic strength: 0.15 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
FMCGUI2.5Lemak A.chemical shift assignment
FMCGUI2.5Lemak A.data analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1234 / NOE intraresidue total count: 293 / NOE long range total count: 349 / NOE medium range total count: 233 / NOE sequential total count: 359 / Hydrogen bond constraints total count: 64 / Protein phi angle constraints total count: 44 / Protein psi angle constraints total count: 44
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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