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- PDB-4d4w: Solution structure of human MBD1 CXXC1 domain -

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Basic information

Entry
Database: PDB / ID: 4d4w
TitleSolution structure of human MBD1 CXXC1 domain
ComponentsMETHYL-CPG-BINDING DOMAIN PROTEIN 1
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


double-stranded methylated DNA binding / ventricular cardiac muscle tissue development / unmethylated CpG binding / DNA methylation-dependent heterochromatin formation / methyl-CpG binding / negative regulation of astrocyte differentiation / response to nutrient levels / SUMOylation of transcription cofactors / response to cocaine / neuron differentiation ...double-stranded methylated DNA binding / ventricular cardiac muscle tissue development / unmethylated CpG binding / DNA methylation-dependent heterochromatin formation / methyl-CpG binding / negative regulation of astrocyte differentiation / response to nutrient levels / SUMOylation of transcription cofactors / response to cocaine / neuron differentiation / nuclear matrix / response to estradiol / transcription by RNA polymerase II / nuclear speck / response to xenobiotic stimulus / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily
Similarity search - Domain/homology
Methyl-CpG-binding domain protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / simulated annealing
AuthorsThomson, R. / Smith, B.O.
CitationJournal: J.Biomol.NMR / Year: 2015
Title: Solution Structure of Human Mbd1 Cxxc1.
Authors: Thomson, R. / Smith, B.O.
History
DepositionOct 31, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Jan 24, 2018Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.page_last / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHYL-CPG-BINDING DOMAIN PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)6,6891
Polymers6,6891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 200NOE ENERGY
RepresentativeModel #2

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Components

#1: Protein METHYL-CPG-BINDING DOMAIN PROTEIN 1 / CXXC-TYPE ZINC FINGER PROTEIN 3 / METHYL-CPG-BINDING PROTEIN MBD1 / PROTEIN CONTAINING METHYL-CPG- ...CXXC-TYPE ZINC FINGER PROTEIN 3 / METHYL-CPG-BINDING PROTEIN MBD1 / PROTEIN CONTAINING METHYL-CPG-BINDING DOMAIN 1 / MBD1_CXXC1


Mass: 6688.834 Da / Num. of mol.: 1 / Fragment: RESIDUES 167-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: CARDIAC SKELETAL MUSCLE / Plasmid: PGEX-6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER / References: UniProt: Q9UIS9
Sequence detailsNIH_MGC_183 HOMO SAPIENS CDNA CLONE IMAGE 30529682

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNHA
221HNHB
331HETNOE 1
441HETNOE 1 REF
551NHSQC
661T1
771T2
881TOCSY 60
991DNOESY
10101NOE 100
111112D NOE 800
12121ME NOE 800
13131NTOCSY
NMR detailsText: STRUCTURE WAS DETERMINED USING DOUBLE RESONANCE NMR SPECTROSCOPY ON 15N-LABELED MBD1 CXXC1

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Sample preparation

DetailsContents: 95% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.25 7.5 1.0 atm293.0 K
20.25 7.5 1.0 atm293.0 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE, JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON, WARRENrefinement
TopSpin1.3structure solution
CNS1.2structure solution
CcpNmr Analysis2.4structure solution
CcpNmr Analysis2.1structure solution
CcpNmr Analysis2.2structure solution
CcpNmr Analysis1structure solution
ARIA2.3structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: NOE ENERGY / Conformers calculated total number: 200 / Conformers submitted total number: 25

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