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- PDB-2l2l: Solution structure of the coiled-coil complex between MBD2 and p6... -

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Basic information

Entry
Database: PDB / ID: 2l2l
TitleSolution structure of the coiled-coil complex between MBD2 and p66alpha
Components
  • Methyl-CpG-binding domain protein 2
  • Transcriptional repressor p66-alpha
KeywordsTRANSFERASE / DNA methylation / coiled-coil / NuRD / MBD2 / p66alpha
Function / homology
Function and homology information


satellite DNA binding / NuRD complex / DNA methylation-dependent heterochromatin formation / methyl-CpG binding / C2H2 zinc finger domain binding / : / RNA Polymerase I Transcription Initiation / Regulation of TP53 Activity through Acetylation / RNA Polymerase I Promoter Opening / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression ...satellite DNA binding / NuRD complex / DNA methylation-dependent heterochromatin formation / methyl-CpG binding / C2H2 zinc finger domain binding / : / RNA Polymerase I Transcription Initiation / Regulation of TP53 Activity through Acetylation / RNA Polymerase I Promoter Opening / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / HDACs deacetylate histones / NoRC negatively regulates rRNA expression / protein-macromolecule adaptor activity / sequence-specific DNA binding / molecular adaptor activity / nuclear speck / chromatin remodeling / protein domain specific binding / negative regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1650 / Transcriptional repressor p66, coiled-coil MBD2-interaction domain / Transcriptional repressor p66 / Coiled-coil and interaction region of P66A and P66B with MBD2 / Methyl-CpG binding protein 2/3, C-terminal domain / Methyl-CpG-binding domain protein 2/3, p55-binding region / C-terminal domain of methyl-CpG binding protein 2 and 3 / p55-binding region of Methyl-CpG-binding domain proteins MBD / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1650 / Transcriptional repressor p66, coiled-coil MBD2-interaction domain / Transcriptional repressor p66 / Coiled-coil and interaction region of P66A and P66B with MBD2 / Methyl-CpG binding protein 2/3, C-terminal domain / Methyl-CpG-binding domain protein 2/3, p55-binding region / C-terminal domain of methyl-CpG binding protein 2 and 3 / p55-binding region of Methyl-CpG-binding domain proteins MBD / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / GATA zinc finger / Zinc finger, GATA-type / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Transcriptional repressor p66-alpha / Methyl-CpG-binding domain protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWilliams Jr., D.C. / Scarsdale Jr., N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: p66Alpha-MBD2 coiled-coil interaction and recruitment of Mi-2 are critical for globin gene silencing by the MBD2-NuRD complex.
Authors: Gnanapragasam, M.N. / Scarsdale, J.N. / Amaya, M.L. / Webb, H.D. / Desai, M.A. / Walavalkar, N.M. / Wang, S.Z. / Zu Zhu, S. / Ginder, G.D. / Williams, D.C.
History
DepositionAug 20, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Feb 5, 2020Group: 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: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional repressor p66-alpha
B: Methyl-CpG-binding domain protein 2


Theoretical massNumber of molelcules
Total (without water)9,2982
Polymers9,2982
Non-polymers00
Water0
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/peptide Transcriptional repressor p66-alpha / Hp66alpha / GATA zinc finger domain-containing protein 2A


Mass: 5116.009 Da / Num. of mol.: 1
Fragment: P66-ALPHA coiled-coil domain (unp residues 137-178)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GATAD2A / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q86YP4
#2: Protein/peptide Methyl-CpG-binding domain protein 2 / / Methyl-CpG-binding protein MBD2 / Demethylase / DMTase


Mass: 4181.787 Da / Num. of mol.: 1 / Fragment: MBD2 coiled-coil domain (unp residues 360-393)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD2 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UBB5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D HN(CA)CB
1413D HBHA(CO)NH
1513D CBCA(CO)NH
1613D HN(CO)CA
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D C(CO)NH
11012D 1H-15N HSQC
11123D HNCO
11223D HNCA
11323D HN(CA)CB
11423D HBHA(CO)NH
11523D HN(CO)CA
11623D (H)CCH-TOCSY
11723D 1H-15N NOESY
11823D 1H-13C NOESY
11923D CBCA(CO)NH
12023D C(CO)NH
12122D 1H-15N HSQC
12233D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-99% 13C; U-99% 15N] p66-alpha, 1.0 mM MBD2, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-100% 13C; U-100% 15N] MBD2, 1.0 mM p66-alpha, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-100% 13C; U-100% 15N; U-80% 2H] p66-alpha, 1.0 mM [U-100% 13C; U-100% 15N; U-80% 2H] MBD2, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMp66-alpha-1[U-99% 13C; U-99% 15N]1
1.0 mMMBD2-21
1.0 mMMBD2-3[U-100% 13C; U-100% 15N]2
1.0 mMp66-alpha-42
1.0 mMp66-alpha-5[U-100% 13C; U-100% 15N; U-80% 2H]3
1.0 mMMBD2-6[U-100% 13C; U-100% 15N; U-80% 2H]3
Sample conditionsIonic strength: 0.02 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityPlusVarianUNITYPLUS5001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
PIPPGarrettdata analysis
PIPPGarrettchemical shift assignment
PIPPGarrettpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 677 / NOE intraresidue total count: 223 / NOE long range total count: 0 / NOE medium range total count: 145 / NOE sequential total count: 203 / Protein chi angle constraints total count: 10 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 58 / Protein psi angle constraints total count: 58
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 3.6 ° / Maximum upper distance constraint violation: 0.39 Å
NMR ensemble rmsDistance rms dev: 0.017 Å / Distance rms dev error: 0.004 Å

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