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- PDB-2ky8: Solution structure and dynamic analysis of chicken MBD2 methyl bi... -

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Basic information

Entry
Database: PDB / ID: 2ky8
TitleSolution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target methylated DNA sequence
Components
  • DNA (5'-D(*GP*AP*GP*CP*(5CM)P*GP*AP*TP*(TED)P*CP*C)-3')
  • DNA (5'-D(*GP*GP*AP*AP*TP*(5CM)P*GP*GP*CP*(TED)P*C)-3')
  • Methyl-CpG-binding domain protein 2
KeywordsTRANSCRIPTION/DNA / DNA Binding domain / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


NuRD complex / methyl-CpG binding / host cell nucleus
Similarity search - Function
Methyl-CpG-binding domain protein 3 / 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 / Methyl-cpg-binding Protein 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain ...Methyl-CpG-binding domain protein 3 / 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 / Methyl-cpg-binding Protein 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Methyl-CpG-binding domain protein 2
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsWilliams Jr., D.C. / Scarsdale Jr., J.N.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target-methylated DNA sequence.
Authors: Scarsdale, J.N. / Webb, H.D. / Ginder, G.D. / Williams, D.C.
History
DepositionMay 18, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 7, 2011Group: Database references
Revision 1.3Feb 5, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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: Methyl-CpG-binding domain protein 2
B: DNA (5'-D(*GP*GP*AP*AP*TP*(5CM)P*GP*GP*CP*(TED)P*C)-3')
C: DNA (5'-D(*GP*AP*GP*CP*(5CM)P*GP*AP*TP*(TED)P*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5965
Polymers15,4863
Non-polymers1102
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 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Methyl-CpG-binding domain protein 2 /


Mass: 8005.200 Da / Num. of mol.: 1 / Fragment: UNP Residues 2-71
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: MBD2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5EFL0
#2: DNA chain DNA (5'-D(*GP*GP*AP*AP*TP*(5CM)P*GP*GP*CP*(TED)P*C)-3')


Mass: 3760.568 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*GP*AP*GP*CP*(5CM)P*GP*AP*TP*(TED)P*CP*C)-3')


Mass: 3720.544 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CO)CA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D (H)CCH-TOCSY
1813D C(CO)NH
1913D C(CO)NH
11013D CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-15N NOESY
11313D 1H-13C NOESY
11412D 13C,15N filtered NOESY
11522D 1H-15N HSQC
11632D 1H-15N HSQC-T1
11742D 1H-15N HSQC-T1
11823D-HNCO-JNH
11913D-HNCO-JNH
12012D 1H-15N HSQC,JNCO
12122D 1H-15N HSQC.JNCO
12213D HNCO,JCOCA
12323D HNCO,JCOCA

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-13C; U-15N; U-2H] cMBD2, 0.8 mM DNA, 12 mg/mL of1 bacteriophage, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-13C; U-15N; U-2H] cMBD2, 0.5 mM DNA, 0.5 mM MANGANESE (II) ION, 90% H2O/10% D2O90% H2O/10% D2O
40.5 mM [U-13C; U-15N; U-2H] cMBD2, 0.5 mM DNA, 0.5 mM CA2+, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMcMBD2-1[U-99% 13C; U-99% 15N]1
1 mMDNA-21
0.8 mMcMBD2-3[U-13C; U-15N; U-2H]2
0.8 mMDNA-42
12 mg/mLpf1 bacteriophage-52
0.5 mMcMBD2-6[U-13C; U-15N; U-2H]3
0.5 mMDNA-73
0.5 mMMANGANESE (II) ION-83
0.5 mMcMBD2-9[U-13C; U-15N; U-2H]4
0.5 mMDNA-104
0.5 mMCA2+-114
Sample conditionsIonic strength: 20 / 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 Clorerefinement
PIPPGarrettchemical shift assignment
PIPPGarrettpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
VNMRVariancollection
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: experimental target function included NOE distances, backbone torsion angle restraints based on chemical shifts, residual dipolar couplings and paramagnetic relaxation enhancement data.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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