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- PDB-1n6j: Structural basis of sequence-specific recruitment of histone deac... -

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Basic information

Entry
Database: PDB / ID: 1n6j
TitleStructural basis of sequence-specific recruitment of histone deacetylases by Myocyte Enhancer Factor-2
Components
  • 5'-D(*AP*GP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*C)-3'
  • 5'-D(*GP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*CP*T)-3'
  • Calcineurin-binding protein Cabin 1
  • Myocyte-specific enhancer factor 2B
KeywordsTRANSCRIPTION/DNA / MADS-box / Protein-DNA complex / histone deacetylases / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


chromatin organization => GO:0006325 / aggresome / muscle organ development / protein phosphatase inhibitor activity / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Myogenesis / histone deacetylase binding / sequence-specific double-stranded DNA binding / cell junction / heart development ...chromatin organization => GO:0006325 / aggresome / muscle organ development / protein phosphatase inhibitor activity / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Myogenesis / histone deacetylase binding / sequence-specific double-stranded DNA binding / cell junction / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / cell differentiation / cell surface receptor signaling pathway / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
Calcineurin-binding protein cabin-1, MEF2-binding domain / Histone transcription regulator 3/CABIN1 / MEF2 binding / SRF-like / Transcription factor, MADS-box / MADS MEF2-like / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. ...Calcineurin-binding protein cabin-1, MEF2-binding domain / Histone transcription regulator 3/CABIN1 / MEF2 binding / SRF-like / Transcription factor, MADS-box / MADS MEF2-like / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. / MADS-box domain profile. / MADS / : / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Myocyte-specific enhancer factor 2B / Calcineurin-binding protein cabin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHan, A. / Pan, F. / Stroud, J.C. / Youn, H.D. / Liu, J.O. / Chen, L.
CitationJournal: Nature / Year: 2003
Title: Sequence-specific recruitment of transcriptional co-repressor Cabin1 by myocyte enhancer factor-2
Authors: Han, A. / Pan, F. / Stroud, J.C. / Youn, H.D. / Liu, J.O. / Chen, L.
History
DepositionNov 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 9, 2015Group: Version format compliance
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*AP*GP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*C)-3'
D: 5'-D(*GP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*CP*T)-3'
A: Myocyte-specific enhancer factor 2B
B: Myocyte-specific enhancer factor 2B
G: Calcineurin-binding protein Cabin 1


Theoretical massNumber of molelcules
Total (without water)34,2075
Polymers34,2075
Non-polymers00
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.140, 70.140, 151.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Number of models2

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Components

#1: DNA chain 5'-D(*AP*GP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*C)-3'


Mass: 4278.815 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*CP*T)-3'


Mass: 4278.815 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Myocyte-specific enhancer factor 2B / Serum response factor-like protein 2 / XMEF2 / RSRFR2


Mass: 10964.712 Da / Num. of mol.: 2 / Fragment: residues 2-91, MADS-box/MEF2S domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEF2B OR XMEF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02080
#4: Protein/peptide Calcineurin-binding protein Cabin 1 / Calcineurin inhibitor / CHAIN


Mass: 3720.275 Da / Num. of mol.: 1 / Fragment: residues 101-132, Cabin1, MEF2-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CABIN1 OR KIAA0330 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6J0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 3500, sodium cholride, BTP, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 350011
2sodium cholride11
3BTP11
4H2O11
5PEG 350012
6sodium cholride12
7H2O12
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6.68 / PH range high: 6.35
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMbis-Tris-propane1reservoirpH6.35-6.68
215 %PEG10001reservoir
350 mM1reservoirNaCl
410 mM1reservoirCaCl2
55 mM1reservoirMgCl2
610 %glycerol1reservoir
75 mMdithiothreitol1reservoir
82 mMspermine1reservoir

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Data collection

DiffractionMean temperature: 101 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 18733 / Num. obs: 18733 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.5 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 38
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.059 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1135 / Rsym value: 0.37 / % possible all: 54
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / % possible obs: 92.7 % / Num. measured all: 364592 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 77.7 % / Rmerge(I) obs: 0.319

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EGW

1egw


Resolution: 2.2→28.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 368477.9 / Data cutoff high rms absF: 368477.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: There are two models represented in this entry (MODEL 1 and MODEL 2) containing 5 chains (ABGCD) each. Molecules ABGCD in MODEL 1 is an alternative conformation to the molecules ABGCD in MODEL 2.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1752 9.7 %RANDOM
Rwork0.243 ---
obs0.243 17987 89.9 %-
all-17987 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.6301 Å2 / ksol: 0.267209 e/Å3
Displacement parametersBiso mean: 53.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.32 Å20 Å20 Å2
2--5.32 Å20 Å2
3----10.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.2→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1705 568 0 228 2501
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it1.691.5
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it2.462
X-RAY DIFFRACTIONc_scangle_it3.22.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 209 9.2 %
Rwork0.301 2069 -
obs--70.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / Num. reflection obs: 18733 / % reflection Rfree: 10 % / Rfactor Rwork: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0066
X-RAY DIFFRACTIONc_angle_deg1.09
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor Rfree: 0.341 / Rfactor Rwork: 0.313 / Num. reflection Rwork: 1613

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