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- PDB-1tqe: Mechanism of recruitment of class II histone deacetylases by myoc... -

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Basic information

Entry
Database: PDB / ID: 1tqe
TitleMechanism of recruitment of class II histone deacetylases by myocyte enhancer factor-2
Components
  • (MEF2 binding site of nur77 promoter) x 2
  • Histone deacetylase 9
  • Myocyte-specific enhancer factor 2B
KeywordsTRANSCRIPTION/PROTEIN BINDING/DNA / MEF2 / HDAC / co-repressor / transcription / TRANSCRIPTION-PROTEIN BINDING-DNA COMPLEX
Function / homology
Function and homology information


regulation of striated muscle cell differentiation / : / negative regulation of cytokine production => GO:0001818 / : / histone H4K16 deacetylase activity / : / regulation of skeletal muscle fiber development / DNA-binding transcription factor binding => GO:0140297 / negative regulation of lipoprotein lipase activity / negative regulation of striated muscle tissue development ...regulation of striated muscle cell differentiation / : / negative regulation of cytokine production => GO:0001818 / : / histone H4K16 deacetylase activity / : / regulation of skeletal muscle fiber development / DNA-binding transcription factor binding => GO:0140297 / negative regulation of lipoprotein lipase activity / negative regulation of striated muscle tissue development / : / peptidyl-lysine deacetylation / histone deacetylase / protein lysine deacetylase activity / muscle organ development / histone deacetylase activity / histone methyltransferase complex / positive regulation of cell migration involved in sprouting angiogenesis / B cell activation / Myogenesis / histone deacetylase complex / transcription factor binding / B cell differentiation / protein kinase C binding / cholesterol homeostasis / determination of adult lifespan / cellular response to insulin stimulus / histone deacetylase binding / transcription corepressor activity / sequence-specific double-stranded DNA binding / cell junction / nervous system development / chromatin organization / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / cell differentiation / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA repair / negative regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Histone deacetylase class II, eukaryotic / SRF-like / Transcription factor, MADS-box / Histone deacetylase, glutamine rich N-terminal domain / Glutamine rich N terminal domain of histone deacetylase 4 / 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. ...Histone deacetylase class II, eukaryotic / SRF-like / Transcription factor, MADS-box / Histone deacetylase, glutamine rich N-terminal domain / Glutamine rich N terminal domain of histone deacetylase 4 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Myocyte-specific enhancer factor 2B / Histone deacetylase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChen, L. / Han, A. / He, J. / Wu, Y. / Liu, J.O.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Mechanism of Recruitment of Class II Histone Deacetylases by Myocyte Enhancer Factor-2.
Authors: Han, A. / He, J. / Wu, Y. / Liu, J.O. / Chen, L.
History
DepositionJun 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 23, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: MEF2 binding site of nur77 promoter
D: MEF2 binding site of nur77 promoter
E: MEF2 binding site of nur77 promoter
F: MEF2 binding site of nur77 promoter
P: Myocyte-specific enhancer factor 2B
Q: Myocyte-specific enhancer factor 2B
X: Histone deacetylase 9
R: Myocyte-specific enhancer factor 2B
S: Myocyte-specific enhancer factor 2B
Y: Histone deacetylase 9


Theoretical massNumber of molelcules
Total (without water)70,51310
Polymers70,51310
Non-polymers00
Water0
1
C: MEF2 binding site of nur77 promoter
D: MEF2 binding site of nur77 promoter
P: Myocyte-specific enhancer factor 2B
Q: Myocyte-specific enhancer factor 2B
X: Histone deacetylase 9


Theoretical massNumber of molelcules
Total (without water)35,2575
Polymers35,2575
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: MEF2 binding site of nur77 promoter
F: MEF2 binding site of nur77 promoter
R: Myocyte-specific enhancer factor 2B
S: Myocyte-specific enhancer factor 2B
Y: Histone deacetylase 9


Theoretical massNumber of molelcules
Total (without water)35,2575
Polymers35,2575
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.797, 66.930, 66.967
Angle α, β, γ (deg.)76.67, 71.83, 71.81
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain MEF2 binding site of nur77 promoter


Mass: 5218.437 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain MEF2 binding site of nur77 promoter


Mass: 5191.394 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein
Myocyte-specific enhancer factor 2B / Serum response factor-like protein 2 / XMEF2 / RSRFR2


Mass: 11038.855 Da / Num. of mol.: 4 / Fragment: residues 1-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): pLysS / References: UniProt: Q02080
#4: Protein/peptide Histone deacetylase 9 / / HD9 / HD7B / Histone deacetylase-related protein / MEF2-interacting transcription repressor MITR


Mass: 2769.174 Da / Num. of mol.: 2 / Fragment: residues 138-158
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): pLysS / References: UniProt: Q99N13

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 315 K / Method: vapor diffusion, hanging drop / pH: 6.35
Details: BTP, PEG, NaCl, glycerol, MgCl2, CaCl2, pH 6.35, VAPOR DIFFUSION, HANGING DROP, temperature 315K
Components of the solutions
IDNameCrystal-IDSol-ID
1BTP11
2PEG11
3H2O11
4NaClSodium chloride12
5glycerol12
6MgCl212
7CaCl212
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 18, 2003 / Details: mirrors
RadiationMonochromator: Ni Mirror and Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 19058 / Num. obs: 17405 / % possible obs: 91.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.04 / Rsym value: 0.034 / Net I/σ(I): 63
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1823 / Rsym value: 0.124 / % possible all: 95

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SCALEPACKdata scaling
CNSrefinement
CrystalClear(MSC/RIGAKU)data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Structure of MEF2A and DNA complex, pdb entry 1egw

1egw


Resolution: 2.7→30 Å / Isotropic thermal model: anisotropic / Cross valid method: throughtout / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1512 -random
Rwork0.263 ---
all-19058 --
obs-17405 91.3 %-
Displacement parametersBiso mean: 88.2 Å2
Baniso -1Baniso -2Baniso -3
1-37.368 Å214.727 Å212.962 Å2
2---18.424 Å2-11.474 Å2
3----18.944 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.69 Å0.501 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 1382 0 0 4730
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcbond_it3.417
X-RAY DIFFRACTIONc_mcangle_it5.656
X-RAY DIFFRACTIONc_scbond_it3.487
X-RAY DIFFRACTIONc_scangle_it5.974
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree: 0.452 / Rfactor Rwork: 0.445 / Total num. of bins used: 6

Resolution (Å)Num. reflection RfreeRfactor Rfree error% reflection obs (%)
2.7-2.91840.796.1
2.9-3.22633.596
3.2-44930.597.6
4-4.61823.998.5
4.6-5.81745.498.7
5.8-302161.797
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param

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