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- PDB-3mu6: Inhibiting the Binding of Class IIa Histone Deacetylases to Myocy... -

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Basic information

Entry
Database: PDB / ID: 3mu6
TitleInhibiting the Binding of Class IIa Histone Deacetylases to Myocyte Enhancer Factor-2 by Small Molecules
Components
  • DNA (5'-D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP*CP*TP*T)-3')
  • DNA (5'-D(*TP*AP*AP*GP*CP*TP*AP*AP*TP*AP*AP*TP*AP*GP*CP*TP*T)-3')
  • Myocyte-specific enhancer factor 2A
KeywordsDNA BINDING PROTEIN/DNA / MADS-box/MEF2 domain / transcription co-factors / protein-DNA complex / protein-protein docking / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


ERK5 cascade / ventricular cardiac myofibril assembly / mitochondrion distribution / cardiac conduction / mitochondrial genome maintenance / dendrite morphogenesis / muscle organ development / histone acetyltransferase binding / Myogenesis / positive regulation of cardiac muscle hypertrophy ...ERK5 cascade / ventricular cardiac myofibril assembly / mitochondrion distribution / cardiac conduction / mitochondrial genome maintenance / dendrite morphogenesis / muscle organ development / histone acetyltransferase binding / Myogenesis / positive regulation of cardiac muscle hypertrophy / SMAD binding / ERK/MAPK targets / cellular response to calcium ion / positive regulation of glucose import / RNA polymerase II transcription regulatory region sequence-specific DNA binding / histone deacetylase binding / MAPK cascade / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / DNA-templated transcription / apoptotic process / chromatin binding / chromatin / positive regulation of gene expression / protein kinase binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
Holliday junction regulator protein family C-terminal / Holliday junction regulator protein family C-terminal repeat / 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. ...Holliday junction regulator protein family C-terminal / Holliday junction regulator protein family C-terminal repeat / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BXL / DNA / DNA (> 10) / Myocyte-specific enhancer factor 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.434 Å
AuthorsJayathilaka, N. / Han, A. / Gaffney, K. / Dey, R. / He, J. / Ye, J. / Gao, T. / Petasis, N.A. / Chen, L.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Inhibition of the function of class IIa HDACs by blocking their interaction with MEF2.
Authors: Jayathilaka, N. / Han, A. / Gaffney, K.J. / Dey, R. / Jarusiewicz, J.A. / Noridomi, K. / Philips, M.A. / Lei, X. / He, J. / Ye, J. / Gao, T. / Petasis, N.A. / Chen, L.
History
DepositionMay 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Jul 25, 2012Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myocyte-specific enhancer factor 2A
B: Myocyte-specific enhancer factor 2A
E: DNA (5'-D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP*CP*TP*T)-3')
F: DNA (5'-D(*TP*AP*AP*GP*CP*TP*AP*AP*TP*AP*AP*TP*AP*GP*CP*TP*T)-3')
C: Myocyte-specific enhancer factor 2A
D: Myocyte-specific enhancer factor 2A
G: DNA (5'-D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP*CP*TP*T)-3')
H: DNA (5'-D(*TP*AP*AP*GP*CP*TP*AP*AP*TP*AP*AP*TP*AP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7699
Polymers54,4318
Non-polymers3371
Water0
1
A: Myocyte-specific enhancer factor 2A
B: Myocyte-specific enhancer factor 2A
E: DNA (5'-D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP*CP*TP*T)-3')
F: DNA (5'-D(*TP*AP*AP*GP*CP*TP*AP*AP*TP*AP*AP*TP*AP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5535
Polymers27,2164
Non-polymers3371
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-57 kcal/mol
Surface area12140 Å2
MethodPISA
2
C: Myocyte-specific enhancer factor 2A
D: Myocyte-specific enhancer factor 2A
G: DNA (5'-D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP*CP*TP*T)-3')
H: DNA (5'-D(*TP*AP*AP*GP*CP*TP*AP*AP*TP*AP*AP*TP*AP*GP*CP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)27,2164
Polymers27,2164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-56 kcal/mol
Surface area12160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.567, 61.622, 61.478
Angle α, β, γ (deg.)114.120, 89.990, 89.950
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13C
23B
33D
14A
24B
15C
25D
16C
26B
36D
17E
27G
18F
28H

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN A RESID 2:60A0
211CHAIN B RESID 2:60B0
112CHAIN C RESID 2:60C0
212CHAIN D RESID 2:60D0
113CHAIN C RESID 2:60C0
213CHAIN B RESID 2:60B0
313CHAIN D RESID 2:60D0
114CHAIN A RESID 68:72A0
214CHAIN B RESID 68:72B0
115CHAIN C RESID 68:72C0
215CHAIN D RESID 68:72D0
116CHAIN C RESID 68:72C0
216CHAIN B RESID 68:72B0
316CHAIN D RESID 68:72D0
117CHAIN EE1 - 17
217CHAIN GG1 - 17
118CHAIN FF1 - 17
218CHAIN HH1 - 17

NCS ensembles :
ID
1
2
3
4
5
6
7
8

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Components

#1: Protein
Myocyte-specific enhancer factor 2A / Serum response factor-like protein 1


Mass: 8402.940 Da / Num. of mol.: 4 / Mutation: E71A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEF2A, MEF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02078
#2: DNA chain DNA (5'-D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP*CP*TP*T)-3')


Mass: 5200.408 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*AP*AP*GP*CP*TP*AP*AP*TP*AP*AP*TP*AP*GP*CP*TP*T)-3')


Mass: 5209.422 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-BXL / (3E)-N~8~-(2-aminophenyl)-N~1~-phenyloct-3-enediamide


Mass: 337.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N3O2

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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: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 291 K / Method: hanging drop / pH: 4.7
Details: 50 mM acetic acid, 142mM NaCl, 5mM MgCl2, 10mM CaCl2, 3.3% Glycerol, 22.5% 3K PEG, pH 4.7, hanging drop, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1acetic acid11
2NaClSodium chloride11
3MgCl211
4CaCl211
5Glycerol11
63K PEG11
7acetic acid12
8NaClSodium chloride12
9MgCl212
10CaCl212
11Glycerol12
123K PEG12

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. obs: 19854 / % possible obs: 95.6 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.067 / Χ2: 2.751 / Net I/σ(I): 18.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.43-2.522.30.25519541.8493.9
2.52-2.622.40.20719591.99193.7
2.62-2.742.40.17119692.0695.6
2.74-2.882.40.15219702.14595.5
2.88-3.062.40.11819882.35695
3.06-3.32.40.06319802.82795.8
3.3-3.632.40.06119853.35395.8
3.63-4.152.30.05620223.77895.5
4.15-5.232.40.04920063.75297.1
5.23-502.40.04320213.32198

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EGW
Resolution: 2.434→33.444 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.801 / SU ML: 0.37 / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 1026 5.18 %
Rwork0.23 --
obs0.231 19819 94.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.402 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso max: 94.66 Å2 / Biso mean: 32.949 Å2 / Biso min: 8.75 Å2
Baniso -1Baniso -2Baniso -3
1--5.58 Å2-0.459 Å20.837 Å2
2--7.447 Å2-11.446 Å2
3----1.867 Å2
Refinement stepCycle: LAST / Resolution: 2.434→33.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 1382 25 0 3751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083946
X-RAY DIFFRACTIONf_angle_d1.335574
X-RAY DIFFRACTIONf_chiral_restr0.068628
X-RAY DIFFRACTIONf_plane_restr0.004456
X-RAY DIFFRACTIONf_dihedral_angle_d23.8411605
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A485X-RAY DIFFRACTIONPOSITIONAL0.019
12B485X-RAY DIFFRACTIONPOSITIONAL0.019
21C485X-RAY DIFFRACTIONPOSITIONAL0.012
22D485X-RAY DIFFRACTIONPOSITIONAL0.012
31C485X-RAY DIFFRACTIONPOSITIONAL0.016
32B485X-RAY DIFFRACTIONPOSITIONAL0.016
33D485X-RAY DIFFRACTIONPOSITIONAL0.012
41A45X-RAY DIFFRACTIONPOSITIONAL0.015
42B45X-RAY DIFFRACTIONPOSITIONAL0.015
51C45X-RAY DIFFRACTIONPOSITIONAL0.008
52D45X-RAY DIFFRACTIONPOSITIONAL0.008
61C45X-RAY DIFFRACTIONPOSITIONAL0.012
62B45X-RAY DIFFRACTIONPOSITIONAL0.012
63D45X-RAY DIFFRACTIONPOSITIONAL0.008
71E345X-RAY DIFFRACTIONPOSITIONAL0.013
72G345X-RAY DIFFRACTIONPOSITIONAL0.013
81F346X-RAY DIFFRACTIONPOSITIONAL0.013
82H346X-RAY DIFFRACTIONPOSITIONAL0.013
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.434-2.5620.3211400.2822584272489
2.562-2.7230.2921420.2592664280695
2.723-2.9330.3181420.2692703284595
2.933-3.2280.2661410.2422707284895
3.228-3.6950.2341270.1962707283496
3.695-4.6530.21760.1852695287196
4.653-33.4470.2021580.1852733289198

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