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- PDB-7wz6: Crystal structure of MyoD-E47 -

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Basic information

Entry
Database: PDB / ID: 7wz6
TitleCrystal structure of MyoD-E47
Components
  • Isoform E47 of Transcription factor E2-alpha
  • Myoblast determination protein 1
KeywordsTRANSCRIPTION / E-box / bHLH domain
Function / homology
Function and homology information


myoblast fate determination / negative regulation of myoblast proliferation / myotube differentiation involved in skeletal muscle regeneration / positive regulation of snRNA transcription by RNA polymerase II / skeletal muscle fiber adaptation / myotube differentiation / positive regulation of skeletal muscle fiber development / positive regulation of skeletal muscle tissue regeneration / cell development / bHLH transcription factor binding ...myoblast fate determination / negative regulation of myoblast proliferation / myotube differentiation involved in skeletal muscle regeneration / positive regulation of snRNA transcription by RNA polymerase II / skeletal muscle fiber adaptation / myotube differentiation / positive regulation of skeletal muscle fiber development / positive regulation of skeletal muscle tissue regeneration / cell development / bHLH transcription factor binding / lymphocyte differentiation / natural killer cell differentiation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / skeletal muscle tissue regeneration / immunoglobulin V(D)J recombination / muscle cell differentiation / cellular response to oxygen levels / Peyer's patch development / vitamin D response element binding / cardiac muscle cell differentiation / Myogenesis / myoblast fusion / mitogen-activated protein kinase kinase kinase binding / cellular response to glucocorticoid stimulus / myoblast differentiation / muscle organ development / DNA-binding transcription activator activity / myofibril / positive regulation of myoblast fusion / positive regulation of muscle cell differentiation / B cell lineage commitment / regulation of alternative mRNA splicing, via spliceosome / E-box binding / skeletal muscle cell differentiation / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / cis-regulatory region sequence-specific DNA binding / positive regulation of cell cycle / skeletal muscle fiber development / gastrulation / positive regulation of B cell proliferation / skeletal muscle tissue development / striated muscle cell differentiation / cellular response to starvation / positive regulation of neuron differentiation / erythrocyte differentiation / cellular response to estradiol stimulus / PDZ domain binding / promoter-specific chromatin binding / nuclear receptor binding / euchromatin / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of DNA-binding transcription factor activity / RNA polymerase II transcription regulator complex / nucleosome / cellular response to tumor necrosis factor / nervous system development / T cell differentiation in thymus / gene expression / regulation of gene expression / 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 / response to lipopolysaccharide / transcription by RNA polymerase II / protein stabilization / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / ubiquitin protein ligase binding / chromatin binding / chromatin / regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Myogenic muscle-specific protein, N-terminal / Myogenic determination factor 5 / Myogenic factor / Myogenic Basic domain / Myogenic determination factor 5 / Basic domain in HLH proteins of MYOD family / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile.
Similarity search - Domain/homology
Myoblast determination protein 1 / Transcription factor E2-alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsZhong, J. / Huang, Y. / Ma, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171186 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structural basis of the bHLH domains of MyoD-E47 heterodimer.
Authors: Zhong, J. / Jin, Z. / Jiang, L. / Zhang, L. / Hu, Z. / Zhang, Y. / Liu, Y. / Ma, J. / Huang, Y.
History
DepositionFeb 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform E47 of Transcription factor E2-alpha
B: Myoblast determination protein 1


Theoretical massNumber of molelcules
Total (without water)15,7482
Polymers15,7482
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-25 kcal/mol
Surface area8580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.898, 66.858, 68.185
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Isoform E47 of Transcription factor E2-alpha / Immunoglobulin enhancer-binding factor E12/E47 / Transcription factor 3 / TCF-3 / Transcription factor A1


Mass: 7903.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tcf3, Alf2, Me2, Tcfe2a / Production host: Escherichia coli (E. coli) / References: UniProt: P15806
#2: Protein Myoblast determination protein 1


Mass: 7845.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myod1, Myod / Production host: Escherichia coli (E. coli) / References: UniProt: P10085
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate (pH 5.5), 0.2 M sodium acetate, 10% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 11081 / % possible obs: 99.3 % / Redundancy: 9.1 % / Biso Wilson estimate: 24.67 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 29.5
Reflection shellResolution: 2.05→2.09 Å / Rmerge(I) obs: 0.448 / Num. unique obs: 531

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1mdy

1mdy


Resolution: 2.05→21.18 Å / SU ML: 0.2295 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.8309
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2486 1061 9.93 %
Rwork0.2179 9629 -
obs0.221 10690 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.5 Å2
Refinement stepCycle: LAST / Resolution: 2.05→21.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms940 0 0 83 1023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022945
X-RAY DIFFRACTIONf_angle_d0.48651258
X-RAY DIFFRACTIONf_chiral_restr0.0318141
X-RAY DIFFRACTIONf_plane_restr0.0017166
X-RAY DIFFRACTIONf_dihedral_angle_d4.1124131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.140.30281050.243967X-RAY DIFFRACTION79
2.14-2.260.25751200.22771126X-RAY DIFFRACTION93.54
2.26-2.40.24851400.22861218X-RAY DIFFRACTION99.41
2.4-2.580.2651350.21781231X-RAY DIFFRACTION99.93
2.58-2.840.29021410.2311244X-RAY DIFFRACTION100
2.84-3.250.25451360.22811237X-RAY DIFFRACTION100
3.25-4.090.21311360.20191270X-RAY DIFFRACTION100
4.09-21.180.24371480.21131336X-RAY DIFFRACTION100

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