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- PDB-7z5k: Transcription factor MYF5 bound to non-symmetrical site -

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Basic information

Entry
Database: PDB / ID: 7z5k
TitleTranscription factor MYF5 bound to non-symmetrical site
Components
  • DNA (5'-D(P*AP*CP*GP*CP*GP*TP*CP*AP*GP*CP*TP*GP*TP*TP*GP*CP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*GP*CP*AP*AP*CP*AP*GP*CP*TP*GP*AP*CP*GP*CP*GP*T)-3')
  • Myogenic factor 5
KeywordsTRANSCRIPTION / DNA-binding domain / transcription factor / complex with DNA
Function / homology
Function and homology information


muscle cell fate commitment / muscle tissue morphogenesis / positive regulation of skeletal muscle fiber development / embryonic skeletal system morphogenesis / regulation of cell-matrix adhesion / camera-type eye development / TGFBR3 expression / cartilage condensation / muscle organ development / Myogenesis ...muscle cell fate commitment / muscle tissue morphogenesis / positive regulation of skeletal muscle fiber development / embryonic skeletal system morphogenesis / regulation of cell-matrix adhesion / camera-type eye development / TGFBR3 expression / cartilage condensation / muscle organ development / Myogenesis / skeletal muscle cell differentiation / positive regulation of myoblast differentiation / somitogenesis / skeletal muscle tissue development / extracellular matrix organization / ossification / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm
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 domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Myogenic factor 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 Å
AuthorsMorgunova, E. / Popov, A. / Yin, Y. / Taipale, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2025
Title: Interfacial water confers transcription factors with dinucleotide specificity.
Authors: Morgunova, E. / Nagy, G. / Yin, Y. / Zhu, F. / Nayak, S.P. / Xiao, T. / Sokolov, I. / Popov, A. / Laughton, C. / Grubmuller, H. / Taipale, J.
History
DepositionMar 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 15, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _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: Myogenic factor 5
B: Myogenic factor 5
E: DNA (5'-D(P*GP*CP*GP*CP*AP*AP*CP*AP*GP*CP*TP*GP*AP*CP*GP*CP*GP*T)-3')
F: DNA (5'-D(P*AP*CP*GP*CP*GP*TP*CP*AP*GP*CP*TP*GP*TP*TP*GP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)24,8114
Polymers24,8114
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-54 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.443, 33.839, 53.541
Angle α, β, γ (deg.)90.000, 91.880, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Myogenic factor 5 / Myf-5 / Class C basic helix-loop-helix protein 2 / bHLHc2


Mass: 6888.085 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYF5, BHLHC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P13349
#2: DNA chain DNA (5'-D(P*GP*CP*GP*CP*AP*AP*CP*AP*GP*CP*TP*GP*AP*CP*GP*CP*GP*T)-3')


Mass: 5526.581 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*AP*CP*GP*CP*GP*TP*CP*AP*GP*CP*TP*GP*TP*TP*GP*CP*GP*C)-3')


Mass: 5508.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.13 Å3/Da / Density % sol: 60.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 13% PEG 1000, 2.5% MPD, 6,25% PEG 400, 0.05M Sodium Acetate, pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.99→46 Å / Num. obs: 26259 / % possible obs: 93.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 57.98 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.069 / Rrim(I) all: 0.154 / Net I/σ(I): 3.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allNum. unique obsCC1/2% possible allRmerge(I) obsRpim(I) allRrim(I) allNet I/σ(I) obs
1.99-2.042.116698010.0155
9.1-464.912442540.99699.10.0960.0520.1113.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.7.2data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MDY

1mdy


Resolution: 2.28→45.998 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 35.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2664 1231 4.69 %
Rwork0.2288 25028 -
obs0.2309 26259 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.93 Å2 / Biso mean: 84.145 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.28→45.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 738 0 76 1758
Biso mean---78.04 -
Num. residues----148
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2801-2.37140.40171420.3639262193
2.3714-2.47940.33781390.3339282297
2.4794-2.61010.39661450.3259285698
2.6101-2.77360.35511250.3286274296
2.7736-2.98770.35521200.2992287798
2.9877-3.28830.35331600.2667280298
3.2883-3.76390.30711100.2399266291
3.7639-4.74140.23641490.193276597
4.7414-45.90.19231410.1715288199

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