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- PDB-7z5i: Transcription factor MYF5 bound to symmetrical site -

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Basic information

Entry
Database: PDB / ID: 7z5i
TitleTranscription factor MYF5 bound to symmetrical site
Components
  • DNA (5'-D(P*AP*CP*GP*CP*GP*TP*CP*AP*GP*CP*TP*GP*AP*CP*GP*CP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*GP*CP*GP*TP*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 / Resolution: 3 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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*GP*TP*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*AP*CP*GP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)24,5864
Polymers24,5864
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-54 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.700, 33.923, 53.729
Angle α, β, γ (deg.)90.000, 91.040, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12E
22F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLUGLUAA81 - 1361 - 56
21SERSERGLUGLUBB81 - 1361 - 56
12DGDGDTDTEC1 - 181 - 18
22DADADCDCFD1 - 181 - 18

NCS ensembles :
ID
1
2

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Components

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


Mass: 6774.927 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 BL21(DE3) (bacteria) / References: UniProt: P13349
#2: DNA chain DNA (5'-D(P*GP*CP*GP*CP*GP*TP*CP*AP*GP*CP*TP*GP*AP*CP*GP*CP*GP*T)-3')


Mass: 5533.566 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*AP*CP*GP*CP*GP*C)-3')


Mass: 5502.556 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.: 3 / 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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: PME 3350, 2% MPD, 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: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.996→83.336 Å / Num. all: 5721 / Num. obs: 5721 / % possible obs: 91.3 % / Redundancy: 2.8 % / Rpim(I) all: 0.047 / Rrim(I) all: 0.083 / Rsym value: 0.067 / Net I/av σ(I): 1.8 / Net I/σ(I): 6.9 / Num. measured all: 15911
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3-3.162.70.9120.822538390.6381.1190.9121.292
3.16-3.352.80.3692.122207990.2530.450.3692.792.1
3.35-3.582.90.244320837210.1680.2980.2443.592.1
3.58-3.872.70.2163.419066970.1510.2650.2164.792.2
3.87-4.242.80.1036.617776440.0710.1260.1037.791.8
4.24-4.742.90.0867.316205590.0590.1050.086991.2
4.74-5.472.70.0659.613695030.0460.0810.06510.290.3
5.47-6.72.90.05810.112724400.040.0710.05812.490.3
6.7-9.482.80.04210.79003220.030.0510.04216.687.6
9.48-53.722.60.0365.15111970.0250.0440.0362287.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
PDB_EXTRACT3.27data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MDY

1mdy


Resolution: 3→53.34 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.934 / SU B: 27.99 / SU ML: 0.469 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.527 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2876 560 9.8 %RANDOM
Rwork0.2272 ---
obs0.2332 5157 90.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 235.81 Å2 / Biso mean: 99.019 Å2 / Biso min: 55.05 Å2
Baniso -1Baniso -2Baniso -3
1-10.36 Å20 Å2-8.35 Å2
2---3.56 Å20 Å2
3----6.5 Å2
Refinement stepCycle: final / Resolution: 3→53.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 738 0 3 1683
Biso mean---89.9 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0121774
X-RAY DIFFRACTIONr_bond_other_d0.0040.0181365
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.432532
X-RAY DIFFRACTIONr_angle_other_deg1.4712.0163169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0265110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.4021870
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.74115210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7621520
X-RAY DIFFRACTIONr_chiral_restr0.0930.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021468
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02420
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A17020.15
12B17020.15
21E15870.09
22F15870.09
LS refinement shellResolution: 3→3.074 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.553 35 -
Rwork0.466 390 -
obs--91.01 %

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