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- PDB-4rs9: Structure of Myc3 N-terminal JAZ-binding domain [44-238] in compl... -

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Basic information

Entry
Database: PDB / ID: 4rs9
TitleStructure of Myc3 N-terminal JAZ-binding domain [44-238] in complex with Jas motif of JAZ9
Components
  • Protein TIFY 7
  • Transcription factor MYC3
KeywordsTRANSCRIPTION REGULATOR / Helix-Sheet-Helix / alpha+beta structural fold / Transcription factor / bind JAZ corepressors or mediator subunit MED25 / Nuclear
Function / homology
Function and homology information


extracellular ATP signaling / stomatal complex development / anthocyanin-containing compound biosynthetic process / response to jasmonic acid / bHLH transcription factor binding / defense response / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription ...extracellular ATP signaling / stomatal complex development / anthocyanin-containing compound biosynthetic process / response to jasmonic acid / bHLH transcription factor binding / defense response / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / nucleus
Similarity search - Function
Tify domain / CO/COL/TOC1, conserved site / TIFY/JAZ family / Transcription factor AIB/MYC-like / tify domain / Jas motif / Tify domain profile. / TIFY / Transcription factor MYC/MYB N-terminal / bHLH-MYC and R2R3-MYB transcription factors N-terminal ...Tify domain / CO/COL/TOC1, conserved site / TIFY/JAZ family / Transcription factor AIB/MYC-like / tify domain / Jas motif / Tify domain profile. / TIFY / Transcription factor MYC/MYB N-terminal / bHLH-MYC and R2R3-MYB transcription factors N-terminal / 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
Protein TIFY 7 / Transcription factor MYC3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKe, J. / Zhang, F. / Zhou, X.E. / Brunzelle, J.S. / Zhou, M. / Xu, H.E. / Melcher, K. / He, S.Y.
CitationJournal: Nature / Year: 2015
Title: Structural basis of JAZ repression of MYC transcription factors in jasmonate signalling.
Authors: Zhang, F. / Yao, J. / Ke, J. / Zhang, L. / Lam, V.Q. / Xin, X.F. / Zhou, X.E. / Chen, J. / Brunzelle, J. / Griffin, P.R. / Zhou, M. / Xu, H.E. / Melcher, K. / He, S.Y.
History
DepositionNov 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor MYC3
B: Protein TIFY 7


Theoretical massNumber of molelcules
Total (without water)24,2102
Polymers24,2102
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-6 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.745, 85.745, 59.983
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Transcription factor MYC3 / Basic helix-loop-helix protein 5 / AtbHLH5 / bHLH 5 / Protein ALTERED TRYPTOPHAN REGULATION 2 / ...Basic helix-loop-helix protein 5 / AtbHLH5 / bHLH 5 / Protein ALTERED TRYPTOPHAN REGULATION 2 / Transcription factor ATR2 / Transcription factor EN 36 / bHLH transcription factor bHLH005


Mass: 21587.623 Da / Num. of mol.: 1
Fragment: N-terminal JAZ-binding domain (UNP residues 44-238)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g46760, ATR2, BHLH5, EN36, MYC3, MZA15.18 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9FIP9
#2: Protein/peptide Protein TIFY 7 / Jasmonate ZIM domain-containing protein 9


Mass: 2622.164 Da / Num. of mol.: 1 / Fragment: Jas motif (UNP residues 218-239) / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q8W4J8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 M Tris, pH 8.5, and 30% (w/v) polyethylene glycol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2013
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 18916 / Num. obs: 18916 / % possible obs: 100 % / Redundancy: 12 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 23.7
Reflection shellResolution: 1.95→2.06 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MD2programdata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Myc3[44-238]

Resolution: 1.95→42.91 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.519 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 971 5.1 %RANDOM
Rwork0.19987 ---
obs0.20149 17922 99.92 %-
all-17936 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å2-0.57 Å2-0 Å2
2---0.57 Å2-0 Å2
3---1.86 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 0 137 1630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191519
X-RAY DIFFRACTIONr_angle_refined_deg1.0081.9242047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9935186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53324.87278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27915258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.392159
X-RAY DIFFRACTIONr_chiral_restr0.0730.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021155
X-RAY DIFFRACTIONr_mcbond_it1.9654.71756
X-RAY DIFFRACTIONr_mcangle_it3.1367.02938
X-RAY DIFFRACTIONr_scbond_it2.3875.064761
X-RAY DIFFRACTIONr_long_range_B_refined6.94544.5826519
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 74 -
Rwork0.291 1317 -
obs--100 %

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