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- PDB-4ywc: Crystal structure of Myc3(5-242) fragment in complex with Jaz9(21... -

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Basic information

Entry
Database: PDB / ID: 4ywc
TitleCrystal structure of Myc3(5-242) fragment in complex with Jaz9(218-239) peptide
Components
  • Protein TIFY 7
  • Transcription factor MYC3
KeywordsTRANSCRIPTION REGULATOR / helix-sheet-helix sandwich fold / Jasmonate signaling / Myc transcription factor / Myc-Jaz complex
Function / homology
Function and homology information


extracellular ATP signaling / anthocyanin-containing compound biosynthetic process / stomatal complex development / bHLH transcription factor binding / response to jasmonic acid / defense response / protein dimerization activity / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription ...extracellular ATP signaling / anthocyanin-containing compound biosynthetic process / stomatal complex development / bHLH transcription factor binding / response to jasmonic acid / defense response / protein dimerization activity / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
Tify domain / CO/COL/TOC1, conserved site / TIFY/JAZ family / tify domain / Jas motif / Tify domain profile. / TIFY / Transcription factor AIB/MYC-like / : / Plant bHLH transcription factor, ACT-like domain ...Tify domain / CO/COL/TOC1, conserved site / TIFY/JAZ family / tify domain / Jas motif / Tify domain profile. / TIFY / Transcription factor AIB/MYC-like / : / Plant bHLH transcription factor, ACT-like domain / Transcription factor MYC/MYB N-terminal / bHLH-MYC and R2R3-MYB transcription factors N-terminal / 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
Protein TIFY 7 / Transcription factor MYC3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKe, J. / Zhang, F. / Brunzelle, J.S. / Xu, H.E. / Melcher, K. / He, S.Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM102545 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI060761 United States
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
DepositionMar 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Sep 23, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,1534
Polymers57,1534
Non-polymers00
Water1,802100
1
A: Transcription factor MYC3
C: Protein TIFY 7


Theoretical massNumber of molelcules
Total (without water)28,5762
Polymers28,5762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-8 kcal/mol
Surface area10630 Å2
MethodPISA
2
B: Transcription factor MYC3
D: Protein TIFY 7


Theoretical massNumber of molelcules
Total (without water)28,5762
Polymers28,5762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-8 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.105, 110.627, 161.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 25954.275 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 5-242)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MYC3, ATR2, BHLH5, EN36, At5g46760, 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.: 2 / Fragment: UNP residues 194-215 / 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.: 100 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.86 % / Description: plate shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: The purified proteins at a concentration of 15 mg/ml are mixed with 0.2 M magnesium nitrate, 20% (w/v) polyethylene glycol 3,350. Crystals of about 100 um in length appeared in 3 days

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 13, 2015
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 21208 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 10.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4RRU

4rru


Resolution: 2.4→49.621 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2951 1022 4.84 %Random selection
Rwork0.239 ---
obs0.2417 21103 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→49.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3086 0 0 100 3186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083132
X-RAY DIFFRACTIONf_angle_d1.2444219
X-RAY DIFFRACTIONf_dihedral_angle_d17.3631107
X-RAY DIFFRACTIONf_chiral_restr0.049466
X-RAY DIFFRACTIONf_plane_restr0.005547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.52660.42131470.35652825X-RAY DIFFRACTION100
2.5266-2.68490.42971350.33952822X-RAY DIFFRACTION99
2.6849-2.89220.3821430.30572827X-RAY DIFFRACTION99
2.8922-3.18320.3411660.28292825X-RAY DIFFRACTION100
3.1832-3.64370.2861280.222876X-RAY DIFFRACTION100
3.6437-4.59010.22851330.19852912X-RAY DIFFRACTION100
4.5901-49.63110.25541700.19872994X-RAY DIFFRACTION100

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