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- PDB-5t0f: Crystal structure of the Myc3 N-terminal domain [44-242] in compl... -

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Basic information

Entry
Database: PDB / ID: 5t0f
TitleCrystal structure of the Myc3 N-terminal domain [44-242] in complex with JAZ10 CMID domain [16-58] from arabidopsis
Components
  • Protein TIFY 9
  • Transcription factor MYC3
KeywordsTRANSCRIPTION / transcriptional repression / jasmonate signaling / MYC3 / JAZ10 CMID / alternative splicing / desensitization
Function / homology
Function and homology information


regulation of defense response / regulation of systemic acquired resistance / regulation of jasmonic acid mediated signaling pathway / extracellular ATP signaling / stomatal complex development / anthocyanin-containing compound biosynthetic process / response to jasmonic acid / bHLH transcription factor binding / defense response / response to wounding ...regulation of defense response / regulation of systemic acquired resistance / regulation of jasmonic acid mediated signaling pathway / extracellular ATP signaling / stomatal complex development / anthocyanin-containing compound biosynthetic process / response to jasmonic acid / bHLH transcription factor binding / defense response / response to wounding / protein dimerization activity / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / 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 9 / 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. / He, S.Y. / Xu, H.E. / Melcher, K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104212 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102545 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK071662 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural insights into alternative splicing-mediated desensitization of jasmonate signaling.
Authors: Zhang, F. / Ke, J. / Zhang, L. / Chen, R. / Sugimoto, K. / Howe, G.A. / Xu, H.E. / Zhou, M. / He, S.Y. / Melcher, K.
History
DepositionAug 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.6Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Transcription factor MYC3
B: Protein TIFY 9


Theoretical massNumber of molelcules
Total (without water)26,8412
Polymers26,8412
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-15 kcal/mol
Surface area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.321, 65.370, 125.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-103-

HOH

Detailsdimer according to size exclusion chromatography

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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: 21872.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MYC3, ATR2, BHLH5, EN36, At5g46760, MZA15.18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FIP9
#2: Protein/peptide Protein TIFY 9 / Jasmonate ZIM domain-containing protein 10 / Protein JASMONATE-ASSOCIATED 1 / Protein JAZ10


Mass: 4967.769 Da / Num. of mol.: 1 / Fragment: UNP residues 16-58
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TIFY9, JAS1, JAZ10, At5g13220, T31B5.40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93ZM9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M Tris, pH 6.0, 20% (w/v) polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 14, 2015
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 9574 / % possible obs: 100 % / Redundancy: 14.3 % / CC1/2: 1 / Rmerge(I) obs: 0.067 / Net I/σ(I): 26.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 14.9 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 3.5 / CC1/2: 0.935 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RQW

4rqw


Resolution: 2.4→31.632 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 30.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2696 870 4.89 %
Rwork0.2259 --
obs0.228 17783 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→31.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 0 13 1529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071538
X-RAY DIFFRACTIONf_angle_d1.1432076
X-RAY DIFFRACTIONf_dihedral_angle_d16.811542
X-RAY DIFFRACTIONf_chiral_restr0.039236
X-RAY DIFFRACTIONf_plane_restr0.004266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.55030.35031390.31262834X-RAY DIFFRACTION100
2.5503-2.74720.3961520.30372773X-RAY DIFFRACTION100
2.7472-3.02340.32421510.29142818X-RAY DIFFRACTION100
3.0234-3.46040.29011720.2532799X-RAY DIFFRACTION100
3.4604-4.3580.2391410.2132856X-RAY DIFFRACTION100
4.358-31.63510.22371150.18572833X-RAY DIFFRACTION100

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