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- PDB-5t0q: Crystal structure of the Myc3 N-terminal domain [44-242] in compl... -

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Basic information

Entry
Database: PDB / ID: 5t0q
TitleCrystal structure of the Myc3 N-terminal domain [44-242] in complex with JAZ10 Jas domain [166-192] 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 systemic acquired resistance / regulation of jasmonic acid mediated signaling pathway / extracellular ATP signaling / anthocyanin-containing compound biosynthetic process / stomatal complex development / bHLH transcription factor binding / response to jasmonic acid / defense response / response to wounding / protein dimerization activity ...regulation of systemic acquired resistance / regulation of jasmonic acid mediated signaling pathway / extracellular ATP signaling / anthocyanin-containing compound biosynthetic process / stomatal complex development / bHLH transcription factor binding / response to jasmonic acid / 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 / 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 9 / Transcription factor MYC3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK071662 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102545 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104212 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)25,1692
Polymers25,1692
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-5 kcal/mol
Surface area9850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.098, 86.098, 57.871
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Detailsheterodimer according to size exclusion column

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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: 3295.879 Da / Num. of mol.: 1 / Fragment: UNP residues 166-192
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


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.46 Å3/Da / Density % sol: 50 % / Description: Square-shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% w/v polyethylene glycol 3,350, 0.2 M magnesium formate dihydrate, pH 7.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2015
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 13793 / % possible obs: 100 % / Redundancy: 11.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.102 / Net I/σ(I): 16.3
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.8 / CC1/2: 0.866 / % possible all: 100

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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: 2.15→28.182 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 27.3
RfactorNum. reflection% reflection
Rfree0.2421 667 4.85 %
Rwork0.1952 --
obs0.1975 13759 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→28.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1489 0 0 107 1596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081515
X-RAY DIFFRACTIONf_angle_d1.0672039
X-RAY DIFFRACTIONf_dihedral_angle_d15.248547
X-RAY DIFFRACTIONf_chiral_restr0.044220
X-RAY DIFFRACTIONf_plane_restr0.005264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1502-2.31620.3351220.28112581X-RAY DIFFRACTION100
2.3162-2.54910.25741350.24532584X-RAY DIFFRACTION100
2.5491-2.91760.2711170.21112599X-RAY DIFFRACTION100
2.9176-3.67460.24831540.18352613X-RAY DIFFRACTION100
3.6746-28.18460.21351390.17272715X-RAY DIFFRACTION100

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