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- PDB-4yz6: Crystal Structure of Myc3[44-238] from Arabidopsis in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4yz6
TitleCrystal Structure of Myc3[44-238] from Arabidopsis in complex with Jaz1 peptide [200-221]
Components
  • Protein TIFY 10A
  • Transcription factor MYC3
KeywordsTRANSCRIPTION REGULATOR / Jasmonate signaling pathway / Myc3 transcription factor / Jaz1 repressor / plant transcriptional regulation
Function / homology
Function and homology information


regulation of cellular response to alkaline pH / extracellular ATP signaling / anthocyanin-containing compound biosynthetic process / stomatal complex development / jasmonic acid mediated signaling pathway / flower development / bHLH transcription factor binding / pollen development / response to jasmonic acid / defense response ...regulation of cellular response to alkaline pH / extracellular ATP signaling / anthocyanin-containing compound biosynthetic process / stomatal complex development / jasmonic acid mediated signaling pathway / flower development / bHLH transcription factor binding / pollen development / response to jasmonic acid / defense response / protein dimerization activity / defense response to bacterium / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / identical protein binding / nucleus / plasma membrane
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
Transcription factor MYC3 / Protein TIFY 10A
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKe, J. / Zhang, F. / Brunzelle, J. / 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 24, 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
B: Protein TIFY 10A


Theoretical massNumber of molelcules
Total (without water)24,2882
Polymers24,2882
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-7 kcal/mol
Surface area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.209, 86.209, 59.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-444-

HOH

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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: 21587.623 Da / Num. of mol.: 1 / Fragment: UNP residues 44-238
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 / References: UniProt: Q9FIP9
#2: Protein/peptide Protein TIFY 10A / Jasmonate ZIM domain-containing protein 1


Mass: 2700.194 Da / Num. of mol.: 1 / Fragment: UNP residues 200-221 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LMA8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The MYC3(44-238)-JAZ1 complex crystals were grown at 20 degree in sitting drops containing 0.2 ul of the purified complex proteins at a concentration of 15 mg/ml and 0.2 ul of well solution ...Details: The MYC3(44-238)-JAZ1 complex crystals were grown at 20 degree in sitting drops containing 0.2 ul of the purified complex proteins at a concentration of 15 mg/ml and 0.2 ul of well solution containing 3.5 M sodium formate. Crystals of about 80 um in length appeared in 2 days

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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: Feb 20, 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: 1.95→50 Å / Num. all: 18921 / Num. obs: 18921 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 29.7
Reflection shellResolution: 1.95→2 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.952 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4RQW

4rqw


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.514 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21712 965 5.1 %RANDOM
Rwork0.18363 ---
obs0.18518 17940 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.609 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å2-0.5 Å2-0 Å2
2---1 Å20 Å2
3---3.24 Å2
Refinement stepCycle: 1 / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 0 160 1682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191549
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0891.9262090
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2075189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03324.62580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29815262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0411510
X-RAY DIFFRACTIONr_chiral_restr0.0670.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021182
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.294.069768
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.6376.054953
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2614.501780
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.53338.4356842
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 70 -
Rwork0.244 1312 -
obs--100 %

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