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

+
Open data


ID or keywords:

Loading...

-
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 / regulation of defense response / extracellular ATP signaling / regulation of jasmonic acid mediated signaling pathway / stomatal complex development / anthocyanin-containing compound biosynthetic process / jasmonic acid mediated signaling pathway / pollen development / flower development / response to jasmonic acid ...regulation of cellular response to alkaline pH / regulation of defense response / extracellular ATP signaling / regulation of jasmonic acid mediated signaling pathway / stomatal complex development / anthocyanin-containing compound biosynthetic process / jasmonic acid mediated signaling pathway / pollen development / flower development / response to jasmonic acid / bHLH transcription factor binding / defense response / response to wounding / protein dimerization activity / transcription cis-regulatory region binding / defense response to bacterium / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / identical protein binding / nucleus / plasma membrane
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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more