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

+
Open data


ID or keywords:

Loading...

-
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 / response to jasmonic acid / bHLH transcription factor binding / 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 / 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 / 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 ...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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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

-
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

+
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://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