[English] 日本語
Yorodumi
- PDB-7fdn: Crystal structure of transcription factor WER in complex with EGL3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fdn
TitleCrystal structure of transcription factor WER in complex with EGL3
ComponentsTranscription factor EGL1
KeywordsTRANSCRIPTION / Transcription factor
Function / homology
Function and homology information


trichome differentiation / jasmonic acid mediated signaling pathway / epidermal cell fate specification / protein dimerization activity / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
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 EGL1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLuo, Q. / Wang, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Plants / Year: 2021
Title: Structural insights into partner selection for MYB and bHLH transcription factor complexes.
Authors: Wang, B. / Luo, Q. / Li, Y. / Du, K. / Wu, Z. / Li, T. / Shen, W.H. / Huang, C.H. / Gan, J. / Dong, A.
History
DepositionJul 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription factor EGL1
B: Transcription factor EGL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,87410
Polymers43,3652
Non-polymers5108
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-44 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.452, 70.452, 88.556
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Transcription factor EGL1 / Basic helix-loop-helix protein 2 / AtMYC146 / AtbHLH2 / bHLH 2 / Protein ENHANCER OF GLABRA 3 / ...Basic helix-loop-helix protein 2 / AtMYC146 / AtbHLH2 / bHLH 2 / Protein ENHANCER OF GLABRA 3 / Transcription factor EN 30 / bHLH transcription factor bHLH002


Mass: 21682.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BHLH2, EGL1, EGL3, EN30, MYC146, At1g63650, F24D7.16 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9CAD0

-
Non-polymers , 5 types, 134 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100 mM CAPS pH 10.5, 200 mM lithium sulfate, and 2 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 38966 / % possible obs: 99.8 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.02 / Rrim(I) all: 0.063 / Χ2: 0.948 / Net I/σ(I): 11.5 / Num. measured all: 379714
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.977.70.95338980.8760.351.0180.94899.2
1.97-2.058.90.82138690.9360.2850.870.93299.8
2.05-2.149.10.53439210.9690.1850.5660.95999.8
2.14-2.2510.30.38238780.9820.1240.4020.96899.8
2.25-2.3910.80.25538920.9920.0810.2681.00299.9
2.39-2.5810.60.17839070.9950.0570.1880.97999.9
2.58-2.8410.30.10639190.9980.0350.1120.99199.7
2.84-3.259.50.05938600.9980.020.0630.97399.9
3.25-4.0910.40.03939150.9990.0130.0410.95299.8
4.09-309.70.0339070.9990.010.0320.75699.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RRU

4rru


Resolution: 1.9→29.54 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.158 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 1732 5.1 %RANDOM
Rwork0.1852 ---
obs0.1873 32189 87.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.25 Å2 / Biso mean: 22.935 Å2 / Biso min: 8.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å2-0 Å2
2--0.03 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.9→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2658 0 25 126 2809
Biso mean--63.55 30.9 -
Num. residues----340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132743
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172512
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.6243723
X-RAY DIFFRACTIONr_angle_other_deg1.4221.575841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69324.046131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2915463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.771510
X-RAY DIFFRACTIONr_chiral_restr0.0820.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023027
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02559
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 81 -
Rwork0.23 1045 -
all-1126 -
obs--38.87 %

+
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