[English] 日本語
Yorodumi
- PDB-6xy5: Ternary complex of 14-3-3 sigma (C38N), Estrogen Related Receptor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xy5
TitleTernary complex of 14-3-3 sigma (C38N), Estrogen Related Receptor gamma (DBD) phosphopeptide, and disulfide PPI stabilizer 5
Components
  • 14-3-3 protein sigma
  • Estrogen Related Receptor gamma phosphopeptide
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / ERRy phosphopeptide / disulfide / stabilization
Function / homology
Function and homology information


AF-2 domain binding / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / nuclear steroid receptor activity / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors ...AF-2 domain binding / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / nuclear steroid receptor activity / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / estrogen response element binding / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / retinoic acid receptor signaling pathway / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / steroid binding / positive regulation of cell adhesion / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Nuclear Receptor transcription pathway / nuclear receptor activity / intrinsic apoptotic signaling pathway in response to DNA damage / sequence-specific double-stranded DNA binding / intracellular protein localization / regulation of protein localization / positive regulation of cold-induced thermogenesis / positive regulation of cell growth / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / cadherin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Oestrogen-related receptor / Retinoic acid receptor / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / Estrogen receptor/oestrogen-related receptor / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein ...Oestrogen-related receptor / Retinoic acid receptor / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / Estrogen receptor/oestrogen-related receptor / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-O4E / 14-3-3 protein sigma / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSomsen, B.A. / Ottmann, C.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)024.001.035 Netherlands
Netherlands Organisation for Scientific Research (NWO)016.150.366 Netherlands
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Fluorescence Anisotropy-Based Tethering for Discovery of Protein-Protein Interaction Stabilizers.
Authors: Sijbesma, E. / Somsen, B.A. / Miley, G.P. / Leijten-van de Gevel, I.A. / Brunsveld, L. / Arkin, M.R. / Ottmann, C.
History
DepositionJan 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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
Revision 1.4Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein sigma
B: Estrogen Related Receptor gamma phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1296
Polymers27,7712
Non-polymers3584
Water6,864381
1
A: 14-3-3 protein sigma
B: Estrogen Related Receptor gamma phosphopeptide
hetero molecules

A: 14-3-3 protein sigma
B: Estrogen Related Receptor gamma phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,25912
Polymers55,5424
Non-polymers7168
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5390 Å2
ΔGint-57 kcal/mol
Surface area23000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.302, 112.109, 62.571
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26553.875 Da / Num. of mol.: 1 / Mutation: C38N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide Estrogen Related Receptor gamma phosphopeptide


Mass: 1217.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62508*PLUS

-
Non-polymers , 4 types, 385 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-O4E / 3-bromanyl-~{N}-methyl-~{N}-(2-sulfanylethyl)benzamide


Mass: 274.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12BrNOS / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.095 M HEPES (pH 7.3), 0.19 M CaCl2, 25% (v/v) PEG 400 and 5% (v/v) glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.3→66.34 Å / Num. obs: 71045 / % possible obs: 99.7 % / Redundancy: 12.6 % / CC1/2: 0.998 / Net I/σ(I): 13.6
Reflection shellResolution: 1.3→1.32 Å / Mean I/σ(I) obs: 4.1 / Num. unique obs: 3575 / CC1/2: 0.912

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P1N

3p1n


Resolution: 1.3→56.054 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.33
RfactorNum. reflection% reflection
Rfree0.1775 6924 5.05 %
Rwork0.1621 --
obs0.1628 71009 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.57 Å2 / Biso mean: 15.8466 Å2 / Biso min: 5.81 Å2
Refinement stepCycle: final / Resolution: 1.3→56.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 17 381 2284
Biso mean--35.19 26.87 -
Num. residues----242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDRfactor Rfree error% reflection obs (%)
1.3-1.31480.25612140.2202X-RAY DIFFRACTION099
1.3148-1.33020.21372480.2139X-RAY DIFFRACTION098
1.3302-1.34650.20162300.2088X-RAY DIFFRACTION0100
1.3465-1.36350.23222280.2034X-RAY DIFFRACTION098
1.3635-1.38150.2112270.2082X-RAY DIFFRACTION099
1.3815-1.40040.19912240.2039X-RAY DIFFRACTION099
1.4004-1.42040.20342350.1996X-RAY DIFFRACTION099
1.4204-1.44160.22022420.1904X-RAY DIFFRACTION0100
1.4416-1.46410.20642470.1787X-RAY DIFFRACTION099
1.4641-1.48810.2092350.1763X-RAY DIFFRACTION099
1.4881-1.51380.17762300.1697X-RAY DIFFRACTION0100
1.5138-1.54130.20812360.1722X-RAY DIFFRACTION099
1.5413-1.5710.21171980.1625X-RAY DIFFRACTION0100
1.571-1.6030.16622370.1612X-RAY DIFFRACTION0100
1.603-1.63790.16622390.1574X-RAY DIFFRACTION0100
1.6379-1.6760.16532210.159X-RAY DIFFRACTION0100
1.676-1.71790.17552200.1523X-RAY DIFFRACTION0100
1.7179-1.76440.19112070.1613X-RAY DIFFRACTION0100
1.7644-1.81630.17022670.1616X-RAY DIFFRACTION0100
1.8163-1.87490.18552530.1627X-RAY DIFFRACTION0100
1.8749-1.94190.20612520.1571X-RAY DIFFRACTION0100
1.9419-2.01970.17852530.1539X-RAY DIFFRACTION0100
2.0197-2.11160.13852240.1447X-RAY DIFFRACTION0100
2.1116-2.22290.16692210.144X-RAY DIFFRACTION0100
2.2229-2.36220.17142260.1359X-RAY DIFFRACTION0100
2.3622-2.54460.162010.1427X-RAY DIFFRACTION0100
2.5446-2.80070.14781960.1547X-RAY DIFFRACTION0100
2.8007-3.20590.15782310.1601X-RAY DIFFRACTION0100
3.2059-4.03890.17062500.1555X-RAY DIFFRACTION0100
4.0389-56.0540.18772320.1749X-RAY DIFFRACTION0100

+
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