[English] 日本語
Yorodumi
- PDB-6hkb: Ternary complex of Estrogen Receptor alpha peptide and 14-3-3 sig... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hkb
TitleTernary complex of Estrogen Receptor alpha peptide and 14-3-3 sigma C42 mutant bound to disulfide fragment PPI stabilizer 3
Components
  • 14-3-3 protein sigma
  • Estrogen receptor
KeywordsPROTEIN BINDING / protein-protein interaction / fragment / tethering / stabilizer
Function / homology
Function and homology information


steroid hormone receptor signaling pathway / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / nuclear estrogen receptor activity / positive regulation of epidermal cell differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / Regulation of GBP-mediated host defense / Developmental Lineage of Mammary Gland Alveolar Cells / regulation of cell-cell adhesion ...steroid hormone receptor signaling pathway / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / nuclear estrogen receptor activity / positive regulation of epidermal cell differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / Regulation of GBP-mediated host defense / Developmental Lineage of Mammary Gland Alveolar Cells / regulation of cell-cell adhesion / TFIIB-class transcription factor binding / negative regulation of smooth muscle cell apoptotic process / establishment of skin barrier / Regulation of localization of FOXO transcription factors / nuclear receptor-mediated steroid hormone signaling pathway / cellular response to estrogen stimulus / Developmental Lineage of Mammary Gland Luminal Epithelial Cells / estrogen response element binding / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / Mitochondrial unfolded protein response (UPRmt) / negative regulation of protein localization to plasma membrane / cAMP/PKA signal transduction / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / estrogen receptor signaling pathway / negative regulation of protein kinase activity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of nitric-oxide synthase activity / steroid binding / positive regulation of protein localization / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / protein export from nucleus / protein localization to chromatin / 14-3-3 protein binding / ESR-mediated signaling / release of cytochrome c from mitochondria / negative regulation of miRNA transcription / positive regulation of cell adhesion / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of innate immune response / positive regulation of protein export from nucleus / TBP-class protein binding / stem cell differentiation / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / transcription corepressor binding / negative regulation of canonical NF-kappaB signal transduction / transcription coregulator binding / TP53 Regulates Metabolic Genes / cellular response to estradiol stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / SUMOylation of intracellular receptors / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein sequestering activity / euchromatin / Nuclear Receptor transcription pathway / response to estrogen / beta-catenin binding / nuclear receptor activity / transcription coactivator binding / positive regulation of nitric oxide biosynthetic process / Constitutive Signaling by Aberrant PI3K in Cancer / intracellular protein localization / sequence-specific double-stranded DNA binding / phospholipase C-activating G protein-coupled receptor signaling pathway / Regulation of RUNX2 expression and activity / Ovarian tumor domain proteases / response to estradiol / PIP3 activates AKT signaling / regulation of protein localization / positive regulation of cell growth / positive regulation of cytosolic calcium ion concentration / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / calmodulin binding / Extra-nuclear estrogen signaling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cadherin binding / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein kinase binding / chromatin / negative regulation of transcription by RNA polymerase II / Golgi apparatus / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 14-3-3 protein sigma / Estrogen receptor/oestrogen-related receptor / 14-3-3 proteins signature 2. ...14-3-3 domain / Delta-Endotoxin; domain 1 / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 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-G8Q / Estrogen receptor / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSijbesma, E. / Hallenbeck, K.K. / Leysen, S. / Arkin, M.R. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research024.001.035 Netherlands
CitationJournal: J. Am. Chem. Soc. / Year: 2019
Title: Site-Directed Fragment-Based Screening for the Discovery of Protein-Protein Interaction Stabilizers.
Authors: Sijbesma, E. / Hallenbeck, K.K. / Leysen, S. / de Vink, P.J. / Skora, L. / Jahnke, W. / Brunsveld, L. / Arkin, M.R. / Ottmann, C.
History
DepositionSep 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein sigma
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8156
Polymers27,4142
Non-polymers4014
Water6,107339
1
A: 14-3-3 protein sigma
B: Estrogen receptor
hetero molecules

A: 14-3-3 protein sigma
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,63012
Polymers54,8284
Non-polymers8038
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4300 Å2
ΔGint-43 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.234, 112.394, 62.439
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-302-

MG

-
Components

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


Mass: 26542.914 Da / Num. of mol.: 1 / Mutation: C38N, N42C
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 receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 870.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P03372
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-G8Q / (1~{R},2~{S})-2-[methyl-[(~{R})-(2-methylpropan-2-yl)oxy-oxidanyl-methyl]amino]-2-phenyl-1-(2-sulfanylethylamino)ethanol


Mass: 328.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H28N2O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 0.095M Hepes, 0.19M CaCl2, 5% glycerol, 26% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→66.37 Å / Num. obs: 32176 / % possible obs: 99.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 10.79 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.084 / Rsym value: 0.075 / Net I/σ(I): 15.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 7.5 / Num. unique obs: 1681 / CC1/2: 0.967 / Rrim(I) all: 0.212 / Rsym value: 0.188 / % possible all: 100

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC3

4jc3


Resolution: 1.7→34.34 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.45
RfactorNum. reflection% reflection
Rfree0.2 1674 5.21 %
Rwork0.1768 --
obs0.178 32128 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.97 Å2 / Biso mean: 13.7022 Å2 / Biso min: 3.82 Å2
Refinement stepCycle: final / Resolution: 1.7→34.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1891 0 25 339 2255
Biso mean--26.28 22.96 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061944
X-RAY DIFFRACTIONf_angle_d0.8832621
X-RAY DIFFRACTIONf_chiral_restr0.045291
X-RAY DIFFRACTIONf_plane_restr0.004337
X-RAY DIFFRACTIONf_dihedral_angle_d3.1271655
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.750.23581430.176824962639100
1.75-1.80650.23681230.180825182641100
1.8065-1.87110.23771290.180225242653100
1.8711-1.9460.21811570.177825032660100
1.946-2.03450.19551390.173525022641100
2.0345-2.14180.17461490.166225112660100
2.1418-2.2760.17351410.165225322673100
2.276-2.45160.20971290.177425392668100
2.4516-2.69830.19621390.186225482687100
2.6983-3.08850.19921520.18625392691100
3.0885-3.89030.20281430.171325972740100
3.8903-34.34710.19181300.17982645277598

+
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