[English] 日本語
Yorodumi
- PDB-2yjd: Stapled peptide bound to Estrogen Receptor Beta -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yjd
TitleStapled peptide bound to Estrogen Receptor Beta
Components
  • ESTROGEN RECEPTOR BETA
  • STAPLED PEPTIDE
KeywordsHORMONE RECEPTOR/PEPTIDE / HORMONE RECEPTOR-PEPTIDE COMPLEX
Function / homology
Function and homology information


receptor antagonist activity / nuclear steroid receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor activity / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts ...receptor antagonist activity / nuclear steroid receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor activity / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / Endogenous sterols / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / steroid binding / ESR-mediated signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / response to progesterone / cellular response to estradiol stimulus / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / negative regulation of cell growth / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / positive regulation of DNA-binding transcription factor activity / Circadian Clock / cell-cell signaling / PIP3 activates AKT signaling / HATs acetylate histones / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling / transcription coactivator activity / protein dimerization activity / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / intracellular membrane-bounded organelle / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily ...Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / 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. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
4-(2-PROPAN-2-YLOXYBENZIMIDAZOL-1-YL)PHENOL / Nuclear receptor coactivator 2 / Estrogen receptor beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.93 Å
AuthorsPhillips, C. / Roberts, L.R. / Schade, M. / Bent, A. / Davies, N.L. / Moore, R. / Pannifer, A.D. / Brown, D.G. / Pickford, A.R. / Irving, S.L.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Design and Structure of Stapled Peptides Binding to Estrogen Receptors.
Authors: Phillips, C. / Roberts, L.R. / Schade, M. / Bazin, R. / Bent, A. / Davies, N.L. / Moore, R. / Pannifer, A.D. / Pickford, A.R. / Prior, S.H. / Read, C.M. / Scott, A. / Brown, D.G. / Xu, B. / Irving, S.L.
History
DepositionMay 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Atomic model / Other

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ESTROGEN RECEPTOR BETA
B: ESTROGEN RECEPTOR BETA
C: STAPLED PEPTIDE
D: STAPLED PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4666
Polymers56,9304
Non-polymers5372
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-37.1 kcal/mol
Surface area25670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.620, 102.620, 102.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.05678, 0.9983, -0.00964), (0.9984, -0.05672, 0.00581), (0.005252, -0.00995, -0.9999)
Vector: -0.5842, 0.4146, -22.29)

-
Components

#1: Protein ESTROGEN RECEPTOR BETA / / ER-BETA / NUCLEAR RECEPTOR SUBFAMILY 3 GROUP A MEMBER 2


Mass: 27109.143 Da / Num. of mol.: 2 / Fragment: LIGAND-BINDING DOMAIN, RESIDUES 261-500
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q92731
#2: Protein/peptide STAPLED PEPTIDE /


Mass: 1355.648 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q15596*PLUS
#3: Chemical ChemComp-YJD / 4-(2-PROPAN-2-YLOXYBENZIMIDAZOL-1-YL)PHENOL


Mass: 268.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H16N2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.16 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→13 Å / Num. obs: 38555 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 12 % / Biso Wilson estimate: 32.86 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7

-
Processing

SoftwareName: BUSTER / Version: 2.9.6 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.93→13.03 Å / Cor.coef. Fo:Fc: 0.9083 / Cor.coef. Fo:Fc free: 0.8857 / SU R Cruickshank DPI: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.181 / SU Rfree Blow DPI: 0.16 / SU Rfree Cruickshank DPI: 0.162
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2602 1944 5.04 %RANDOM
Rwork0.2246 ---
obs0.2264 38555 96.87 %-
Displacement parametersBiso mean: 35.27 Å2
Baniso -1Baniso -2Baniso -3
1--3.642 Å20 Å20 Å2
2---3.642 Å20 Å2
3---7.284 Å2
Refine analyzeLuzzati coordinate error obs: 0.299 Å
Refinement stepCycle: LAST / Resolution: 1.93→13.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3714 0 40 206 3960
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013824HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.155168HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1300SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes118HARMONIC2
X-RAY DIFFRACTIONt_gen_planes536HARMONIC5
X-RAY DIFFRACTIONt_it3824HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.43
X-RAY DIFFRACTIONt_other_torsion20.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion486SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4611SEMIHARMONIC4
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.3115 122 4.98 %
Rwork0.269 2326 -
all0.2711 2448 -
obs--96.87 %

+
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