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- PDB-2yjd: Stapled peptide bound to Estrogen Receptor Beta -

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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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor activity / nuclear steroid receptor activity / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol ...receptor antagonist activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor activity / nuclear steroid receptor activity / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / regulation of lipid metabolic process / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Recycling of bile acids and salts / estrogen receptor signaling pathway / transcription regulator inhibitor activity / cellular response to hormone stimulus / steroid binding / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / positive regulation of adipose tissue development / bile acid and bile salt transport / BMAL1:CLOCK,NPAS2 activates circadian expression / regulation of cellular response to insulin stimulus / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / SUMOylation of transcription cofactors / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / Activation of gene expression by SREBF (SREBP) / ESR-mediated signaling / negative regulation of smoothened signaling pathway / nuclear receptor binding / cellular response to estradiol stimulus / circadian regulation of gene expression / Heme signaling / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / negative regulation of cell growth / Nuclear Receptor transcription pathway / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / mRNA transcription by RNA polymerase II / nuclear receptor activity / transcription coregulator activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / cell-cell signaling / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Estrogen-dependent gene expression / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / Extra-nuclear estrogen signaling / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / 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 / Nuclear receptor coactivators bHLH domain / PAS domain / : / Nuclear receptor coactivator, interlocking / 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 / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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 / 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
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)

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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


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

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

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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

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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 %

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