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- PDB-7oq8: Ternary complex of 14-3-3 sigma, Estrogen Receptor alfa phosphope... -

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Basic information

Entry
Database: PDB / ID: 7oq8
TitleTernary complex of 14-3-3 sigma, Estrogen Receptor alfa phosphopeptide, and WQ178
Components
  • 14-3-3 protein sigma
  • Estrogen receptor
KeywordsSIGNALING PROTEIN / protein-peptide complex small-molecule
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / regulation of epidermal cell division / protein kinase C inhibitor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / regulation of epidermal cell division / protein kinase C inhibitor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / positive regulation of epidermal cell differentiation / epithelial cell proliferation involved in mammary gland duct elongation / keratinocyte development / epithelial cell development / keratinization / prostate epithelial cord elongation / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / TFIIB-class transcription factor binding / Regulation of localization of FOXO transcription factors / androgen metabolic process / steroid hormone receptor signaling pathway / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / mammary gland alveolus development / estrogen receptor signaling pathway / establishment of skin barrier / cellular response to estrogen stimulus / estrogen response element binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / : / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / nuclear receptor-mediated steroid hormone signaling pathway / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / RHO GTPases activate PKNs / protein localization to chromatin / 14-3-3 protein binding / protein kinase A signaling / protein sequestering activity / TBP-class protein binding / negative regulation of innate immune response / nitric-oxide synthase regulator activity / steroid binding / protein export from nucleus / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / stem cell proliferation / cellular response to estradiol stimulus / transcription coregulator binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / stem cell differentiation / nuclear estrogen receptor binding / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / SUMOylation of intracellular receptors / euchromatin / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of DNA-binding transcription factor activity / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / response to estrogen / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / ATPase binding / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling
Similarity search - Function
Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / 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. ...Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / 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 / 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
Similarity search - Domain/homology
Chem-0B7 / Estrogen receptor / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsCentorrino, F. / Ottmann, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675179European Union
CitationJournal: To Be Published
Title: A crystallography-based study of fragment extensions into the 14-3-3 binding groove
Authors: Centorrino, F. / Wu, Q. / Cossar, P. / Brunsveld, L. / Ottmann, C.
History
DepositionJun 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 2.0Jan 31, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_strand_id / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_common_name / _pdbx_distant_solvent_atoms.auth_asym_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.auth_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_torsion.auth_asym_id / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq_dif.pdbx_pdb_strand_id
Revision 2.1Mar 13, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,8718
Polymers30,0132
Non-polymers8576
Water4,774265
1
C: 14-3-3 protein sigma
B: Estrogen receptor
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)61,74116
Polymers60,0274
Non-polymers1,71512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)82.018, 110.832, 60.932
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11C-301-

MG

21C-655-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules CB

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


Mass: 28286.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31947
#2: Protein/peptide Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 1726.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P03372

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Non-polymers , 4 types, 271 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / 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-0B7 / ~{N}-[(5-carbamimidoyl-3-phenyl-thiophen-2-yl)methyl]-1~{H}-indole-6-carboxamide


Mass: 374.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H18N4OS / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.095 M Hepes pH7.5, 26%PEG 400, 0.19 M CaCl2, and 5 % Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.43→65.93 Å / Num. obs: 51452 / % possible obs: 99.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.39 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.058 / Net I/σ(I): 8.9
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.896 / Mean I/σ(I) obs: 1 / Num. unique obs: 2542 / CC1/2: 0.467 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC3

4jc3


Resolution: 1.43→65.93 Å / SU ML: 0.1763 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.1369 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2056 3688 3.88 %
Rwork0.1797 91297 -
obs0.1807 51437 95.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.63 Å2
Refinement stepCycle: LAST / Resolution: 1.43→65.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 62 265 2119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791943
X-RAY DIFFRACTIONf_angle_d1.20192637
X-RAY DIFFRACTIONf_chiral_restr0.0609287
X-RAY DIFFRACTIONf_plane_restr0.0056344
X-RAY DIFFRACTIONf_dihedral_angle_d20.9671711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.450.38051450.32913609X-RAY DIFFRACTION97.96
1.45-1.470.32231430.31873588X-RAY DIFFRACTION97.24
1.47-1.490.3441430.29113574X-RAY DIFFRACTION97
1.49-1.510.27831430.27833514X-RAY DIFFRACTION96.16
1.51-1.540.31921380.27813466X-RAY DIFFRACTION94.3
1.54-1.560.28781370.27123405X-RAY DIFFRACTION93.06
1.56-1.590.2781310.25813199X-RAY DIFFRACTION87.61
1.59-1.620.23031380.23033275X-RAY DIFFRACTION89.67
1.62-1.650.22851400.22853495X-RAY DIFFRACTION93.81
1.65-1.680.27081440.22133600X-RAY DIFFRACTION98.6
1.68-1.720.2221440.21673562X-RAY DIFFRACTION98.67
1.72-1.760.22571450.2173618X-RAY DIFFRACTION98.77
1.76-1.80.21851530.20313659X-RAY DIFFRACTION98.76
1.8-1.850.21521510.20253587X-RAY DIFFRACTION98.37
1.85-1.90.22281460.19163606X-RAY DIFFRACTION97.91
1.9-1.970.2381370.18413587X-RAY DIFFRACTION97.64
1.97-2.040.19041480.17713544X-RAY DIFFRACTION96.67
2.04-2.120.18621380.16743400X-RAY DIFFRACTION93.52
2.12-2.210.17351190.15883207X-RAY DIFFRACTION86.52
2.21-2.330.1841340.14543352X-RAY DIFFRACTION91.42
2.33-2.480.17621490.15133615X-RAY DIFFRACTION98.92
2.48-2.670.16871500.1573641X-RAY DIFFRACTION99.29
2.67-2.940.20091440.15573627X-RAY DIFFRACTION99.11
2.94-3.360.17661440.16023640X-RAY DIFFRACTION99.03
3.36-4.240.17661380.14663364X-RAY DIFFRACTION91.53
4.24-65.930.2161460.1743563X-RAY DIFFRACTION96.99

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