[English] 日本語
Yorodumi
- PDB-2ocf: Human estrogen receptor alpha ligand-binding domain in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ocf
TitleHuman estrogen receptor alpha ligand-binding domain in complex with estradiol and the E2#23 FN3 monobody
Components
  • Estrogen receptor
  • Fibronectin
KeywordsHORMONE/GROWTH FACTOR / Estrogen Receptor / LBD / monobody / estradiol / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


fibronectin fibril / negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / positive regulation of substrate-dependent cell migration, cell attachment to substrate / cell-substrate junction assembly / neural crest cell migration involved in autonomic nervous system development / fibrinogen complex / Fibronectin matrix formation / blood coagulation, fibrin clot formation / enteric nervous system development ...fibronectin fibril / negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / positive regulation of substrate-dependent cell migration, cell attachment to substrate / cell-substrate junction assembly / neural crest cell migration involved in autonomic nervous system development / fibrinogen complex / Fibronectin matrix formation / blood coagulation, fibrin clot formation / enteric nervous system development / Attachment of bacteria to epithelial cells / integrin activation / neural crest cell migration / ALK mutants bind TKIs / proteoglycan binding / Molecules associated with elastic fibres / MET activates PTK2 signaling / steroid hormone receptor signaling pathway / endodermal cell differentiation / peptidase activator activity / response to muscle activity / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / nuclear estrogen receptor activity / extracellular matrix structural constituent / biological process involved in interaction with symbiont / Developmental Lineage of Mammary Gland Alveolar Cells / endoplasmic reticulum-Golgi intermediate compartment / GRB2:SOS provides linkage to MAPK signaling for Integrins / TFIIB-class transcription factor binding / negative regulation of smooth muscle cell apoptotic process / basement membrane / regulation of protein phosphorylation / nuclear receptor-mediated steroid hormone signaling pathway / Non-integrin membrane-ECM interactions / cellular response to estrogen stimulus / Developmental Lineage of Mammary Gland Luminal Epithelial Cells / estrogen response element binding / regulation of ERK1 and ERK2 cascade / Integrin cell surface interactions / ECM proteoglycans / Mitochondrial unfolded protein response (UPRmt) / endothelial cell migration / substrate adhesion-dependent cell spreading / Nuclear signaling by ERBB4 / cell-matrix adhesion / estrogen receptor signaling pathway / RNA polymerase II preinitiation complex assembly / Degradation of the extracellular matrix / collagen binding / positive regulation of nitric-oxide synthase activity / steroid binding / stem cell differentiation / Integrin signaling / protein localization to chromatin / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / 14-3-3 protein binding / ESR-mediated signaling / negative regulation of miRNA transcription / platelet alpha granule lumen / integrin-mediated signaling pathway / positive regulation of fibroblast proliferation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / TBP-class protein binding / nuclear estrogen receptor binding / nitric-oxide synthase regulator activity / acute-phase response / transcription corepressor binding / negative regulation of canonical NF-kappaB signal transduction / Cell surface interactions at the vascular wall / transcription coregulator binding / Developmental Lineage of Pancreatic Ductal Cells / cellular response to estradiol stimulus / SUMOylation of intracellular receptors / Post-translational protein phosphorylation / response to wounding / euchromatin / Signaling by high-kinase activity BRAF mutants / Nuclear Receptor transcription pathway / MAP2K and MAPK activation / response to estrogen / beta-catenin binding / integrin binding / nuclear receptor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / transcription coactivator binding / positive regulation of nitric oxide biosynthetic process / Constitutive Signaling by Aberrant PI3K in Cancer / heart development / regulation of cell shape / sequence-specific double-stranded DNA binding / phospholipase C-activating G protein-coupled receptor signaling pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Regulation of RUNX2 expression and activity / Signaling by BRAF and RAF1 fusions
Similarity search - Function
Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. ...Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / : / Kringle-like fold / Fibronectin type III domain / Retinoid X Receptor / Retinoid X Receptor / EGF-like domain signature 1. / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ESTRADIOL / Fibronectin / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsRajan, S.S. / Kuruvilla, S.M. / Sharma, S.K. / Kim, Y. / Huang, J. / Koide, A. / Koide, S. / Joachimiak, A. / Greene, G.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Probing protein conformational changes in living cells by using designer binding proteins: application to the estrogen receptor.
Authors: Koide, A. / Abbatiello, S. / Rothgery, L. / Koide, S.
History
DepositionDec 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell
Item: _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE AUTHORS STATE THAT THE C-TERMINAL RESIDUES 549-595 FROM CHAIN A AND N-TERMINAL CLONING ... SEQUENCE AUTHORS STATE THAT THE C-TERMINAL RESIDUES 549-595 FROM CHAIN A AND N-TERMINAL CLONING ARTIFACT FROM CHAIN D ARE MISSING IN COORDINATES DUE TO LACK OF ELECTRON DENSITY.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Estrogen receptor
D: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1973
Polymers46,9252
Non-polymers2721
Water19811
1
A: Estrogen receptor
D: Fibronectin
hetero molecules

A: Estrogen receptor
D: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3956
Polymers93,8504
Non-polymers5452
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)119.219, 119.219, 132.999
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe biological assembly is a dimer where the second monomer is generated by the two fold axis: y,x,1/3-z

-
Components

#1: Protein Estrogen receptor / ER / Estradiol receptor / ER-alpha


Mass: 33679.223 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain, Residues 298-595 / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03372
#2: Protein Fibronectin / FN / Cold-insoluble globulin / CIG


Mass: 13245.792 Da / Num. of mol.: 1
Fragment: E2#23 FN3 MONOBODY, Fibronectin type III Domain 10, Residues 1447-1540
Mutation: R1452T, D1453K, R1524L, G1525R, D1526L, S1527M, P1528L, S1530G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CIG, FN1, FN / Production host: Escherichia coli (E. coli) / References: UniProt: P02751
#3: Chemical ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24O2 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.5M NaCl, 0.1M Imidazole, pH 8.0, 0.2M Zn(OAc)2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2006 / Details: Bent Conical Si-Mirror (Rh-coated)
RadiationMonochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 12253 / % possible obs: 99.6 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 23.19
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 3 / Num. unique all: 1191

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
XFITdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1ZKY, 1FNF

1zky

1fnf


Resolution: 2.95→48.11 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.906 / SU B: 30.308 / SU ML: 0.262 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.871 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25091 575 4.7 %RANDOM
Rwork0.19146 ---
obs0.19429 11540 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.996 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20.91 Å20 Å2
2--1.82 Å20 Å2
3----2.73 Å2
Refinement stepCycle: LAST / Resolution: 2.95→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 20 11 2590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222642
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9943587
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6515323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25123.725102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.80215471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0921515
X-RAY DIFFRACTIONr_chiral_restr0.0850.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021895
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2720.31281
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3380.51852
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.5148
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3220.326
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.57
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.0321.51647
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it10.43522638
X-RAY DIFFRACTIONr_scbond_it17.69531091
X-RAY DIFFRACTIONr_scangle_it23.3564.5949
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 35 -
Rwork0.223 837 -
obs--98.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.12350.7614-0.54455.2687-0.29484.0149-0.1174-0.34540.47310.24550.22920.2350.19330.2339-0.1118-0.1960.1407-0.0044-0.3136-0.0143-0.328956.2651-11.49075.8417
21.499-0.3834-0.0476.5792-0.62490.39060.1321-0.0313-0.10490.73250.01210.2698-0.12040.0363-0.14420.02990.12390.0454-0.10630.0289-0.230648.9006-27.039824.8286
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA305 - 5488 - 251
2X-RAY DIFFRACTION2DB2 - 9429 - 121

+
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