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- PDB-2ocf: Human estrogen receptor alpha ligand-binding domain in complex wi... -

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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


negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking ...negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking / integrin activation / ALK mutants bind TKIs / cell-substrate junction assembly / biological process involved in interaction with symbiont / Molecules associated with elastic fibres / proteoglycan binding / extracellular matrix structural constituent / MET activates PTK2 signaling / regulation of epithelial cell apoptotic process / Syndecan interactions / 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 / p130Cas linkage to MAPK signaling for integrins / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / endodermal cell differentiation / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / GRB2:SOS provides linkage to MAPK signaling for Integrins / TFIIB-class transcription factor binding / androgen metabolic process / Non-integrin membrane-ECM interactions / steroid hormone mediated signaling pathway / Signaling by ALK fusions and activated point mutants / basement membrane / ECM proteoglycans / endoplasmic reticulum-Golgi intermediate compartment / mammary gland alveolus development / positive regulation of axon extension / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / Integrin cell surface interactions / estrogen response element binding / Nuclear signaling by ERBB4 / Nuclear events stimulated by ALK signaling in cancer / positive regulation of phospholipase C activity / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / collagen binding / TBP-class protein binding / extracellular matrix / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / steroid binding / Degradation of the extracellular matrix / nitric-oxide synthase regulator activity / Integrin signaling / substrate adhesion-dependent cell spreading / ESR-mediated signaling / cell-matrix adhesion / regulation of ERK1 and ERK2 cascade / 14-3-3 protein binding / transcription corepressor binding / negative regulation of miRNA transcription / platelet alpha granule lumen / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / integrin-mediated signaling pathway / nuclear estrogen receptor binding / transcription coregulator binding / stem cell differentiation / Post-translational protein phosphorylation / acute-phase response / Cell surface interactions at the vascular wall / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / euchromatin / SUMOylation of intracellular receptors / wound healing / MAP2K and MAPK activation / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / beta-catenin binding / response to wounding / Nuclear Receptor transcription pathway / response to estrogen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / GPER1 signaling / male gonad development / Regulation of RUNX2 expression and activity
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-II collagen-binding domain profile. ...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 / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Kringle-like fold / EGF-like domain signature 1. / Fibronectin type III domain / Fibronectin type 3 domain / Retinoid X Receptor / Retinoid X Receptor / 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 / 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 / Immunoglobulins / Immunoglobulin-like fold / 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
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Estradiol


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


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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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: 2.91 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

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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

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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

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