[English] 日本語
Yorodumi
- PDB-2ovh: Progesterone Receptor with Bound Asoprisnil and a Peptide from th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ovh
TitleProgesterone Receptor with Bound Asoprisnil and a Peptide from the Co-Repressor SMRT
Components
  • Progesterone receptor
  • SMRT peptide
KeywordsTRANSCRIPTION / Progesterone receptor / PR / Nuclear Receptor / Steroid Receptor / Co-Repressor / Asoprisnil
Function / homology
Function and homology information


glandular epithelial cell maturation / tertiary branching involved in mammary gland duct morphogenesis / ovulation from ovarian follicle / negative regulation of phosphorylation / paracrine signaling / maintenance of protein location in nucleus / regulation of epithelial cell proliferation / nuclear steroid receptor activity / lung alveolus development / progesterone receptor signaling pathway ...glandular epithelial cell maturation / tertiary branching involved in mammary gland duct morphogenesis / ovulation from ovarian follicle / negative regulation of phosphorylation / paracrine signaling / maintenance of protein location in nucleus / regulation of epithelial cell proliferation / nuclear steroid receptor activity / lung alveolus development / progesterone receptor signaling pathway / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / G protein-coupled receptor activity / SUMOylation of intracellular receptors / transcription coactivator binding / Nuclear Receptor transcription pathway / nuclear receptor activity / cell-cell signaling / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / mitochondrial outer membrane / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / signaling receptor binding / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Progesterone receptor / Progesterone receptor / 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 ...Progesterone receptor / Progesterone receptor / 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
Chem-AS0 / Progesterone receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMadauss, K.P. / Deng, S.-J. / Short, S.A. / Stewart, E.L. / Williams, S.P.
CitationJournal: Mol.Endocrinol. / Year: 2007
Title: A structural and in vitro characterization of asoprisnil: a selective progesterone receptor modulator.
Authors: Madauss, K.P. / Grygielko, E.T. / Deng, S.J. / Sulpizio, A.C. / Stanley, T.B. / Wu, C. / Short, S.A. / Thompson, S.K. / Stewart, E.L. / Laping, N.J. / Williams, S.P. / Bray, J.D.
History
DepositionFeb 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Progesterone receptor
B: SMRT peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9173
Polymers31,4672
Non-polymers4501
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-14 kcal/mol
Surface area12500 Å2
MethodPISA
2
A: Progesterone receptor
B: SMRT peptide
hetero molecules

A: Progesterone receptor
B: SMRT peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8336
Polymers62,9344
Non-polymers8992
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area6410 Å2
ΔGint-35 kcal/mol
Surface area22750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.475, 87.475, 90.599
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Progesterone receptor / PR


Mass: 29554.633 Da / Num. of mol.: 1 / Fragment: PR LBD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGR, NR3C3 / Plasmid: pHis GST / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06401
#2: Protein/peptide SMRT peptide


Mass: 1912.345 Da / Num. of mol.: 1 / Fragment: SMRT peptide (residues 2337-2352) / Source method: obtained synthetically / Details: SMRT peptide
#3: Chemical ChemComp-AS0 / 4-[(11BETA,17BETA)-17-METHOXY-17-(METHOXYMETHYL)-3-OXOESTRA-4,9-DIEN-11-YL]BENZALDEHYDE OXIME


Mass: 449.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H35NO4 / Details: asoprisnil
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris, 0.4M NaCl, 10% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 7, 2004
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 6.5 % / Av σ(I) over netI: 8.8 / Number: 175007 / Rmerge(I) obs: 0.084 / Χ2: 1.08 / D res high: 2 Å / D res low: 50 Å / Num. obs: 26720 / % possible obs: 97
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.315098.710.0381.1677
3.424.3110010.0461.1687.4
2.993.4210010.0731.1527.4
2.712.9910010.1211.0687.4
2.522.7110010.1631.0737.3
2.372.5210010.2051.0187.3
2.252.3710010.2491.0036.9
2.152.2599.610.3050.9966
2.072.1594.610.3690.9754.6
22.0776.610.4151.0023.2
ReflectionResolution: 2→50 Å / Num. all: 27495 / Num. obs: 26720 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.084 / Χ2: 1.075 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.073.20.41520791.00276.6
2.07-2.154.60.36925490.97594.6
2.15-2.2560.30527120.99699.6
2.25-2.376.90.24927381.003100
2.37-2.527.30.20527291.018100
2.52-2.717.30.16327331.073100
2.71-2.997.40.12127481.068100
2.99-3.427.40.07327541.152100
3.42-4.317.40.04627981.168100
4.31-5070.03828801.16798.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
CNX2002refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PR LBD from 1A28 with residues 900-933 removed

1a28


Resolution: 2→20 Å / FOM work R set: 0.868 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1770 6.4 %Random
Rwork0.198 ---
all0.2 27495 --
obs0.2 25438 92.5 %-
Displacement parametersBiso mean: 27.405 Å2
Baniso -1Baniso -2Baniso -3
1-0.024 Å2-0.066 Å20 Å2
2--0.024 Å20 Å2
3----0.049 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 33 210 2296
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.136
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 35

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2-2.020.282340.278395429
2.02-2.040.284430.291473516
2.04-2.060.361310.276519550
2.06-2.080.303390.275569608
2.08-2.110.307480.25612660
2.11-2.130.245450.249638683
2.13-2.150.29390.222639678
2.15-2.180.224480.218675723
2.18-2.210.261560.218669725
2.21-2.240.248600.222660720
2.24-2.270.261490.211652701
2.27-2.30.252610.207681742
2.3-2.330.238440.205694738
2.33-2.370.251430.191693736
2.37-2.410.243510.208705756
2.41-2.450.307440.222686730
2.45-2.50.268470.212681728
2.5-2.540.236640.201699763
2.54-2.60.206470.207700747
2.6-2.650.181470.185700747
2.65-2.710.282580.203705763
2.71-2.780.201660.202678744
2.78-2.860.221550.193727782
2.86-2.940.264510.194695746
2.94-3.030.221530.205725778
3.03-3.140.212450.189725770
3.14-3.270.186510.185724775
3.27-3.420.19450.18735780
3.42-3.590.244500.183739789
3.59-3.820.216540.174742796
3.82-4.110.215660.159714780
4.11-4.520.163570.164743800
4.52-5.160.138460.16745791
5.16-6.470.226680.252743811
6.47-200.203650.208788853
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5aso.par

+
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://pdbjlvh1.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