[English] 日本語
Yorodumi
- PDB-1ymt: Mouse SF-1 LBD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ymt
TitleMouse SF-1 LBD
Components
  • Nuclear receptor 0B2
  • Steroidogenic factor 1
KeywordsTRANSCRIPTION / nuclear receptor / SF-1 / ligand-binding domain / ligand / phosphatidyl glycerol / co-repressor peptide
Function / homology
Function and homology information


response to gonadotropin-releasing hormone / Sertoli cell differentiation / SUMOylation of intracellular receptors / negative regulation of female gonad development / Nuclear Receptor transcription pathway / sex determination / positive regulation of male gonad development / luteinization / tissue development / Leydig cell differentiation ...response to gonadotropin-releasing hormone / Sertoli cell differentiation / SUMOylation of intracellular receptors / negative regulation of female gonad development / Nuclear Receptor transcription pathway / sex determination / positive regulation of male gonad development / luteinization / tissue development / Leydig cell differentiation / male sex determination / maintenance of protein location in nucleus / peroxisome proliferator activated receptor binding / hormone metabolic process / nuclear thyroid hormone receptor binding / adrenal gland development / bile acid and bile salt transport / female gonad development / calcineurin-mediated signaling / animal organ regeneration / nuclear retinoid X receptor binding / transcription regulator inhibitor activity / response to glucose / Notch signaling pathway / hormone-mediated signaling pathway / transcription coregulator binding / negative regulation of DNA-binding transcription factor activity / circadian regulation of gene expression / : / positive regulation of insulin secretion / phospholipid binding / RNA polymerase II transcription regulator complex / nuclear receptor activity / circadian rhythm / male gonad development / transcription corepressor activity / response to ethanol / transcription by RNA polymerase II / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein-containing complex binding / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear receptor subfamily 0 group B member 1/2 / Nuclear hormone receptor family 5 / Retinoid X Receptor / Retinoid X Receptor / 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 receptor subfamily 0 group B member 1/2 / Nuclear hormone receptor family 5 / Retinoid X Receptor / Retinoid X Receptor / 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
Chem-DR9 / Steroidogenic factor 1 / Nuclear receptor subfamily 0 group B member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKrylova, I.N. / Sablin, E.P. / Moore, J. / Xu, R.X. / Waitt, G.M. / Juzumiene, D. / Bynum, J.M. / Fletterick, R.J. / Willson, T.M. / Ingraham, H.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: Structural analyses reveal phosphatidyl inositols as ligands for the NR5 orphan receptors SF-1 and LRH-1
Authors: Krylova, I.N. / Sablin, E.P. / Moore, J. / Xu, R.X. / Waitt, G.M. / MacKay, J.A. / Juzumiene, D. / Bynum, J.M. / Madauss, K. / Montana, V. / Lebedeva, L. / Suzawa, M. / Williams, J.D. / ...Authors: Krylova, I.N. / Sablin, E.P. / Moore, J. / Xu, R.X. / Waitt, G.M. / MacKay, J.A. / Juzumiene, D. / Bynum, J.M. / Madauss, K. / Montana, V. / Lebedeva, L. / Suzawa, M. / Williams, J.D. / Williams, S.P. / Guy, R.K. / Thornton, J.W. / Fletterick, R.J. / Willson, T.M. / Ingraham, H.A.
History
DepositionJan 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Steroidogenic factor 1
B: Nuclear receptor 0B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3253
Polymers29,5782
Non-polymers7471
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-27 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.853, 73.853, 117.014
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-946-

HOH

DetailsPolypeptide monomer (chain A) bound to phospholipid (chain C) represents biological assembly

-
Components

#1: Protein Steroidogenic factor 1 / STF-1 / SF-1 / Adrenal 4 binding protein / Steroid hormone receptor Ad4BP / Fushi tarazu factor ...STF-1 / SF-1 / Adrenal 4 binding protein / Steroid hormone receptor Ad4BP / Fushi tarazu factor homolog 1 / Embryonal LTR binding protein / ELP / Embryonal long terminal repeat- binding protein / Steroid hydroxylase positive regulator


Mass: 27992.281 Da / Num. of mol.: 1 / Fragment: mSF-1 LBD (residues 219-462) / Mutation: C302S, C408S, C413S, C423S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nr5a1, Ftzf1 / Production host: Escherichia coli (E. coli) / References: UniProt: P33242
#2: Protein/peptide Nuclear receptor 0B2 / Orphan nuclear receptor SHP / Small heterodimer partner


Mass: 1585.889 Da / Num. of mol.: 1 / Fragment: mSHP peptide (residues 17-30) / Source method: obtained synthetically / Details: mSHP peptide, RPTILYALLSPSPR (a.a. 17-30) / References: UniProt: Q62227
#3: Chemical ChemComp-DR9 / 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL / (2R)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(9E)-HEXADEC-9-ENOYLOXY]PROPYL (9E)-OCTADEC-9-ENOATE


Mass: 746.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H75O10P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.7 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8 mg/ml mSF-1, 6X molar excess of mSHP peptide, 0.1 M Tris, 14% PEG 8000, 5% isopropanol, 15% xylitol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.03326 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03326 Å / Relative weight: 1
ReflectionResolution: 1.2→25 Å / Num. all: 101414 / Num. obs: 95280 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 38
Reflection shellResolution: 1.2→1.32 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PK5 (mLRH-1 LBD)

1pk5


Resolution: 1.2→24.09 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 339886.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4822 5.1 %RANDOM
Rwork0.197 ---
all0.203 101414 --
obs0.197 95280 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.4456 Å2 / ksol: 0.360209 e/Å3
Displacement parametersBiso mean: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2--0.7 Å20 Å2
3----1.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.2→24.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2233 0 51 467 2751
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_improper_angle_d2.39
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it2.972
X-RAY DIFFRACTIONc_scangle_it4.062.5
LS refinement shellResolution: 1.2→1.32 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.307 1122 5.3 %
Rwork0.311 20170 -
obs--85.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3C16_1_C18_1.PARC16_1_C18_1.TOP

+
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