[English] 日本語
Yorodumi
- PDB-3f5c: Structure of Dax-1:LRH-1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f5c
TitleStructure of Dax-1:LRH-1 complex
Components
  • Nuclear receptor subfamily 0 group B member 1
  • Nuclear receptor subfamily 5 group A member 2
KeywordsTRANSCRIPTION / nuclear receptor / transcriptional corepressor / regulatory complex / DNA-binding / Lipid-binding / Metal-binding / Nucleus / Receptor / Transcription regulation / Zinc / Zinc-finger / Cytoplasm / Repressor
Function / homology
Function and homology information


nuclear receptor binding => GO:0016922 / DNA hairpin binding / Sertoli cell differentiation / : / negative regulation of steroid biosynthetic process / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / AF-2 domain binding / sex determination / pancreas morphogenesis ...nuclear receptor binding => GO:0016922 / DNA hairpin binding / Sertoli cell differentiation / : / negative regulation of steroid biosynthetic process / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / AF-2 domain binding / sex determination / pancreas morphogenesis / calcineurin-mediated signaling / gonad development / acinar cell differentiation / tissue development / negative regulation of intracellular steroid hormone receptor signaling pathway / Leydig cell differentiation / male sex determination / intracellular receptor signaling pathway / bile acid metabolic process / adrenal gland development / transcription factor binding / centriolar satellite / response to immobilization stress / positive regulation of viral genome replication / hormone-mediated signaling pathway / cellular response to leukemia inhibitory factor / transcription coregulator binding / cholesterol homeostasis / protein localization / negative regulation of DNA-binding transcription factor activity / phospholipid binding / RNA polymerase II transcription regulator complex / transcription corepressor activity / nuclear receptor activity / male gonad development / regulation of cell population proliferation / spermatogenesis / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Nuclear receptor repeat / Nuclear receptor repeat / 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 / Zinc finger, C4 type (two domains) ...Nuclear receptor repeat / Nuclear receptor repeat / 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 / 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
Nuclear receptor subfamily 5 group A member 2 / Nuclear receptor subfamily 0 group B member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFletterick, R.J. / Sablin, E.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: The structure of corepressor Dax-1 bound to its target nuclear receptor LRH-1.
Authors: Sablin, E.P. / Woods, A. / Krylova, I.N. / Hwang, P. / Ingraham, H.A. / Fletterick, R.J.
History
DepositionNov 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 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: Nuclear receptor subfamily 5 group A member 2
B: Nuclear receptor subfamily 0 group B member 1
C: Nuclear receptor subfamily 0 group B member 1


Theoretical massNumber of molelcules
Total (without water)89,4823
Polymers89,4823
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.355, 103.355, 117.455
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein Nuclear receptor subfamily 5 group A member 2 / Liver receptor homolog 1 / LRH-1


Mass: 28731.969 Da / Num. of mol.: 1 / Fragment: UNP residues 313-560 / Mutation: I525L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nr5a2, Lrh1 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: P45448
#2: Protein Nuclear receptor subfamily 0 group B member 1 / Nuclear receptor DAX-1


Mass: 30375.004 Da / Num. of mol.: 2 / Fragment: UNP residues 205-472
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nr0b1, Ahch, Dax1 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: Q61066

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 20% PEG 8000, 1 mM Deoxy-BigChap, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2005 / Details: mirrors
RadiationMonochromator: KHOZU Double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. all: 24752 / Num. obs: 24366 / % possible obs: 98.44 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.8
Reflection shellResolution: 3→3.1 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
PHENIXrefinement
CNSrefinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PK5

1pk5


Resolution: 3→24.785 Å / SU ML: 0.59 / σ(F): 0.08 / Phase error: 33.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2792 700 2.87 %
Rwork0.222 --
obs0.2236 24366 98.44 %
all-24752 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.487 Å2 / ksol: 0.273 e/Å3
Refinement stepCycle: LAST / Resolution: 3→24.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4936 0 0 0 4936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115036
X-RAY DIFFRACTIONf_angle_d1.2536813
X-RAY DIFFRACTIONf_dihedral_angle_d15.3821863
X-RAY DIFFRACTIONf_chiral_restr0.073781
X-RAY DIFFRACTIONf_plane_restr0.006861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.23140.40251150.38274579X-RAY DIFFRACTION95
3.2314-3.55580.33931390.34749X-RAY DIFFRACTION99
3.5558-4.06830.27861430.22024730X-RAY DIFFRACTION99
4.0683-5.11820.23421740.16674745X-RAY DIFFRACTION99
5.1182-24.78610.25671290.18734863X-RAY DIFFRACTION100
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)
15.4661-1.69361.48935.5721-0.01463.6729-0.2929-0.47080.88020.90520.1252-0.5328-0.38660.14420.08450.4680.1362-0.23370.3151-0.26720.437884.906941.126169.0478
25.69630.6719-0.59443.48321.13992.94960.19130.1125-0.0504-0.1627-0.12640.08860.14190.1101-0.02610.36060.1241-0.17580.31210.21930.142956.003143.500247.575
30.39340.7796-0.97655.1574.40036.1197-0.2029-0.1129-0.1102-0.08060.129-0.462-0.01850.2999-0.02210.19470.0271-0.06270.3417-0.24440.651487.90323.93245.0439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

+
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