[English] 日本語
Yorodumi
- PDB-1pk5: Crystal structure of the orphan nuclear receptor LRH-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pk5
TitleCrystal structure of the orphan nuclear receptor LRH-1
ComponentsOrphan nuclear receptor NR5A2
KeywordsGENE REGULATION / nuclear receptor / ligand-binding domain / LRH-1
Function / homology
Function and homology information


SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / positive regulation of viral genome replication / hormone-mediated signaling pathway / cellular response to leukemia inhibitory factor ...SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / positive regulation of viral genome replication / hormone-mediated signaling pathway / cellular response to leukemia inhibitory factor / transcription coregulator binding / cholesterol homeostasis / phospholipid binding / RNA polymerase II transcription regulator complex / nuclear receptor activity / regulation of cell population proliferation / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
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 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSablin, E.P. / Krylova, I.N. / Fletterick, R.J. / Ingraham, H.A.
CitationJournal: Mol.Cell / Year: 2003
Title: Structural basis for ligand-independent activation of the orphan nuclear receptor LRH-1
Authors: Sablin, E.P. / Krylova, I.N. / Fletterick, R.J. / Ingraham, H.A.
History
DepositionJun 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE Author maintains residue I525 in sequence database should be L525

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Orphan nuclear receptor NR5A2
B: Orphan nuclear receptor NR5A2


Theoretical massNumber of molelcules
Total (without water)57,4642
Polymers57,4642
Non-polymers00
Water2,846158
1
A: Orphan nuclear receptor NR5A2


Theoretical massNumber of molelcules
Total (without water)28,7321
Polymers28,7321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Orphan nuclear receptor NR5A2


Theoretical massNumber of molelcules
Total (without water)28,7321
Polymers28,7321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.775, 127.542, 53.213
Angle α, β, γ (deg.)90.00, 91.72, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Orphan nuclear receptor NR5A2 / Liver receptor homolog / LRH-1


Mass: 28731.969 Da / Num. of mol.: 2 / Fragment: LRH-1 LBD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: NR5A2 OR LRH1 / Plasmid: pBHI-pf1 / Production host: Escherichia coli (E. coli) / References: UniProt: P45448
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: PEG 4000, glycerol, TRIS, isopropanol, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
215 %glycerol1reservoir
321 %PEG40001reservoir
4100 mMTris1reservoirpH8.8
55 %isopropanol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 26, 2002 / Details: KOHZU: DOUBLE CRYSTAL SI(III)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 18102 / Num. obs: 17939 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 45.9 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 24.4
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 5.7 / Rsym value: 0.169 / % possible all: 97.1
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 17954 / % possible obs: 98.2 %
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / % possible obs: 88.8 %

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RXR ALPHA (PDB ID 1FBY)

1fby


Resolution: 2.4→24.55 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 693 3.9 %RANDOM
Rwork0.208 ---
all0.215 18102 --
obs0.208 17939 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.3806 Å2 / ksol: 0.355359 e/Å3
Displacement parametersBiso mean: 48.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.18 Å20 Å2-9.52 Å2
2---6.21 Å20 Å2
3---11.39 Å2
Refine analyzeLuzzati coordinate error free: 0.33 Å / Luzzati sigma a free: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.4→24.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3893 0 0 158 4051
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_mcbond_it2.21.5
X-RAY DIFFRACTIONc_mcangle_it3.412
X-RAY DIFFRACTIONc_scbond_it3.562
X-RAY DIFFRACTIONc_scangle_it5.172.5
LS refinement shellResolution: 2.4→2.55 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 114 -
Rwork0.243 2922 -
obs-2922 97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.57
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.22

+
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