[English] 日本語
Yorodumi
- PDB-1s0x: Crystal structure of the human RORalpha ligand binding domain in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1s0x
TitleCrystal structure of the human RORalpha ligand binding domain in complex with cholesterol sulfate at 2.2A
ComponentsNuclear receptor ROR-alpha
Keywordshormone/growth factor receptor / THREE-LAYERED ALPHA HELICAL SANDWICH / NUCLEAR HORMONE RECEPTOR / ORPHAN RECEPTOR / LIGAND BINDING DOMAIN / hormone-growth factor receptor COMPLEX
Function / homology
Function and homology information


cGMP metabolic process / cerebellar Purkinje cell differentiation / cerebellar granule cell precursor proliferation / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-modulated transcription factor activity / positive regulation of circadian rhythm / oxysterol binding / muscle cell differentiation ...cGMP metabolic process / cerebellar Purkinje cell differentiation / cerebellar granule cell precursor proliferation / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-modulated transcription factor activity / positive regulation of circadian rhythm / oxysterol binding / muscle cell differentiation / regulation of smoothened signaling pathway / triglyceride homeostasis / regulation of macrophage activation / negative regulation of fat cell differentiation / positive regulation of vascular endothelial growth factor production / regulation of glucose metabolic process / cellular response to interleukin-1 / intracellular receptor signaling pathway / : / nitric oxide biosynthetic process / negative regulation of canonical NF-kappaB signal transduction / xenobiotic metabolic process / cholesterol homeostasis / transcription corepressor binding / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / circadian regulation of gene expression / Heme signaling / PPARA activates gene expression / beta-catenin binding / Nuclear Receptor transcription pathway / negative regulation of inflammatory response / transcription coactivator binding / nuclear receptor activity / cellular response to tumor necrosis factor / : / angiogenesis / Interleukin-4 and Interleukin-13 signaling / cellular response to hypoxia / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / 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 ROR / Retinoid-related orphan receptors, DNA-binding domain / 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
CHOLEST-5-EN-3-YL HYDROGEN SULFATE / Nuclear receptor ROR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsKallen, J. / Schlaeppi, J.M. / Bitsch, F. / Delhon, I. / Fournier, B.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of the human RORalpha Ligand binding domain in complex with cholesterol sulfate at 2.2 A
Authors: Kallen, J. / Schlaeppi, J.M. / Bitsch, F. / Delhon, I. / Fournier, B.
#1: Journal: Structure / Year: 2002
Title: X-ray structure of the hRORalpha LBD at 1.63A: Structural and functional data that cholesterol or a cholesterol derivative is the natural ligand of RORalpha
Authors: Kallen, J. / Schlaeppi, J.-M. / Bitsch, F. / Geisse, S. / Geiser, M. / Delhon, I. / Fournier, B.
History
DepositionJan 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: 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 1.4Sep 20, 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 ROR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9812
Polymers31,5141
Non-polymers4671
Water4,612256
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.400, 49.900, 60.700
Angle α, β, γ (deg.)90.00, 97.80, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly is monomer

-
Components

#1: Protein Nuclear receptor ROR-alpha / Nuclear receptor RZR-alpha


Mass: 31514.279 Da / Num. of mol.: 1 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RORA, NR1F1, RZRA / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P35398
#2: Chemical ChemComp-C3S / CHOLEST-5-EN-3-YL HYDROGEN SULFATE / CHOLESTEROL-SULFATE


Mass: 466.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.78 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
117.6 mg/mlprotein1drop
20.2 M1reservoirMgCl2
316 MPEG40001reservoir
40.1 MTris-HCl1reservoirpH8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.92 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 17, 2002
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 16541 / Num. obs: 16541 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 16.2
Reflection shellResolution: 2.2→2.28 Å / % possible all: 99.4
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 57993
Reflection shell
*PLUS
% possible obs: 99.4 %

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1N83

1n83


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.909 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20874 830 5 %RANDOM
Rwork0.19672 ---
all0.19734 15671 --
obs0.19734 15671 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.919 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å2-0.79 Å2
2---0.15 Å20 Å2
3----2.06 Å2
Refine analyzeLuzzati coordinate error free: 0.181 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 32 256 2354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212145
X-RAY DIFFRACTIONr_bond_other_d0.0010.021917
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9672897
X-RAY DIFFRACTIONr_angle_other_deg0.74334474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3013250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22215411
X-RAY DIFFRACTIONr_chiral_restr0.0790.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022313
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02431
X-RAY DIFFRACTIONr_nbd_refined0.2550.3563
X-RAY DIFFRACTIONr_nbd_other0.2090.31831
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.5186
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3230.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.310.342
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3920.58
X-RAY DIFFRACTIONr_mcbond_it0.8331.51252
X-RAY DIFFRACTIONr_mcangle_it1.66922023
X-RAY DIFFRACTIONr_scbond_it2.5093893
X-RAY DIFFRACTIONr_scangle_it4.2074.5874
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.275 75
Rwork0.295 1130
obs-1130
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.41

+
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