[English] 日本語
Yorodumi
- PDB-3w0y: Crystal Structure Analysis of Vitamin D receptor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3w0y
TitleCrystal Structure Analysis of Vitamin D receptor
ComponentsVitamin D3 receptor
KeywordsHORMONE RECEPTOR / Vitamin D receptor
Function / homology
Function and homology information


regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / bile acid nuclear receptor activity / response to bile acid / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / vitamin D response element binding ...regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / bile acid nuclear receptor activity / response to bile acid / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / vitamin D response element binding / lithocholic acid binding / positive regulation of keratinocyte differentiation / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / intestinal absorption / bile acid signaling pathway / mammary gland branching involved in pregnancy / decidualization / negative regulation of keratinocyte proliferation / positive regulation of bone mineralization / nuclear retinoid X receptor binding / lactation / skeletal system development / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / cell morphogenesis / intracellular calcium ion homeostasis / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / calcium ion transport / nuclear receptor activity / cell differentiation / receptor complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Vitamin D receptor / VDR, 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 / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Vitamin D receptor / VDR, 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 / 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-DS4 / Vitamin D3 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.98 Å
AuthorsItoh, S. / Iijima, S.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure Analysis of Vitamin D receptor
Authors: Kashiwagi, H. / Ono, Y. / Itoh, S. / Iijima, S. / Ichikawa, F. / Harada, S. / Takeda, S. / Sekiguchi, N. / Ishigai, M. / Takahashi, T.
History
DepositionNov 5, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vitamin D3 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3432
Polymers28,7461
Non-polymers5971
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.217, 51.124, 132.664
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Vitamin D3 receptor / VDR / 1 / 25-dihydroxyvitamin D3 receptor / Nuclear receptor subfamily 1 group I member 1


Mass: 28746.260 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 120-164, 216-423
Source method: isolated from a genetically manipulated source
Details: FUSION PROTEIN OF RESIDUES 120-164 AND RESIDUES 216-423
Source: (gene. exp.) Homo sapiens (human) / Gene: VDR, NR1I1 / Production host: Escherichia coli (E. coli) / References: UniProt: P11473
#2: Chemical ChemComp-DS4 / [3-fluoro-2'-methyl-4'-(3-{3-methyl-4-[(1E)-4,4,4-trifluoro-3-hydroxy-3-(trifluoromethyl)but-1-en-1-yl]phenyl}pentan-3-yl)biphenyl-4-yl]acetic acid


Mass: 596.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H31F7O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.67 Å3/Da / Density % sol: 53.88 % / Mosaicity: 0.819 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 10, 2005
RadiationMonochromator: Silicone / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 22329 / % possible obs: 90.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 27.57 Å2 / Rmerge(I) obs: 0.088 / Χ2: 2.467 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.91-1.983.60.55521112.829186.9
1.98-2.063.70.32822010.934190.7
2.06-2.153.80.32321933.119190.7
2.15-2.263.80.25222062.464190.4
2.26-2.413.80.15822011.583190.4
2.41-2.593.80.12921921.848190.1
2.59-2.853.80.1122162.031189.5
2.85-3.273.80.08122772.247191.8
3.27-4.113.80.06823063.92192
4.11-503.70.04724263.603191.1

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.11.2refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
BUSTER2.11.2refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.98→33.87 Å / Cor.coef. Fo:Fc: 0.9495 / Cor.coef. Fo:Fc free: 0.9355 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.186 / SU Rfree Blow DPI: 0.159 / SU Rfree Cruickshank DPI: 0.151
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1021 5.07 %RANDOM
Rwork0.1745 ---
obs0.1767 20132 90.83 %-
Displacement parametersBiso max: 98.71 Å2 / Biso mean: 29.7263 Å2 / Biso min: 12.22 Å2
Baniso -1Baniso -2Baniso -3
1-1.5086 Å20 Å20 Å2
2---0.4228 Å20 Å2
3----1.0858 Å2
Refine analyzeLuzzati coordinate error obs: 0.188 Å
Refinement stepCycle: LAST / Resolution: 1.98→33.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 42 281 2316
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d729SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes53HARMONIC2
X-RAY DIFFRACTIONt_gen_planes289HARMONIC5
X-RAY DIFFRACTIONt_it2078HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion268SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2724SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2078HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2817HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion16.28
LS refinement shellResolution: 1.98→2.09 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2464 151 5.25 %
Rwork0.1833 2727 -
all0.1867 2878 -
obs--90.83 %

+
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