[English] 日本語
Yorodumi
- PDB-3vt8: Crystal structures of rat VDR-LBD with W282R mutation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vt8
TitleCrystal structures of rat VDR-LBD with W282R mutation
Components
  • COACTIVATOR PEPTIDE DRIP
  • Vitamin D3 receptor
KeywordsHORMONE RECEPTOR / Transcription
Function / homology
Function and homology information


negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / bile acid nuclear receptor activity / response to bile acid / dense fibrillar component / positive regulation of parathyroid hormone secretion / phosphate ion transmembrane transport / apoptotic process involved in mammary gland involution ...negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / bile acid nuclear receptor activity / response to bile acid / dense fibrillar component / positive regulation of parathyroid hormone secretion / phosphate ion transmembrane transport / apoptotic process involved in mammary gland involution / cellular response to vitamin D / vitamin D binding / calcitriol binding / positive regulation of apoptotic process involved in mammary gland involution / vitamin D response element binding / lithocholic acid binding / positive regulation of keratinocyte differentiation / negative regulation of ossification / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / bile acid signaling pathway / intestinal absorption / response to aldosterone / mammary gland branching involved in pregnancy / regulation of calcium ion transport / decidualization / negative regulation of keratinocyte proliferation / heterochromatin / nuclear retinoid X receptor binding / T-tubule / lactation / skeletal system development / apoptotic signaling pathway / animal organ morphogenesis / euchromatin / mRNA transcription by RNA polymerase II / cell morphogenesis / nuclear matrix / response to calcium ion / intracellular calcium ion homeostasis / RNA polymerase II transcription regulator complex / cellular response to amyloid-beta / calcium ion transport / nuclear receptor activity / response to estradiol / heart development / sequence-specific DNA binding / cell differentiation / receptor complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus
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-YI3 / Vitamin D3 receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNakabayashi, M. / Shimizu, M. / Ikura, T. / Ito, N.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands.
Authors: Nakabayashi, M. / Tsukahara, Y. / Iwasaki-Miyamoto, Y. / Mihori-Shimazaki, M. / Yamada, S. / Inaba, S. / Oda, M. / Shimizu, M. / Makishima, M. / Tokiwa, H. / Ikura, T. / Ito, N.
History
DepositionMay 19, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vitamin D3 receptor
C: COACTIVATOR PEPTIDE DRIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5983
Polymers32,1372
Non-polymers4611
Water1,71195
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-10 kcal/mol
Surface area12020 Å2
MethodPISA
2
A: Vitamin D3 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0272
Polymers30,5661
Non-polymers4611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.068, 42.052, 41.868
Angle α, β, γ (deg.)90.00, 95.62, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 30566.021 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 116-423 / Mutation: W282R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nr1i1, Vdr / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P13053
#2: Protein/peptide COACTIVATOR PEPTIDE DRIP


Mass: 1570.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PEPTIDE SYNTHESIS
#3: Chemical ChemComp-YI3 / (1R,3R,7E,9beta,17beta)-9-butyl-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9,10-secoestra-5,7-diene-1,3-diol


Mass: 460.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H52O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MOPS-Na, di-Ammonium Citrate, PEG 4000, 2-propanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorDate: Feb 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 15047 / Biso Wilson estimate: 16.6 Å2
Reflection shellResolution: 2.1→2.18 Å

-
Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZLC

2zlc


Resolution: 2.1→38.26 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100897.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1520 10.1 %RANDOM
Rwork0.189 ---
obs0.189 15047 94.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.0914 Å2 / ksol: 0.363018 e/Å3
Displacement parametersBiso mean: 33.8 Å2
Baniso -1Baniso -2Baniso -3
1--12.42 Å20 Å2-1.62 Å2
2--14.94 Å20 Å2
3----2.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.1→38.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 0 33 95 2089
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.951.5
X-RAY DIFFRACTIONc_mcangle_it2.922
X-RAY DIFFRACTIONc_scbond_it5.714
X-RAY DIFFRACTIONc_scangle_it6.985
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 230 9.8 %
Rwork0.248 2112 -
obs--89.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3YI3.paramYI3.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