[English] 日本語
Yorodumi
- PDB-2o4r: Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2o4r
TitleCrystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII 17-20E and the NR2 Box of DRIP 205
Components
  • Peroxisome proliferator-activated receptor-binding protein
  • Vitamin D3 receptor
KeywordsHORMONE/GROWTH FACTOR RECEPTOR / Nuclear receptor-ligand complex / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX
Function / homology
Function and homology information


positive regulation of parathyroid hormone secretion / negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / androgen biosynthetic process / regulation of RNA biosynthetic process / SUMOylation of intracellular receptors / retinal pigment epithelium development / Nuclear Receptor transcription pathway / thyroid hormone receptor signaling pathway / response to bile acid ...positive regulation of parathyroid hormone secretion / negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / androgen biosynthetic process / regulation of RNA biosynthetic process / SUMOylation of intracellular receptors / retinal pigment epithelium development / Nuclear Receptor transcription pathway / thyroid hormone receptor signaling pathway / response to bile acid / dense fibrillar component / cellular response to vitamin D / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / positive regulation of keratinocyte differentiation / ventricular trabecula myocardium morphogenesis / vitamin D binding / mediator complex / Generic Transcription Pathway / nuclear retinoic acid receptor binding / response to aldosterone / lens development in camera-type eye / cellular response to thyroid hormone stimulus / vitamin D receptor signaling pathway / positive regulation of vitamin D receptor signaling pathway / phosphate ion transmembrane transport / megakaryocyte development / negative regulation of ossification / nuclear vitamin D receptor binding / peroxisome proliferator activated receptor binding / intestinal absorption / nuclear thyroid hormone receptor binding / cellular response to steroid hormone stimulus / negative regulation of neuron differentiation / histone acetyltransferase binding / mammary gland branching involved in pregnancy / LBD domain binding / RSV-host interactions / decidualization / regulation of calcium ion transport / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of keratinocyte proliferation / keratinocyte differentiation / general transcription initiation factor binding / positive regulation of transcription initiation by RNA polymerase II / fat cell differentiation / nuclear retinoid X receptor binding / ubiquitin ligase complex / retinoic acid receptor signaling pathway / RNA polymerase II preinitiation complex assembly / erythrocyte development / intracellular receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / heterochromatin / lactation / BMAL1:CLOCK,NPAS2 activates circadian expression / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Activation of gene expression by SREBF (SREBP) / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / positive regulation of erythrocyte differentiation / T-tubule / cellular response to epidermal growth factor stimulus / animal organ morphogenesis / nuclear estrogen receptor binding / nuclear receptor binding / skeletal system development / apoptotic signaling pathway / transcription coregulator activity / Heme signaling / positive regulation of transcription elongation by RNA polymerase II / PPARA activates gene expression / promoter-specific chromatin binding / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / euchromatin / Nuclear Receptor transcription pathway / protein-DNA complex / Transcriptional regulation of white adipocyte differentiation / chromatin DNA binding / response to calcium ion / caveola / mRNA transcription by RNA polymerase II / cell morphogenesis / nuclear receptor activity / RNA polymerase II transcription regulator complex / transcription coactivator binding / cellular response to amyloid-beta / intracellular calcium ion homeostasis / nuclear matrix / calcium ion transport / transcription corepressor activity / response to estradiol / ubiquitin protein ligase activity / heart development / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / angiogenesis / Estrogen-dependent gene expression
Similarity search - Function
: / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / Vitamin D receptor / VDR, DNA-binding domain / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. ...: / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / 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 / 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
Chem-VD5 / Vitamin D3 receptor / Mediator of RNA polymerase II transcription subunit 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.98 Å
AuthorsVanhooke, J.L. / Benning, M.M. / DeLuca, H.F.
Citation
Journal: Arch.Biochem.Biophys. / Year: 2007
Title: New analogs of 2-methylene-19-nor-(20S)-1,25-dihydroxyvitamin D(3) with conformationally restricted side chains: Evaluation of biological activity and structural determination of VDR-bound conformations.
Authors: Vanhooke, J.L. / Tadi, B.P. / Benning, M.M. / Plum, L.A. / Deluca, H.F.
#1: Journal: Biochemistry / Year: 2004
Title: Molecular Structure of the Rat Vitamin D Receptor Ligand Binding Domain Complexed with 2-Carbon-Substituted Vitamin D3 Hormone Analogues and a LXXLL-Containing Coactivator Peptide
Authors: Vanhooke, J.L. / Benning, M.M. / Bauer, C.B. / Pike, J.W. / DeLuca, H.F.
History
DepositionDec 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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: Peroxisome proliferator-activated receptor-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9693
Polymers34,5552
Non-polymers4151
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-11 kcal/mol
Surface area11790 Å2
MethodPISA
2
A: Vitamin D3 receptor
C: Peroxisome proliferator-activated receptor-binding protein
hetero molecules

A: Vitamin D3 receptor
C: Peroxisome proliferator-activated receptor-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9386
Polymers69,1094
Non-polymers8292
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5800 Å2
ΔGint-42 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.000, 43.000, 42.000
Angle α, β, γ (deg.)90.000, 96.000, 90.000
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is composed of one molecule of VDR (chain A), one molecule of the synthetic peptide (chain C), and one ligand molecule (residue name VD5). The asymmetric unit contains one biological unit.

-
Components

#1: Protein Vitamin D3 receptor / VDR / 1 / 25-dihydroxyvitamin D3 receptor


Mass: 32983.730 Da / Num. of mol.: 1 / Fragment: ligand binding domain
Mutation: residues Ser165 through Pro211 are deleted from the protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vdr, Nr1i1 / Plasmid: pET-29B / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) Codon Plus RIL / References: UniProt: P13053
#2: Protein/peptide Peroxisome proliferator-activated receptor-binding protein / PBP / PPAR-binding protein / Thyroid hormone receptor-associated protein complex 220 kDa component ...PBP / PPAR-binding protein / Thyroid hormone receptor-associated protein complex 220 kDa component / Trap220 / Thyroid receptor-interacting protein 2 / TRIP-2 / p53 regulatory protein RB18A / Vitamin D receptor-interacting protein complex component DRIP205 / Activator- recruited cofactor 205 kDa component / ARC205


Mass: 1570.898 Da / Num. of mol.: 1 / Fragment: DRIP 205 NR2 Box Peptide / Source method: obtained synthetically / Details: synthesized at UW-Madison Biotechnology Center / References: UniProt: Q15648
#3: Chemical ChemComp-VD5 / (1R,3R,7E,17E)-17-(5-hydroxy-1,5-dimethylhexylidene)-2-methylene-9,10-secoestra-5,7-diene-1,3-diol


Mass: 414.621 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H42O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 295 K / Method: macroseeding in batch / pH: 7
Details: PEG 4000, MOPS, Ammonium Citrate, Isopropanol, pH 7.0, macroseeding in batch, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: BRUKER PROTEUM R / Detector: CCD / Date: Nov 30, 2005 / Details: Montel Optics
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→42.5 Å / Num. all: 19228 / Num. obs: 19195 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 7.03 % / Rsym value: 0.0447 / Net I/σ(I): 22.77
Reflection shellResolution: 1.98→2.08 Å / Redundancy: 3.61 % / Mean I/σ(I) obs: 4.49 / Num. unique all: 2611 / Rsym value: 0.186 / % possible all: 99.6

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
SAINTdata reduction
LSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1RJK

1rjk


Resolution: 1.98→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.149 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 956 5.1 %RANDOM
Rwork0.186 ---
obs0.189 18621 96.4 %-
all-18621 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.771 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å20 Å2-0.19 Å2
2--2.72 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.98→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 30 166 2195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222072
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9962806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8795248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03324.72591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01515375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1331510
X-RAY DIFFRACTIONr_chiral_restr0.0840.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021526
X-RAY DIFFRACTIONr_nbd_refined0.210.21036
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2153
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.25
X-RAY DIFFRACTIONr_mcbond_it0.9321.51302
X-RAY DIFFRACTIONr_mcangle_it1.57922039
X-RAY DIFFRACTIONr_scbond_it2.4363860
X-RAY DIFFRACTIONr_scangle_it3.8654.5767
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 41 -
Rwork0.208 708 -
obs-749 52.45 %

+
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