[English] 日本語
Yorodumi
- PDB-1rk3: crystal structure of the rat vitamin D receptor ligand binding do... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rk3
Titlecrystal structure of the rat vitamin D receptor ligand binding domain complexed with 1,25-dihydroxyvitamin D3 and a synthetic peptide containing the NR2 box of DRIP 205
Components
  • Peroxisome proliferator-activated receptor binding protein
  • Vitamin D3 receptor
Keywordshormone/growth factor receptor / nuclear receptor-ligand complex / nuclear receptor-coactivator interactions / hormone-growth factor receptor COMPLEX
Function / homology
Function and homology information


negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / SUMOylation of intracellular receptors / retinal pigment epithelium development / Nuclear Receptor transcription pathway ...negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / SUMOylation of intracellular receptors / retinal pigment epithelium development / Nuclear Receptor transcription pathway / G0 to G1 transition / thyroid hormone receptor signaling pathway / response to bile acid / mammary gland branching involved in thelarche / dense fibrillar component / core mediator complex / positive regulation of parathyroid hormone secretion / regulation of vitamin D receptor signaling pathway / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / vitamin D binding / calcitriol binding / cellular response to vitamin D / lithocholic acid binding / nuclear retinoic acid receptor binding / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / positive regulation of hepatocyte proliferation / ventricular trabecula myocardium morphogenesis / mediator complex / positive regulation of keratinocyte differentiation / thyroid hormone generation / Generic Transcription Pathway / response to aldosterone / phosphate ion transmembrane transport / peroxisome proliferator activated receptor binding / embryonic heart tube development / cellular response to thyroid hormone stimulus / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / negative regulation of ossification / embryonic hindlimb morphogenesis / nuclear thyroid hormone receptor binding / lens development in camera-type eye / intestinal absorption / embryonic hemopoiesis / megakaryocyte development / cellular response to hepatocyte growth factor stimulus / cellular response to steroid hormone stimulus / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of neuron differentiation / epithelial cell proliferation involved in mammary gland duct elongation / histone acetyltransferase binding / erythrocyte development / RSV-host interactions / LBD domain binding / fat cell differentiation / mammary gland branching involved in pregnancy / decidualization / nuclear steroid receptor activity / regulation of calcium ion transport / monocyte differentiation / general transcription initiation factor binding / animal organ regeneration / hematopoietic stem cell differentiation / ubiquitin ligase complex / negative regulation of keratinocyte proliferation / positive regulation of transcription initiation by RNA polymerase II / nuclear receptor-mediated steroid hormone signaling pathway / embryonic placenta development / nuclear retinoid X receptor binding / heterochromatin / RNA polymerase II preinitiation complex assembly / retinoic acid receptor signaling pathway / keratinocyte differentiation / intracellular receptor signaling pathway / lactation / : / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / T-tubule / BMAL1:CLOCK,NPAS2 activates circadian expression / Activation of gene expression by SREBF (SREBP) / positive regulation of erythrocyte differentiation / cellular response to epidermal growth factor stimulus / animal organ morphogenesis / nuclear estrogen receptor binding / nuclear receptor binding / skeletal system development / transcription coregulator activity / apoptotic signaling pathway / promoter-specific chromatin binding / positive regulation of transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / Heme signaling / liver development / euchromatin / Transcriptional activation of mitochondrial biogenesis / PPARA activates 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-VDX / 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: 2.2 Å
AuthorsVanhooke, J.L. / M Benning, M. / Bauer, C.B. / Pike, J.W. / DeLuca, H.F.
CitationJournal: Biochemistry / Year: 2004
Title: Molecular Structure of the Rat Vitamin D Receptor Ligand Binding Domain Complexed with 2-Carbon-Substituted Vitamin D(3) 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
DepositionNov 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 23, 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)34,9713
Polymers34,5552
Non-polymers4171
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-8 kcal/mol
Surface area11750 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)69,9436
Polymers69,1094
Non-polymers8332
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5810 Å2
ΔGint-35 kcal/mol
Surface area21920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.726, 44.154, 42.072
Angle α, β, γ (deg.)90.00, 96.13, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe asymmetric unit contains one biological unit. The biological unit is composed of one molecule of VDR, one ligand molecule, and one molecule of the synthetic peptide

-
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: Chain A, DEL(165-211)
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) CodonPlus 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 / TRIP2 / 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 / References: UniProt: Q15648
#3: Chemical ChemComp-VDX / 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL / 1,25 DIHYDROXY VITAMIN D3


Mass: 416.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, MOPS, ammonium citrate, isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: BRUKER PROTEUM R / Detector: CCD / Date: Oct 24, 2002
RadiationMonochromator: Montel optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→42.44 Å / Num. all: 14565 / Num. obs: 14475 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Rsym value: 0.052 / Net I/σ(I): 10.9
Reflection shellResolution: 2.2→2.3 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.198 / % possible all: 95

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SAINTdata reduction
LSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1RJK

1rjk


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.508 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24255 727 5 %RANDOM
Rwork0.19048 ---
all0.19303 14468 --
obs0.19303 14468 99.42 %-
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: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.19 Å20 Å2-0.62 Å2
2--3.31 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 30 92 2110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212061
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.992791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1115247
X-RAY DIFFRACTIONr_chiral_restr0.0890.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021507
X-RAY DIFFRACTIONr_nbd_refined0.2080.2923
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.294
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.21
X-RAY DIFFRACTIONr_mcbond_it0.8221.51253
X-RAY DIFFRACTIONr_mcangle_it1.56522032
X-RAY DIFFRACTIONr_scbond_it2.4383808
X-RAY DIFFRACTIONr_scangle_it3.9984.5759
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.271 41
Rwork0.199 936
obs-977

+
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