[English] 日本語
Yorodumi
- PDB-9m1a: Vitamin D receptor complex with a diethyldiphenylsilane derivative -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9m1a
TitleVitamin D receptor complex with a diethyldiphenylsilane derivative
Components
  • Mediator of RNA polymerase II transcription subunit 1
  • Vitamin D3 receptor
KeywordsTRANSCRIPTION / Vitamin D receptor
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 / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type ...: / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / Vitamin D receptor / VDR, DNA-binding domain / : / 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
Similarity search - Domain/homology
: / Vitamin D3 receptor / Mediator of RNA polymerase II transcription subunit 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsThilakarathne, N.M.H.N. / Hanazono, Y. / Ito, N. / Kagechika, H. / Fujii, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Med.Chem. / Year: 2025
Title: Structure-activity relationship and crystallographic analyses of non-secosteroidal vitamin D receptor ligands bearing diphenylsilane core as a hydrophobic pharmacophore.
Authors: Mudiyanselage, H.N.T.N. / Misawa, T. / Ochiai, K. / Demizu, Y. / Hanazono, Y. / Ito, N. / Fujii, S.
History
DepositionFeb 25, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vitamin D3 receptor
C: Mediator of RNA polymerase II transcription subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6833
Polymers32,1662
Non-polymers5171
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-10 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.307, 41.785, 42.274
Angle α, β, γ (deg.)90.000, 96.276, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

-
Components

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


Mass: 30595.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vdr, Nr1i1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13053
#2: Protein/peptide Mediator of RNA polymerase II transcription subunit 1


Mass: 1570.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15648
#3: Chemical ChemComp-A1L78 / (4~{S})-5-[4-[diethyl-[4-(2-ethyl-2-oxidanyl-butoxy)-3-methyl-phenyl]silyl]-2-methyl-phenoxy]-4-oxidanyl-pentanoic acid


Mass: 516.742 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H44O6Si / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Tacsimate, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.78→42.02 Å / Num. obs: 25689 / % possible obs: 99.1 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Net I/σ(I): 14.6
Reflection shellResolution: 1.78→1.82 Å / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2 / Num. unique obs: 1464 / CC1/2: 0.998 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZLC

2zlc


Resolution: 1.78→40.32 Å / SU ML: 0.1922 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4696 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2112 1284 5 %
Rwork0.1793 24386 -
obs0.1808 25670 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.68 Å2
Refinement stepCycle: LAST / Resolution: 1.78→40.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2015 0 36 159 2210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612224
X-RAY DIFFRACTIONf_angle_d0.78293025
X-RAY DIFFRACTIONf_chiral_restr0.043332
X-RAY DIFFRACTIONf_plane_restr0.004393
X-RAY DIFFRACTIONf_dihedral_angle_d26.8915867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.850.3191420.26172709X-RAY DIFFRACTION99.51
1.85-1.940.27311410.22992684X-RAY DIFFRACTION99.61
1.94-2.040.23271440.20052719X-RAY DIFFRACTION99.51
2.04-2.170.23461420.18232703X-RAY DIFFRACTION99.68
2.17-2.330.21931440.17932718X-RAY DIFFRACTION99.55
2.33-2.570.19341410.17772700X-RAY DIFFRACTION99.02
2.57-2.940.19781430.16542718X-RAY DIFFRACTION99
2.94-3.70.19981420.16192691X-RAY DIFFRACTION97.56
3.7-40.320.20151450.17872744X-RAY DIFFRACTION96.62
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.172785917990.4781292812510.05612328867231.15967946992-0.05325719872561.393368795830.08802821278330.00491531710307-0.1513259383710.002500489383950.00959523132775-0.0351947164295-0.1108105536780.0999026592955-0.07336716630590.213553859734-0.0215014900123-0.0184422859870.213344079364-0.0208285408850.2007696487319.08628137240.37108550185219.2038845438
25.911756643723.538901623940.1172039411775.133533023050.7744353976130.1899234478410.01225392888120.242018098281-0.589337272620.0443666911676-0.171573257311-0.185212153180.2818117669020.1012867860310.1200516492110.2830791600770.03944080431950.008416635607030.409322751595-0.09276310046280.4135112132665.52668090153-10.438734116611.0649910331
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain C

+
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