[English] 日本語
Yorodumi
- PDB-7vqp: Vitamin D receptor complexed with a lithocholic acid derivative -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vqp
TitleVitamin D receptor complexed with a lithocholic acid derivative
Components
  • Mediator of RNA polymerase II transcription subunit 1
  • Vitamin D3 receptor
KeywordsTRANSCRIPTION / vitamin D Receptor / lithocholic acid
Function / homology
Function and homology information


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 / mammary gland branching involved in thelarche / retinal pigment epithelium development / G0 to G1 transition / thyroid hormone receptor signaling pathway / core mediator complex ...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 / mammary gland branching involved in thelarche / retinal pigment epithelium development / G0 to G1 transition / thyroid hormone receptor signaling pathway / core mediator complex / regulation of vitamin D receptor signaling pathway / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / mediator complex / nuclear retinoic acid receptor binding / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / cellular response to thyroid hormone stimulus / embryonic hindlimb morphogenesis / peroxisome proliferator activated receptor binding / positive regulation of hepatocyte proliferation / nuclear vitamin D receptor binding / lens development in camera-type eye / nuclear thyroid hormone receptor binding / positive regulation of intracellular estrogen receptor signaling pathway / embryonic hemopoiesis / megakaryocyte development / cellular response to steroid hormone stimulus / cellular response to hepatocyte growth factor stimulus / histone acetyltransferase binding / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / RSV-host interactions / fat cell differentiation / mammary gland branching involved in pregnancy / monocyte differentiation / general transcription initiation factor binding / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / negative regulation of keratinocyte proliferation / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / animal organ regeneration / erythrocyte development / nuclear receptor-mediated steroid hormone signaling pathway / ubiquitin ligase complex / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / lactation / cellular response to epidermal growth factor stimulus / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / positive regulation of erythrocyte differentiation / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / liver development / nuclear receptor binding / promoter-specific chromatin binding / nuclear estrogen receptor binding / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / brain development / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / transcription coactivator binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / protein import into nucleus / transcription corepressor activity / ubiquitin protein ligase activity / Circadian Clock / angiogenesis / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / protein ubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus
Similarity search - Function
: / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1
Similarity search - Domain/homology
Chem-7SW / 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: 1.94 Å
AuthorsKato, K. / Numoto, N. / Kagechika, H. / Tanatani, A. / Ito, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biomolecules / Year: 2022
Title: Lithocholic Acid Amides as Potent Vitamin D Receptor Agonists.
Authors: Yoshihara, A. / Kawasaki, H. / Masuno, H. / Takada, K. / Numoto, N. / Ito, N. / Hirata, N. / Kanda, Y. / Ishizawa, M. / Makishima, M. / Kagechika, H. / Tanatani, A.
History
DepositionOct 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
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)32,6703
Polymers32,1662
Non-polymers5041
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-10 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.805, 37.581, 40.913
Angle α, β, γ (deg.)90.000, 98.590, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Vitamin D3 receptor


Mass: 30595.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli BL21(DE3) (bacteria)
#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-7SW / 3-((R)-4-((3R,5R,8R,9S,10S,13R,14S,17R)-3-(2-hydroxy-2-methylpropyl)-10,13-dimethylhexadecahydro-1H-cyclopenta[a]phenanthren-17-yl)pentanamido)propanoic acid


Mass: 503.757 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H53NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 34.04 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M MOPS-NaOH, 0.1-0.4 M sodium formate, 12-22% (w/v) PEG4000, 5% (v/v) ethylene glycol

-
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: Feb 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.94→40 Å / Num. obs: 17530 / % possible obs: 98.4 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rsym value: 0.056 / Net I/σ(I): 8.6
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1183 / CC1/2: 0.876 / Rsym value: 0.567 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZLC

2zlc


Resolution: 1.94→40 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.607 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / ESU R: 0.196 / ESU R Free: 0.166
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2424 848 4.839 %
Rwork0.207 16675 -
all0.209 --
obs-17523 98.058 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 33.815 Å2
Baniso -1Baniso -2Baniso -3
1-0.109 Å20 Å2-0.06 Å2
2---0.11 Å2-0 Å2
3---0.018 Å2
Refinement stepCycle: LAST / Resolution: 1.94→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1927 0 36 10 1973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132013
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161972
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.6672727
X-RAY DIFFRACTIONr_angle_other_deg1.3061.6194574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5815239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26823.54296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37515372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.235159
X-RAY DIFFRACTIONr_chiral_restr0.0770.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022174
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02406
X-RAY DIFFRACTIONr_nbd_refined0.2080.2458
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.21823
X-RAY DIFFRACTIONr_nbtor_refined0.160.2979
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2946
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.234
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2090.29
X-RAY DIFFRACTIONr_nbd_other0.1620.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1120.22
X-RAY DIFFRACTIONr_mcbond_it2.5643.323965
X-RAY DIFFRACTIONr_mcbond_other2.5623.32964
X-RAY DIFFRACTIONr_mcangle_it3.6924.9531201
X-RAY DIFFRACTIONr_mcangle_other3.6914.9561202
X-RAY DIFFRACTIONr_scbond_it3.4053.771048
X-RAY DIFFRACTIONr_scbond_other3.4013.7681047
X-RAY DIFFRACTIONr_scangle_it5.1765.4761526
X-RAY DIFFRACTIONr_scangle_other5.1745.4771527
X-RAY DIFFRACTIONr_lrange_it6.6939.8262198
X-RAY DIFFRACTIONr_lrange_other6.68839.8412199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.454590.3371228X-RAY DIFFRACTION98.0198
1.99-2.0450.347590.3221193X-RAY DIFFRACTION98.6604
2.045-2.1040.318610.2821092X-RAY DIFFRACTION94.9753
2.104-2.1680.282570.2381136X-RAY DIFFRACTION99.0042
2.168-2.2390.31520.2211112X-RAY DIFFRACTION98.5605
2.239-2.3180.245610.2041052X-RAY DIFFRACTION97.7173
2.318-2.4050.249540.1981014X-RAY DIFFRACTION98.524
2.405-2.5030.298450.193978X-RAY DIFFRACTION97.2433
2.503-2.6130.251340.19952X-RAY DIFFRACTION98.5015
2.613-2.740.246480.184907X-RAY DIFFRACTION97.9487
2.74-2.8880.31420.189887X-RAY DIFFRACTION99.8925
2.888-3.0620.255390.199820X-RAY DIFFRACTION99.652
3.062-3.2720.231490.199763X-RAY DIFFRACTION99.388
3.272-3.5320.279390.213710X-RAY DIFFRACTION97.2727
3.532-3.8660.238370.201667X-RAY DIFFRACTION98.4615
3.866-4.3180.186280.181598X-RAY DIFFRACTION97.9656
4.318-4.9760.158350.171519X-RAY DIFFRACTION94.863
4.976-6.0710.194200.243464X-RAY DIFFRACTION98.374
6.071-8.4880.243220.197356X-RAY DIFFRACTION98.1818
8.488-400.17670.183227X-RAY DIFFRACTION97.0954

+
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