[English] 日本語
Yorodumi
- PDB-8pz7: crystal structure of VDR complex with D-Bishomo-1a,25-dihydroxyvi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pz7
Titlecrystal structure of VDR complex with D-Bishomo-1a,25-dihydroxyvitamin D3 Analog 57
Components
  • Nuclear receptor coactivator 2
  • Vitamin D3 receptor A
KeywordsTRANSCRIPTION / nuclear receptor / vdr / agonist
Function / homology
Function and homology information


heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / lithocholic acid binding / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / hematopoietic stem cell proliferation / heart looping / locomotor rhythm ...heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / lithocholic acid binding / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / hematopoietic stem cell proliferation / heart looping / locomotor rhythm / aryl hydrocarbon receptor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / calcium ion homeostasis / cellular response to hormone stimulus / Recycling of bile acids and salts / positive regulation of adipose tissue development / : / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / ossification / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / : / response to progesterone / nuclear receptor binding / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / nuclear receptor activity / : / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / transcription regulator complex / Estrogen-dependent gene expression / transcription coactivator activity / cell differentiation / nuclear body / protein dimerization activity / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Vitamin D receptor / VDR, DNA-binding domain / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator ...Vitamin D receptor / VDR, DNA-binding domain / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / : / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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
Chem-IG0 / Nuclear receptor coactivator 2 / Vitamin D3 receptor A
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsRochel, N.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE17-0009-01 France
CitationJournal: Eur.J.Med.Chem. / Year: 2024
Title: Design, synthesis, and biological activity of D-bishomo-1 alpha ,25-dihydroxyvitamin D 3 analogs and their crystal structures with the vitamin D nuclear receptor.
Authors: Fabisiak, A. / Brzeminski, P. / Sicinski, R.R. / Rochel, N. / Maj, E. / Filip-Psurska, B. / Wietrzyk, J. / Plum, L.A. / DeLuca, H.F.
History
DepositionJul 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vitamin D3 receptor A
B: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0873
Polymers35,6412
Non-polymers4471
Water43224
1
A: Vitamin D3 receptor A
B: Nuclear receptor coactivator 2
hetero molecules

A: Vitamin D3 receptor A
B: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1746
Polymers71,2814
Non-polymers8932
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area4060 Å2
ΔGint-32 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.240, 66.240, 264.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

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


Mass: 34060.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: vdra, nr1i1a, vdr / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9PTN2
#2: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1579.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-IG0 / (1~{R},3~{R})-5-[(2~{E})-2-[(4~{a}~{R},5~{R},9~{a}~{S})-4~{a}-methyl-5-[(2~{R})-6-methyl-6-oxidanyl-heptan-2-yl]-3,4,5,8,9,9~{a}-hexahydro-2~{H}-benzo[7]annulen-1-ylidene]ethylidene]-2-methyl-cyclohexane-1,3-diol


Mass: 446.706 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H50O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.37 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: NH4Acetate 3.5M, BisTrisPropane 0.1M pH 7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.93→48.07 Å / Num. obs: 8045 / % possible obs: 99.6 % / Redundancy: 2 % / CC1/2: 1 / Net I/σ(I): 25.4
Reflection shellResolution: 2.93→3.04 Å / Num. unique obs: 750 / CC1/2: 0.948

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.93→48.06 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.24 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2571 802 10.03 %
Rwork0.1962 --
obs0.2023 7998 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.93→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 32 24 2049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.914
X-RAY DIFFRACTIONf_dihedral_angle_d17.72807
X-RAY DIFFRACTIONf_chiral_restr0.05315
X-RAY DIFFRACTIONf_plane_restr0.01354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.93-3.120.36491240.33281116X-RAY DIFFRACTION96
3.12-3.360.33971310.23621169X-RAY DIFFRACTION100
3.36-3.70.28081310.21471176X-RAY DIFFRACTION99
3.7-4.230.26411320.18591182X-RAY DIFFRACTION100
4.23-5.330.2271340.16611212X-RAY DIFFRACTION100
5.33-48.060.23461500.18721341X-RAY DIFFRACTION100
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)
12.7507-0.5997-2.27736.725-5.80017.90240.31020.07891.64750.4103-0.06150.598-1.4529-0.4352-0.36990.7591-0.12870.16811.0158-0.18990.9277-39.487839.66096.3595
25.27322.40983.86458.05053.82593.4550.3796-0.40040.00120.0819-0.09961.3932-0.4917-1.6529-0.29250.65020.0267-0.0571.0904-0.14830.971-41.609723.3696-10.7686
32.96412.27913.53285.7909-1.30858.27290.1875-0.9726-0.5904-0.3787-0.03350.21521.3338-0.5185-0.29370.9673-0.12220.13830.8254-0.08740.7903-31.291411.2078-16.8035
45.4132-1.2114-1.98433.37210.11877.4870.1394-0.5531-0.02780.2338-0.19740.28690.0959-0.15970.07730.5528-0.08390.05450.6637-0.03760.4051-29.918527.7498-4.7352
52.51861.6542-1.98123.36041.13785.86340.0274-0.2033-0.95840.896-0.66080.57151.78-0.48420.67911.4101-0.20510.14710.7276-0.02551.124-32.837310.7331-8.4653
69.6904-2.6062-3.78823.00832.63356.8983-0.8207-0.9843-0.48670.7370.43710.13280.76970.14860.3360.9038-0.0155-0.06230.7683-0.00450.5829-31.155821.75075.9224
77.4047-2.0787-3.69762.66063.33587.7658-0.1688-1.29590.3450.69360.3298-0.20420.32821.2115-0.16770.7929-0.033-0.0290.974-0.06960.5722-24.372330.07357.3383
84.01020.60570.11116.01253.44566.2056-0.0189-0.1757-0.22680.19990.3904-0.73770.32420.8516-0.26620.68080.07930.10160.8191-0.04020.6527-19.116322.0786-16.9235
97.3373.2957-0.96574.95033.61364.84640.8046-0.25990.89990.0998-0.1138-0.0264-1.76911.1559-0.71431.0773-0.1007-0.0020.6952-0.07810.7481-23.605938.1852-15.3095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 155 through 174 )
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 184 )
3X-RAY DIFFRACTION3chain 'A' and (resid 185 through 254 )
4X-RAY DIFFRACTION4chain 'A' and (resid 255 through 315 )
5X-RAY DIFFRACTION5chain 'A' and (resid 316 through 334 )
6X-RAY DIFFRACTION6chain 'A' and (resid 335 through 366 )
7X-RAY DIFFRACTION7chain 'A' and (resid 367 through 431 )
8X-RAY DIFFRACTION8chain 'A' and (resid 432 through 451 )
9X-RAY DIFFRACTION9chain 'B' and (resid 686 through 695 )

+
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