[English] 日本語
Yorodumi
- PDB-2zmh: Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2zmh
TitleCrystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism
Components
  • Mediator of RNA polymerase II transcription subunit 1
  • Vitamin D3 receptor
KeywordsTRANSCRIPTION / NUCLEAR RECEPTOR-ANTAGONIST COMPLEX / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Transcription regulation / Zinc / Zinc-finger / Activator
Function / homology
Function and homology information


negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / response to bile acid / dense fibrillar component / positive regulation of parathyroid hormone secretion / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / cellular response to vitamin D ...negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / response to bile acid / dense fibrillar component / positive regulation of parathyroid hormone secretion / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / cellular response to vitamin D / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / vitamin D binding / lithocholic acid binding / bile acid nuclear receptor activity / mediator complex / positive regulation of keratinocyte differentiation / negative regulation of ossification / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / intestinal absorption / response to aldosterone / mammary gland branching involved in pregnancy / regulation of calcium ion transport / decidualization / negative regulation of keratinocyte proliferation / heterochromatin / nuclear retinoid X receptor binding / T-tubule / lactation / skeletal system development / apoptotic signaling pathway / animal organ morphogenesis / transcription coregulator activity / mRNA transcription by RNA polymerase II / cell morphogenesis / euchromatin / caveola / nuclear matrix / response to calcium ion / intracellular calcium ion homeostasis / RNA polymerase II transcription regulator complex / nuclear receptor activity / cellular response to amyloid-beta / calcium ion transport / response to estradiol / heart development / sequence-specific DNA binding / cell differentiation / receptor complex / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus
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 / Zinc finger, C4 type (two domains) / 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-NYA / Mediator of RNA polymerase II transcription subunit 1 / Vitamin D3 receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNakabayashi, M. / Yamada, S. / Tanaka, T. / Igarashi, M. / Yoshimoto, N. / Ikura, T. / Ito, N. / Makishima, M. / Tokiwa, H. / DeLuca, H.F. / Shimizu, M.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Crystal structures of rat vitamin d receptor bound to adamantyl vitamin d analogs: structural basis for vitamin d receptor antagonism and partial agonism
Authors: Nakabayashi, M. / Yamada, S. / Yoshimoto, N. / Tanaka, T. / Igarashi, M. / Ikura, T. / Ito, N. / Makishima, M. / Tokiwa, H. / DeLuca, H.F. / Shimizu, M.
History
DepositionApr 18, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Mediator of RNA polymerase II transcription subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6733
Polymers32,1662
Non-polymers5071
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-8 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.643, 42.334, 42.066
Angle α, β, γ (deg.)90.00, 95.47, 90.00
Int Tables number5
Space group name H-MC121

-
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 / Fragment: LIGAND BINDING DOMAIN, UNP residues 116-423 / Mutation: Deletion UNP residues 165-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vdr, Nr1i1 / Plasmid: PET-14B / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P13053
#2: Protein/peptide Mediator of RNA polymerase II transcription subunit 1 / Mediator complex subunit 1 / PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR


Mass: 1570.898 Da / Num. of mol.: 1 / Fragment: DRIP 205 NR2 BOX PEPTIDE, UNP residues 624-636 / Source method: obtained synthetically / Details: Synthetic peptide / References: UniProt: A1L0Z0
#3: Chemical ChemComp-NYA / (1R,3R,7E,17beta)-17-{(1R,2E,4R)-4-hydroxy-1-methyl-4-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]but-2-en-1-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol


Mass: 506.759 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H50O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.13 Å3/Da / Density % sol: 42.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, MOPS, sodium formate, ethyleneglycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 16132 / Biso Wilson estimate: 18.9 Å2

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40.82 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 173193.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1533 10.1 %RANDOM
Rwork0.222 ---
obs0.222 15250 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.7317 Å2 / ksol: 0.37117 e/Å3
Displacement parametersBiso mean: 41.7 Å2
Baniso -1Baniso -2Baniso -3
1--12.58 Å20 Å2-4.65 Å2
2--14.94 Å20 Å2
3----2.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.1→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2015 0 37 31 2083
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scbond_it4.084
X-RAY DIFFRACTIONc_scangle_it5.195
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 238 9.6 %
Rwork0.298 2233 -
obs--92.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep2.paramprotein2.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3108b4_par.param108b4_top.top

+
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