[English] 日本語
Yorodumi
- PDB-6jez: Covalent labeling of rVDR-LBD by turn-on fluorescent probe mediat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jez
TitleCovalent labeling of rVDR-LBD by turn-on fluorescent probe mediated by conjugate addition and cyclization
Components
  • Mediator of RNA polymerase II transcription subunit 1
  • Vitamin D3 receptor,Vitamin D3 receptor
KeywordsHORMONE / turn-on fluorescent probe / TCC probe / covalent labeling / histidine
Function / homology
Function and homology information


negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / enucleate erythrocyte development / regulation of RNA biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / 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 / regulation of RNA biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / 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 / mammary gland branching involved in thelarche / thyroid hormone receptor signaling pathway / response to bile acid / 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 / cellular response to vitamin D / calcitriol binding / 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 / phosphate ion transmembrane transport / response to aldosterone / 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 / histone acetyltransferase binding / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / RSV-host interactions / erythrocyte development / 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 / mRNA transcription by RNA polymerase II / positive regulation of transcription elongation 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
7-(diethylamino)chromen-2-one / Chem-YSV / 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: 2.3 Å
AuthorsKojima, H. / Yamamoto, K. / Itoh, T.
CitationJournal: Cell Chem Biol / Year: 2020
Title: Cyclization Reaction-Based Turn-on Probe for Covalent Labeling of Target Proteins.
Authors: Kojima, H. / Fujita, Y. / Takeuchi, R. / Ikebe, Y. / Ohashi, N. / Yamamoto, K. / Itoh, T.
History
DepositionFeb 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,8004
Polymers32,1662
Non-polymers6342
Water1,09961
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-10 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.930, 43.390, 42.000
Angle α, β, γ (deg.)90.00, 95.30, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Vitamin D3 receptor,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 / Activator-recruited cofactor 205 kDa component / ARC205 / Mediator complex subunit 1 / Peroxisome ...Activator-recruited cofactor 205 kDa component / ARC205 / Mediator complex subunit 1 / Peroxisome proliferator-activated receptor-binding protein / PPAR-binding protein / Thyroid hormone receptor-associated protein complex 220 kDa component / Trap220 / Thyroid receptor-interacting protein 2 / TRIP-2 / Vitamin D receptor-interacting protein complex component DRIP205 / p53 regulatory protein RB18A


Mass: 1570.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15648
#3: Chemical ChemComp-YSV / (1R,3R)-5-(2-((1R,3aS,7aR,E)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-2- methylenecyclohexane-1,3-diol / 2-methylidene-19-nor-1alpha,25-dihydroxyvitamin D3


Mass: 416.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O3
#4: Chemical ChemComp-EJO / 7-(diethylamino)chromen-2-one


Mass: 217.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MOPS-Na pH 7.0, 0.1 M sodium formate, 15% PEG4000, 5% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→41.75 Å / Num. obs: 12346 / % possible obs: 98.9 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.029 / Net I/σ(I): 23.2
Reflection shellResolution: 2.3→2.39 Å / Rmerge(I) obs: 0.109 / Num. unique obs: 1377 / CC1/2: 0.989 / Rpim(I) all: 0.066

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZLC

2zlc


Resolution: 2.3→29.18 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.874 / SU B: 16.123 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.255 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25594 592 4.8 %RANDOM
Rwork0.20234 ---
obs0.20486 11749 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.774 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0 Å20.08 Å2
2---0.09 Å2-0 Å2
3---0.41 Å2
Refinement stepCycle: 1 / Resolution: 2.3→29.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1998 0 46 61 2105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192096
X-RAY DIFFRACTIONr_bond_other_d0.0020.022043
X-RAY DIFFRACTIONr_angle_refined_deg1.7052.0042841
X-RAY DIFFRACTIONr_angle_other_deg0.87734716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7685250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27324.78392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.13215375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1611510
X-RAY DIFFRACTIONr_chiral_restr0.090.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212296
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02453
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2351.7691003
X-RAY DIFFRACTIONr_mcbond_other1.2351.771004
X-RAY DIFFRACTIONr_mcangle_it1.9892.6381250
X-RAY DIFFRACTIONr_mcangle_other1.9892.6391250
X-RAY DIFFRACTIONr_scbond_it1.4851.9141093
X-RAY DIFFRACTIONr_scbond_other1.4841.9151094
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3472.8041591
X-RAY DIFFRACTIONr_long_range_B_refined3.62514.2962439
X-RAY DIFFRACTIONr_long_range_B_other3.62514.2982435
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 34 -
Rwork0.218 866 -
obs--100 %
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)
13.68070.1875-0.43291.34910.03371.8442-0.0186-0.0747-0.08250.04660.0111-0.0272-0.01680.03610.00750.0923-0.011-0.02970.01330.00770.012419.42210.202919.049
27.38961.3814-5.35325.9472-3.304710.6705-0.0640.1878-0.2708-0.3845-0.20030.00590.9618-0.19960.26430.23260.0125-0.01490.2761-0.09690.21676.119-10.364810.7041
35.6975-2.02092.54655.77023.00324.158-0.0459-0.39410.12450.1837-0.0219-0.03990.1033-0.30570.06780.08870.04550.00480.08350.03460.071413.04913.942824.8295
471.206524.92914.44768.77455.06232.9318-0.47820.34891.7323-0.24060.14720.4987-0.10020.07730.3310.2495-0.00010.07540.38880.00070.393918.61949.85871.6552
53.1398-0.2198-0.28890.47890.31441.2985-0.02550.00760.05480.00320.028-0.0493-0.04680.0363-0.00250.1901-0.0357-0.01480.06050.00590.074218.52262.724218.3041
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A123 - 420
2X-RAY DIFFRACTION2C625 - 635
3X-RAY DIFFRACTION3A501
4X-RAY DIFFRACTION4A502
5X-RAY DIFFRACTION5A601 - 658
6X-RAY DIFFRACTION5C701 - 703

+
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