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- PDB-6jez: Covalent labeling of rVDR-LBD by turn-on fluorescent probe mediat... -

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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 / 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 / thyroid hormone generation / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / response to aldosterone / peroxisome proliferator activated receptor binding / phosphate ion transmembrane transport / 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 / embryonic hindlimb morphogenesis / negative regulation of ossification / 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 / LBD domain binding / RSV-host interactions / 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 / negative regulation of keratinocyte proliferation / positive regulation of transcription initiation by RNA polymerase II / ubiquitin ligase complex / 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 / liver development / mRNA transcription by RNA polymerase II / Heme signaling / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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