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- PDB-5gic: Crystal structure of VDR in complex with DLAM-2P -

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Basic information

Entry
Database: PDB / ID: 5gic
TitleCrystal structure of VDR in complex with DLAM-2P
Components
  • SRC1
  • Vitamin D3 receptor
KeywordsTRANSCRIPTION / nuclear receptor
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 / mammary gland branching involved in thelarche / retinal pigment epithelium development / SUMOylation of intracellular receptors ...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 / mammary gland branching involved in thelarche / retinal pigment epithelium development / SUMOylation of intracellular receptors / G0 to G1 transition / Nuclear Receptor transcription pathway / 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 / 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 / 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 / negative regulation of ossification / positive regulation of vitamin D receptor signaling pathway / embryonic hindlimb morphogenesis / peroxisome proliferator activated receptor binding / positive regulation of hepatocyte proliferation / vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / intestinal absorption / 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 / response to aldosterone / 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 / regulation of calcium ion transport / decidualization / 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 / heterochromatin / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / ubiquitin ligase complex / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / T-tubule / 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 / skeletal system development / apoptotic signaling pathway / nuclear receptor binding / promoter-specific chromatin binding / nuclear estrogen receptor binding / positive regulation of transcription elongation by RNA polymerase II / animal organ morphogenesis / transcription coregulator activity / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / euchromatin / brain development / PPARA activates gene expression / Cytoprotection by HMOX1
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-DLC / 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 / Resolution: 2.352 Å
AuthorsShimizu, T. / Asano, L.
CitationJournal: Febs Lett. / Year: 2016
Title: Regulation of the vitamin D receptor by vitamin D lactam derivatives.
Authors: Asano, L. / Waku, T. / Abe, R. / Kuwabara, N. / Ito, I. / Yanagisawa, J. / Nagasawa, K. / Shimizu, T.
History
DepositionJun 23, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site
Revision 2.0May 17, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vitamin D3 receptor
C: SRC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1323
Polymers29,5842
Non-polymers5481
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.315, 42.444, 42.106
Angle α, β, γ (deg.)90.00, 96.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 28371.539 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 124-164,UNP RESIDUES 212-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vdr, Nr1i1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13053
#2: Protein/peptide SRC1


Mass: 1212.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15648*PLUS
#3: Chemical ChemComp-DLC / (3~{R},5~{S})-5-[(2~{R})-2-[(1~{R},3~{a}~{S},4~{Z},7~{a}~{R})-7~{a}-methyl-4-[(2~{E})-2-[(3~{S},5~{R})-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]propyl]-3-methyl-3-oxidanyl-1-(2-phenylethyl)pyrrolidin-2-one


Mass: 547.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C35H49NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris-HCl, PEG 8000, NaCl

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jan 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 11424 / % possible obs: 99 % / Redundancy: 3.6 % / Net I/σ(I): 10.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementResolution: 2.352→30 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.59 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2506 2149 9.99 %
Rwork0.2169 --
obs0.2202 11424 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.352→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 40 30 1968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041981
X-RAY DIFFRACTIONf_angle_d0.9222700
X-RAY DIFFRACTIONf_dihedral_angle_d16.1251213
X-RAY DIFFRACTIONf_chiral_restr0.044319
X-RAY DIFFRACTIONf_plane_restr0.005343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3522-2.40680.32431290.36421161X-RAY DIFFRACTION90
2.4068-2.4670.37261390.33111306X-RAY DIFFRACTION98
2.467-2.53370.38521450.34071302X-RAY DIFFRACTION99
2.5337-2.60820.32221500.3271336X-RAY DIFFRACTION98
2.6082-2.69230.29421410.28611261X-RAY DIFFRACTION98
2.6923-2.78850.34781490.28631327X-RAY DIFFRACTION98
2.7885-2.90.32111380.26551259X-RAY DIFFRACTION98
2.9-3.03190.29151530.27531357X-RAY DIFFRACTION99
3.0319-3.19160.30681470.26291277X-RAY DIFFRACTION99
3.1916-3.39130.25171420.23321279X-RAY DIFFRACTION98
3.3913-3.65270.21621450.20781321X-RAY DIFFRACTION98
3.6527-4.01950.2431440.18651294X-RAY DIFFRACTION99
4.0195-4.59940.19061480.15781313X-RAY DIFFRACTION98
4.5994-5.78790.21981410.17571288X-RAY DIFFRACTION98
5.7879-30.01250.2071380.16621287X-RAY DIFFRACTION96
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)
15.34420.2267-0.61951.1473-1.01933.2685-0.0506-0.15020.12850.252-0.22-0.2594-0.38-0.0968-0.04390.4831-0.01860.00890.4004-0.06090.4302-18.61686.2788.5007
26.0429-0.52660.08622.1683-0.34682.63690.04070.0781-0.1530.0498-0.08060.0836-0.19490.12030.05930.35610.0101-0.03070.4347-0.00650.3984-17.89-0.0143.6297
34.2311-0.6856-0.55720.7548-0.81791.99130.61381.27020.0857-0.58510.4303-0.6022-1.03070.39680.02550.8464-0.0060.16520.68530.21540.952-13.650210.9699-9.4112
45.03150.41990.47712.4623-1.13742.8885-0.26720.72350.04560.1090.05480.04540.0077-0.3477-0.00010.52340.0786-0.01880.69140.07460.3821-25.59473.7392-9.3554
56.0775-0.0770.36451.8873-0.04643.83930.05480.2042-0.70720.1921-0.25710.36310.0458-0.4841-0.00340.3821-0.01520.01620.4814-0.02620.4381-27.6741-4.93856.4292
65.6808-1.38810.47712.7049-1.1743.5676-0.0073-1.0278-0.68160.0790.2090.6555-0.0195-0.9582-0.1230.33230.0153-0.00240.72840.08930.5503-37.9399-2.68139.5388
74.9043-0.0297-0.92141.7376-0.16812.99020.40261.1125-0.5446-0.3981-0.32480.0341-0.2078-0.11890.04220.3980.0696-0.06940.6734-0.19970.4535-23.751-5.4424-5.913
86.6988-0.5628-0.89612.4681-0.24954.5761-0.32831.5178-0.6065-0.4053-0.4309-0.19050.5924-0.03630.26030.41540.05080.05270.9045-0.03680.5537-4.3309-5.5972-4.0353
96.8316-0.050.00082.8225-0.67823.7889-0.0725-0.7253-1.2792-0.3479-0.3991-0.69030.83810.39030.24910.42730.06-0.00871.16670.2310.8908-7.8822-10.06710.9727
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 124 through 222 )
2X-RAY DIFFRACTION2chain 'A' and (resid 223 through 283 )
3X-RAY DIFFRACTION3chain 'A' and (resid 284 through 301 )
4X-RAY DIFFRACTION4chain 'A' and (resid 302 through 319 )
5X-RAY DIFFRACTION5chain 'A' and (resid 320 through 345 )
6X-RAY DIFFRACTION6chain 'A' and (resid 346 through 374 )
7X-RAY DIFFRACTION7chain 'A' and (resid 375 through 402 )
8X-RAY DIFFRACTION8chain 'A' and (resid 403 through 420 )
9X-RAY DIFFRACTION9chain 'C' and (resid 626 through 635 )

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