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- PDB-5h1e: Interaction between vitamin D receptor and coactivator peptide SRC2-3 -

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Basic information

Entry
Database: PDB / ID: 5h1e
TitleInteraction between vitamin D receptor and coactivator peptide SRC2-3
Components
  • Nuclear receptor coactivator 2 peptide
  • Vitamin D3 receptor
KeywordsTRANSCRIPTION / Vitamin D3 / VDRE / RXR / co-factors / TIF2
Function / homology
Function and homology information


negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / bile acid nuclear receptor activity / response to bile acid / dense fibrillar component / positive regulation of parathyroid hormone secretion / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport ...negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / bile acid nuclear receptor activity / 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 / vitamin D binding / calcitriol binding / lithocholic acid binding / positive regulation of keratinocyte differentiation / negative regulation of ossification / vitamin D receptor signaling pathway / positive regulation of vitamin D receptor signaling pathway / bile acid signaling pathway / intestinal absorption / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / response to aldosterone / locomotor rhythm / mammary gland branching involved in pregnancy / regulation of calcium ion transport / aryl hydrocarbon receptor binding / decidualization / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / negative regulation of keratinocyte proliferation / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / heterochromatin / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / Recycling of bile acids and salts / cellular response to hormone stimulus / T-tubule / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / lactation / Regulation of lipid metabolism by PPARalpha / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / skeletal system development / response to progesterone / nuclear receptor binding / apoptotic signaling pathway / animal organ morphogenesis / circadian regulation of gene expression / Heme signaling / mRNA transcription by RNA polymerase II / euchromatin / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PPARA activates gene expression / Cytoprotection by HMOX1 / nuclear matrix / Transcriptional regulation of white adipocyte differentiation / intracellular calcium ion homeostasis / response to calcium ion / RNA polymerase II transcription regulator complex / cellular response to amyloid-beta / nuclear receptor activity / calcium ion transport / Circadian Clock / response to estradiol / heart development / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / cell differentiation / receptor complex / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / 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 / protein-containing complex / DNA binding
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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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-VDX / Vitamin D3 receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsEgawa, D. / Itoh, T. / Kato, A. / Kataoka, S. / Anami, Y. / Yamamoto, K.
CitationJournal: Bioorg. Med. Chem. / Year: 2017
Title: SRC2-3 binds to vitamin D receptor with high sensitivity and strong affinity
Authors: Egawa, D. / Itoh, T. / Kato, A. / Kataoka, S. / Anami, Y. / Yamamoto, K.
History
DepositionOct 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,6063
Polymers32,1892
Non-polymers4171
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-6 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.770, 42.880, 42.210
Angle α, β, γ (deg.)90.00, 95.83, 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: 30595.037 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 116-164, 212-423
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 Nuclear receptor coactivator 2 peptide / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1593.844 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 740-752 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-VDX / 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL / 1,25 DIHYDROXY VITAMIN D3


Mass: 416.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MOP-Na, Na-Formate, PEG 4000, Ethleneglycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→41.99 Å / Num. obs: 6752 / % possible obs: 78 % / Redundancy: 2 % / Net I/σ(I): 73.3

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Processing

SoftwareName: REFMAC / Version: 5.8.0103 / Classification: refinement
RefinementResolution: 2.6→41.99 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.911 / SU B: 33.372 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24834 469 6.9 %RANDOM
Rwork0.23901 ---
obs0.23966 6283 77.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.152 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.61 Å2
2---2.26 Å2-0 Å2
3---2.11 Å2
Refinement stepCycle: 1 / Resolution: 2.6→41.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 30 38 2061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192087
X-RAY DIFFRACTIONr_bond_other_d0.0070.022032
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9972830
X-RAY DIFFRACTIONr_angle_other_deg1.0534690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0495250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16524.31695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.08915376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6961513
X-RAY DIFFRACTIONr_chiral_restr0.0750.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212293
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02456
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_it0.7482.011003
X-RAY DIFFRACTIONr_mcbond_other0.7492.0111002
X-RAY DIFFRACTIONr_mcangle_it1.1563.0141252
X-RAY DIFFRACTIONr_mcangle_other1.1553.0141253
X-RAY DIFFRACTIONr_scbond_it0.6222.0481084
X-RAY DIFFRACTIONr_scbond_other0.6222.0481085
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9673.0581579
X-RAY DIFFRACTIONr_long_range_B_refined1.74718.9158540
X-RAY DIFFRACTIONr_long_range_B_other1.74518.9168536
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 32 -
Rwork0.326 476 -
obs--78.4 %
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)
12.9404-0.0224-0.48291.145-0.08411.2808-0.024-0.0218-0.04750.0102-0.0032-0.0019-0.03170.00640.02730.2098-0.0169-0.05430.22560.01520.080119.46970.353819.1244
22.36881.74181.10532.8861-1.57784.5222-0.0979-0.072-0.20830.0298-0.0491-0.17210.05750.10450.14690.28360.03360.0080.2939-0.01780.33086.1349-10.625510.5453
32.27791.4594-3.7616.8046-3.70996.4983-0.20110.39910.16010.2410.4431-0.11430.2072-0.713-0.2420.2624-0.0155-0.06280.35610.00720.234213.29444.122325.0408
42.0754-0.03970.59070.78940.2191.1907-0.11070.17210.01150.01520.08540.0512-0.0909-0.0920.02540.2174-0.00830.06070.16550.02830.027518.41480.127215.8009
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A123 - 419
2X-RAY DIFFRACTION2C741 - 750
3X-RAY DIFFRACTION3A501
4X-RAY DIFFRACTION4A601 - 633
5X-RAY DIFFRACTION4C801 - 805

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