[English] 日本語
Yorodumi
- PDB-5h1e: Interaction between vitamin D receptor and coactivator peptide SRC2-3 -

+
Open data


ID or keywords:

Loading...

-
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 / response to bile acid / dense fibrillar component / positive regulation of parathyroid hormone secretion / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / 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 / positive regulation of apoptotic process involved in mammary gland involution / cellular response to vitamin D / vitamin D binding / calcitriol binding / lithocholic acid binding / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / phosphate ion transmembrane transport / positive regulation of keratinocyte differentiation / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / intestinal absorption / negative regulation of ossification / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / response to aldosterone / locomotor rhythm / mammary gland branching involved in pregnancy / aryl hydrocarbon receptor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / regulation of calcium ion transport / decidualization / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / negative regulation of keratinocyte proliferation / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / heterochromatin / transcription regulator inhibitor activity / retinoic acid receptor signaling pathway / cellular response to hormone stimulus / Recycling of bile acids and salts / intracellular receptor signaling pathway / positive regulation of adipose tissue development / : / lactation / Regulation of lipid metabolism by PPARalpha / T-tubule / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / animal organ morphogenesis / nuclear receptor binding / skeletal system development / negative regulation of smoothened signaling pathway / apoptotic signaling pathway / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / euchromatin / PPARA activates gene expression / cell morphogenesis / Cytoprotection by HMOX1 / caveola / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / nuclear matrix / intracellular calcium ion homeostasis / response to calcium ion / nuclear receptor activity / cellular response to amyloid-beta / calcium ion transport / : / response to estradiol / HATs acetylate histones / heart development / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding / cell differentiation / transcription coactivator activity / receptor complex / protein dimerization activity / nuclear body / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin
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 / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / : / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / 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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


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

-
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

-
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

+
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