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- PDB-3gyt: Nuclear receptor DAF-12 from parasitic nematode Strongyloides ste... -

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Basic information

Entry
Database: PDB / ID: 3gyt
TitleNuclear receptor DAF-12 from parasitic nematode Strongyloides stercoralis in complex with its physiological ligand dafachronic acid delta 4
Components
  • Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily
  • SRC1
KeywordsTRANSCRIPTION / nuclear receptor / ligand binding domain / dafachronic acid / SRC1 / nematode / Strongyloides stercoralis / DNA-binding / Metal-binding / Nucleus / Receptor / Transcription regulation / Zinc / Zinc-finger
Function / homology
Function and homology information


labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / estrous cycle ...labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / estrous cycle / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / progesterone receptor signaling pathway / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / response to retinoic acid / histone acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / estrogen receptor signaling pathway / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / regulation of cellular response to insulin stimulus / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / response to progesterone / nuclear receptor binding / nuclear estrogen receptor binding / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / nuclear receptor activity / male gonad development / Circadian Clock / response to estradiol / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / transcription coactivator activity / cell differentiation / protein dimerization activity / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Nuclear receptor coactivator 1 / 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 ...Nuclear receptor coactivator 1 / 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 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 / 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-DL4 / Nuclear receptor coactivator 1 / Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily
Similarity search - Component
Biological speciesStrongyloides stercoralis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsZhou, X.E. / Wang, Z. / Suino-Powell, K. / Motola, D.L. / Conneely, A. / Ogata, C. / Sharma, K.K. / Auchus, R.J. / Kliewer, S.A. / Xu, H.E. / Mangelsdorf, D.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Identification of the nuclear receptor DAF-12 as a therapeutic target in parasitic nematodes.
Authors: Wang, Z. / Zhou, X.E. / Motola, D.L. / Gao, X. / Suino-Powell, K. / Conneely, A. / Ogata, C. / Sharma, K.K. / Auchus, R.J. / Lok, J.B. / Hawdon, J.M. / Kliewer, S.A. / Xu, H.E. / Mangelsdorf, D.J.
History
DepositionApr 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily
B: SRC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7133
Polymers29,2992
Non-polymers4151
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-6 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.947, 118.947, 40.225
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily


Mass: 27797.859 Da / Num. of mol.: 1 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Strongyloides stercoralis (invertebrata)
Gene: daf-12 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9XZJ5
#2: Protein/peptide SRC1


Mass: 1500.715 Da / Num. of mol.: 1 / Fragment: Nuclear receptor binding motif 4 / Source method: obtained synthetically / References: UniProt: Q15788*PLUS
#3: Chemical ChemComp-DL4 / (14beta,17alpha,25R)-3-oxocholest-4-en-26-oic acid


Mass: 414.621 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H42O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 8000, ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 3, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 13012 / % possible obs: 99.964 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.172 / Net I/σ(I): 23.915
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 7.34 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.4 Å14.99 Å
Translation3.4 Å14.99 Å

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.893 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.54 / SU ML: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflection
Rfree0.232 910 7 %
Rwork0.192 --
obs0.195 12999 100 %
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.19 Å20 Å2
2--0.39 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 30 168 2220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222087
X-RAY DIFFRACTIONr_bond_other_d0.0060.021938
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.9872812
X-RAY DIFFRACTIONr_angle_other_deg3.83534529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9725250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.76524.79698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58915398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1991512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022257
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02404
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_it1.2161.51253
X-RAY DIFFRACTIONr_mcbond_other0.2571.5513
X-RAY DIFFRACTIONr_mcangle_it2.40422019
X-RAY DIFFRACTIONr_scbond_it3.3433834
X-RAY DIFFRACTIONr_scangle_it5.5124.5793
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å
RfactorNum. reflection% reflection
Rfree0.287 71 -
Rwork0.207 896 -
obs--99.9 %

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