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- PDB-3up0: Nuclear receptor DAF-12 from hookworm Ancylostoma ceylanicum in c... -

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Basic information

Entry
Database: PDB / ID: 3up0
TitleNuclear receptor DAF-12 from hookworm Ancylostoma ceylanicum in complex with (25S)-delta7-dafachronic acid
Components
  • Nuclear receptor coactivator 2
  • aceDAF-12
KeywordsSTEROID BINDING PROTEIN/TRANSCRIPTION / nematode / STEROID BINDING PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol ...RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / response to progesterone / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / Circadian Clock / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / transcription coactivator activity / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / chromatin binding / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
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 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 / PAS domain superfamily / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-D7S / aceDAF-12 / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesAncylostoma ceylanicum (invertebrata)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhi, X. / Zhou, X.E. / Melcher, K. / Motola, D.L. / Gelmedin, V. / Hawdon, J. / Kliewer, S.A. / Mangelsdorf, D.J. / Xu, H.E.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Conservation of Ligand Binding Reveals a Bile Acid-like Signaling Pathway in Nematodes.
Authors: Zhi, X. / Zhou, X.E. / Melcher, K. / Motola, D.L. / Gelmedin, V. / Hawdon, J. / Kliewer, S.A. / Mangelsdorf, D.J. / Xu, H.E.
History
DepositionNov 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: aceDAF-12
P: Nuclear receptor coactivator 2
B: aceDAF-12
Q: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7896
Polymers58,9594
Non-polymers8292
Water9,620534
1
A: aceDAF-12
P: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8943
Polymers29,4802
Non-polymers4151
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-5 kcal/mol
Surface area12220 Å2
MethodPISA
2
B: aceDAF-12
Q: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8943
Polymers29,4802
Non-polymers4151
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-5 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.012, 85.163, 66.127
Angle α, β, γ (deg.)90.000, 107.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein aceDAF-12


Mass: 27770.740 Da / Num. of mol.: 2 / Fragment: Ligand binding domain
Mutation: K475A, K505R, K550G, K642Q, C553S, C607S, C625S, C661S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ancylostoma ceylanicum (invertebrata) / Gene: daf-12 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H0USY8*PLUS
#2: Protein/peptide Nuclear receptor coactivator 2 / / SRC2 / steroid receptor coactivator-2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / ...SRC2 / steroid receptor coactivator-2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1708.931 Da / Num. of mol.: 2
Fragment: nuclear receptor binding motif (UNP residues 740-753)
Source method: obtained synthetically / Details: SRC2 / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-D7S / (5beta,14beta,17alpha,25S)-3-oxocholest-7-en-26-oic acid / (25S)-delta7-dafachronic acid


Mass: 414.621 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H42O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 293 K / Method: sitting drop / pH: 5.1
Details: 26% w/v PEG2000, 0.2 M ammonium acetate, pH 5.1, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 10, 2009
RadiationMonochromator: Kohzu Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.597→45.89 Å / Num. all: 67287 / Num. obs: 67280 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.597→1.66 Å / Rmerge(I) obs: 0.609 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→45.89 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.614 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 4855 7.2 %RANDOM
Rwork0.1834 ---
all0.1848 67287 --
obs0.1848 66973 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 60.85 Å2 / Biso mean: 19.3318 Å2 / Biso min: 5.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.15 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4093 0 60 534 4687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224226
X-RAY DIFFRACTIONr_bond_other_d0.0010.022978
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9935695
X-RAY DIFFRACTIONr_angle_other_deg0.89337234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.085505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.60324.028211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.04215785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2911538
X-RAY DIFFRACTIONr_chiral_restr0.0860.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024637
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02861
X-RAY DIFFRACTIONr_mcbond_it1.0351.52541
X-RAY DIFFRACTIONr_mcbond_other0.2511.51018
X-RAY DIFFRACTIONr_mcangle_it1.95324090
X-RAY DIFFRACTIONr_scbond_it2.97331685
X-RAY DIFFRACTIONr_scangle_it4.8844.51605
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 357 -
Rwork0.23 4544 -
all-4901 -
obs--100 %

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