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- PDB-3o1d: Structure-function study of Gemini derivatives with two different... -

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Basic information

Entry
Database: PDB / ID: 3o1d
TitleStructure-function study of Gemini derivatives with two different side chains at C-20, Gemini-0072 and Gemini-0097.
Components
  • Nuclear receptor coactivator 2
  • Vitamin D3 receptor A
KeywordsTRANSCRIPTION/TRANSCRIPTION ACTIVATOR / Transcription factor / vitamin D / Nucleus / TRANSCRIPTION-TRANSCRIPTION ACTIVATOR complex
Function / homology
Function and homology information


heart jogging / Vitamin D (calciferol) metabolism / : / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / lithocholic acid binding / hematopoietic stem cell proliferation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / heart looping ...heart jogging / Vitamin D (calciferol) metabolism / : / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / lithocholic acid binding / hematopoietic stem cell proliferation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / heart looping / 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 / calcium ion homeostasis / 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 / ossification / 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 / nuclear receptor activity / Circadian Clock / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / cell differentiation / transcription coactivator activity / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / DNA-templated transcription / 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 / zinc ion binding / nucleoplasm / nucleus / cytoplasm
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 / PAS domain superfamily / 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-G72 / Nuclear receptor coactivator 2 / Vitamin D3 receptor A
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4007 Å
AuthorsHuet, T. / Moras, D. / Rochel, N.
CitationJournal: Medchemcomm / Year: 2011
Title: Structure-function study of gemini derivatives with two different side chains at C-20, Gemini-0072 and Gemini-0097.
Authors: Huet, T. / Maehr, H. / Lee, H.J. / Uskokovic, M.R. / Suh, N. / Moras, D. / Rochel, N.
History
DepositionJul 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Mar 10, 2021Group: Advisory / Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id ..._struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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 A
B: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2353
Polymers35,6412
Non-polymers5951
Water1,13563
1
A: Vitamin D3 receptor A
B: Nuclear receptor coactivator 2
hetero molecules

A: Vitamin D3 receptor A
B: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4706
Polymers71,2814
Non-polymers1,1892
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3860 Å2
ΔGint-35 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.108, 66.108, 264.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 34060.672 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain (UNP Residues 156-453)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: vdra, nr1i1a, vdr / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9PTN2
#2: Protein/peptide Nuclear receptor coactivator 2 / / NCoA-2 / Transcriptional intermediary factor 2 / hTIF2 / Class E basic helix-loop-helix protein 75 / bHLHe75


Mass: 1579.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 13-MER PEPTIDE / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-G72 / (1R,3R,7E,17beta)-17-[(1S)-6,6,6-trifluoro-5-hydroxy-1-(4-hydroxy-4-methylpentyl)-5-(trifluoromethyl)hex-3-yn-1-yl]-9,10-secoestra-5,7-diene-1,3-diol / 1,25-dihydroxy-20S-21(3-trideuteromethyl-3-hydroxy-4,4,4-trideuterobutyl)-23-yne-26,27-hexafluoro-19-nor-cholecalciferol / Gemini-0072


Mass: 594.669 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H44F6O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM BIS-TRIS pH6.5, 1.6 M lithium sulfate, 50 mM magnesium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 11, 2008
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 14413 / Num. obs: 13853 / % possible obs: 96.2 % / Observed criterion σ(I): 14.8
Reflection shellResolution: 2.4→2.49 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4007→24.884 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 25.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2671 699 5.08 %RANDOM
Rwork0.209 ---
obs0.2118 13747 96.16 %-
all-14413 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.384 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.183 Å2-0 Å2-0 Å2
2--9.183 Å2-0 Å2
3----18.3661 Å2
Refinement stepCycle: LAST / Resolution: 2.4007→24.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 41 63 2116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032099
X-RAY DIFFRACTIONf_angle_d0.8612840
X-RAY DIFFRACTIONf_dihedral_angle_d18.254815
X-RAY DIFFRACTIONf_chiral_restr0.05324
X-RAY DIFFRACTIONf_plane_restr0.002356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4007-2.58590.34361580.28852569X-RAY DIFFRACTION99
2.5859-2.84580.31061620.26162611X-RAY DIFFRACTION99
2.8458-3.25680.28191190.2272680X-RAY DIFFRACTION100
3.2568-4.10030.28591190.19932497X-RAY DIFFRACTION91
4.1003-24.88550.22051410.17812691X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: 8.8392 Å / Origin y: 36.7782 Å / Origin z: 42.1761 Å
111213212223313233
T0.3494 Å20.1158 Å2-0.0604 Å2-0.4349 Å2-0.0483 Å2--0.3239 Å2
L0.8624 °2-0.0416 °20.3517 °2-2.0688 °21.6098 °2--2.829 °2
S-0.1703 Å °-0.3865 Å °-0.0078 Å °0.3948 Å °0.0823 Å °-0.0116 Å °0.2387 Å °-0.1112 Å °0.0547 Å °
Refinement TLS groupSelection details: all

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