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- PDB-3o1e: Structure-function of Gemini derivatives with two different side ... -

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Basic information

Entry
Database: PDB / ID: 3o1e
TitleStructure-function 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 / calcitriol binding / vitamin D binding / lithocholic acid binding / hematopoietic stem cell proliferation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / heart looping / locomotor rhythm ...heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / calcitriol binding / vitamin D 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 / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / calcium ion homeostasis / Recycling of bile acids and salts / cellular response to hormone stimulus / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / regulation of cellular response to insulin stimulus / ossification / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / 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 / transcription coactivator activity / cell differentiation / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / 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 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 / 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-H97 / 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: 2.5001 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 ...Advisory / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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 A
B: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2353
Polymers35,6412
Non-polymers5951
Water36020
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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area4030 Å2
ΔGint-28 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.842, 65.842, 263.718
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-H97 / (1R,3R,7E,17beta)-17-[(1R)-6,6,6-trifluoro-5-hydroxy-1-(4-hydroxy-4-methylpentyl)-5-(trifluoromethyl)hex-3-yn-1-yl]-9,1 0-secoestra-5,7-diene-1,3-diol / 1,25-dihydroxy-20R-21(3-trideuteromethyl-3-hydroxy-4,4,4-trideuterobutyl)-23-yne-26,27-hexafluoro-19-nor-cholecalcifero l (Gemini--0097)


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


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.87 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-110.9334
SYNCHROTRONESRF ID14-120.9334
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDDec 11, 2008
ADSC QUANTUM 2102CCDDec 11, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1diamondSINGLE WAVELENGTHMx-ray1
2diamondSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 12894 / Num. obs: 12720 / % possible obs: 98.7 % / Observed criterion σ(I): 18.1
Reflection shellResolution: 2.5→2.59 Å / % possible all: 100

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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: 2.5001→24.79 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 25.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2715 604 4.86 %RANDOM
Rwork0.2055 ---
obs0.2088 12417 98.74 %-
all-12894 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.698 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.2228 Å2-0 Å2-0 Å2
2--7.2228 Å2-0 Å2
3----14.4456 Å2
Refinement stepCycle: LAST / Resolution: 2.5001→24.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 41 20 2062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072098
X-RAY DIFFRACTIONf_angle_d1.2572837
X-RAY DIFFRACTIONf_dihedral_angle_d18.903812
X-RAY DIFFRACTIONf_chiral_restr0.075323
X-RAY DIFFRACTIONf_plane_restr0.005356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.75140.32931540.24982891X-RAY DIFFRACTION100
2.7514-3.14880.31041380.2292904X-RAY DIFFRACTION100
3.1488-3.96460.27821680.20632928X-RAY DIFFRACTION99
3.9646-24.7910.24321440.18483090X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 8.7394 Å / Origin y: 37.4858 Å / Origin z: 42.2286 Å
111213212223313233
T0.3442 Å20.1387 Å2-0.0705 Å2-0.4586 Å2-0.0619 Å2--0.3106 Å2
L1.3842 °2-0.4881 °2-0.1119 °2-2.1663 °21.2776 °2--2.6897 °2
S-0.1884 Å °-0.4529 Å °0.0752 Å °0.4316 Å °0.1828 Å °0.0011 Å °0.2463 Å °-0.0648 Å °0.0046 Å °
Refinement TLS groupSelection details: all

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