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- PDB-4is8: Divergent sequence tunes ligand sensitivity in phospholipid-regul... -

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Basic information

Entry
Database: PDB / ID: 4is8
TitleDivergent sequence tunes ligand sensitivity in phospholipid-regulated hormone receptors
ComponentsNuclear receptor subfamily 5 group A member 2
KeywordsTRANSCRIPTION / LIGAND BINDING DOMAIN
Function / homology
Function and homology information


Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / embryo development ending in birth or egg hatching / homeostatic process / positive regulation of viral genome replication / hormone-mediated signaling pathway ...Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / embryo development ending in birth or egg hatching / homeostatic process / positive regulation of viral genome replication / hormone-mediated signaling pathway / cellular response to leukemia inhibitory factor / transcription coregulator binding / cholesterol homeostasis / SUMOylation of intracellular receptors / phospholipid binding / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear hormone receptor family 5 / 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 family 5 / 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
Nuclear receptor subfamily 5 group A member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsMusille, P.M. / Pathak, M.C. / Ortlund, E.A.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Divergent Sequence Tunes Ligand Sensitivity in Phospholipid-regulated Hormone Receptors.
Authors: Musille, P.M. / Pathak, M. / Lauer, J.L. / Griffin, P.R. / Ortlund, E.A.
History
DepositionJan 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Jul 31, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor subfamily 5 group A member 2
B: Nuclear receptor subfamily 5 group A member 2


Theoretical massNumber of molelcules
Total (without water)55,6902
Polymers55,6902
Non-polymers00
Water724
1
A: Nuclear receptor subfamily 5 group A member 2


Theoretical massNumber of molelcules
Total (without water)27,8451
Polymers27,8451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nuclear receptor subfamily 5 group A member 2


Theoretical massNumber of molelcules
Total (without water)27,8451
Polymers27,8451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.305, 120.029, 123.838
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nuclear receptor subfamily 5 group A member 2 / Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor ...Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor / Hepatocytic transcription factor / Liver receptor homolog 1 / LRH-1


Mass: 27845.133 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN / Mutation: Q419H,A420T,G421E,A422V,T423A,L424F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B1F, CPF, FTF, NR5A2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00482
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsHUMAN LRH1 (UNP O00482) LBD RESIDUES 419-424 (QAGATL) REPLACED BY MOUSE LRH1 (UNP P45448) LBD ...HUMAN LRH1 (UNP O00482) LBD RESIDUES 419-424 (QAGATL) REPLACED BY MOUSE LRH1 (UNP P45448) LBD RESIDUES 438-443 (HTEVAF)

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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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 9.5%-15% PEG3350, 5% GLYCEROL, 50 MM BIS-TRIS, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 14223 / Redundancy: 4.4 % / Net I/σ(I): 11.8

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Processing

Software
NameClassification
SERGUIdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→30 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.923 / SU B: 13.466 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1383 10.1 %RANDOM
Rwork0.224 ---
obs0.225 12337 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.49 Å2
Baniso -1Baniso -2Baniso -3
1-16.41 Å20 Å20 Å2
2---20.76 Å20 Å2
3---4.36 Å2
Refinement stepCycle: LAST / Resolution: 2.78→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3748 0 0 4 3752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223816
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9685152
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5785454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.77225.426188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.40115716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.531514
X-RAY DIFFRACTIONr_chiral_restr0.0640.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212826
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.2511.52294
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.44723702
X-RAY DIFFRACTIONr_scbond_it0.06431522
X-RAY DIFFRACTIONr_scangle_it0.1164.51450
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.78→2.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 82 -
Rwork0.252 678 -
obs--73.57 %

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