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- PDB-4oni: Structure of Human Orphan Receptor LRH1 bound to two bacterial ph... -

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Basic information

Entry
Database: PDB / ID: 4oni
TitleStructure of Human Orphan Receptor LRH1 bound to two bacterial phospholipids
Components(Nuclear receptor subfamily ...) x 2
KeywordsNUCLEAR PROTEIN / alpha helical sandwich fold / Nuclear receptor / Co-factor binding
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 / bile acid and bile salt transport / transcription regulator inhibitor activity / peroxisome proliferator activated receptor binding / embryo development ending in birth or egg hatching ...Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / bile acid and bile salt transport / transcription regulator inhibitor activity / peroxisome proliferator activated receptor binding / embryo development ending in birth or egg hatching / nuclear thyroid hormone receptor binding / homeostatic process / animal organ regeneration / positive regulation of viral genome replication / response to glucose / nuclear retinoid X receptor binding / Notch signaling pathway / hormone-mediated signaling pathway / cholesterol metabolic process / cellular response to leukemia inhibitory factor / cholesterol homeostasis / transcription coregulator binding / phospholipid binding / circadian regulation of gene expression / SUMOylation of intracellular receptors / positive regulation of insulin secretion / negative regulation of DNA-binding transcription factor activity / response to organic cyclic compound / Nuclear Receptor transcription pathway / circadian rhythm / RNA polymerase II transcription regulator complex / transcription corepressor activity / nuclear receptor activity / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / 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 / protein domain specific binding / negative regulation of gene expression / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / chromatin / protein-containing complex binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear receptor subfamily 0 group B member 1/2 / 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 receptor subfamily 0 group B member 1/2 / 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
Chem-EPH / Chem-P6L / Nuclear receptor subfamily 5 group A member 2 / Nuclear receptor subfamily 0 group B member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsGorman, M.A. / Parker, M.W. / Kusumo, S.
CitationJournal: To be Published
Title: Human nuclear receptor LRH1 bound to phosopholipids and SHP peptide
Authors: Gorman, M.A. / Parker, M.W. / Kusumo, S.
History
DepositionJan 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor subfamily 5 group A member 2
C: Nuclear receptor subfamily 0 group B member 2
B: Nuclear receptor subfamily 5 group A member 2
D: Nuclear receptor subfamily 0 group B member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,21710
Polymers62,2904
Non-polymers1,9276
Water6,341352
1
A: Nuclear receptor subfamily 5 group A member 2
C: Nuclear receptor subfamily 0 group B member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1316
Polymers31,1452
Non-polymers9864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-21 kcal/mol
Surface area12950 Å2
MethodPISA
2
B: Nuclear receptor subfamily 5 group A member 2
D: Nuclear receptor subfamily 0 group B member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0864
Polymers31,1452
Non-polymers9412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-25 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.867, 59.856, 73.940
Angle α, β, γ (deg.)90.000, 93.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Nuclear receptor subfamily ... , 2 types, 4 molecules ABCD

#1: Protein Nuclear receptor subfamily 5 group A member 2 / Orphan nuclear receptor NR5A2 / Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F ...Orphan nuclear receptor NR5A2 / Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor / Hepatocytic transcription factor / Liver receptor homolog 1 / LRH-1


Mass: 29196.541 Da / Num. of mol.: 2 / Fragment: Ligand Binding Domain, UNP residues 291-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR5A2 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Star Rosetta / References: UniProt: O00482
#2: Protein/peptide Nuclear receptor subfamily 0 group B member 2 / Nuclear receptor NR0B2 / Orphan nuclear receptor SHP / Small heterodimer partner


Mass: 1948.269 Da / Num. of mol.: 2 / Fragment: NR Box1, UNP residues 12-30 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15466

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Non-polymers , 5 types, 358 molecules

#3: Chemical ChemComp-EPH / L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 709.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H68NO8P / Comment: phospholipid*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-P6L / (2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL (8E)-OCTADEC-8-ENOATE


Mass: 746.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H75O10P / Comment: phospholipid*YM
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.26 Å3/Da / Density % sol: 45.67 % / Mosaicity: 0.16 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 20-30% PEG 3350, Bis Tris, 5% glycerol, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.96 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.8→73.772 Å / Num. all: 49141 / Num. obs: 49141 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rsym value: 0.119 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.95.10.8920.7970.92757554520.3930.8920.7972.472.4
1.9-2.0160.5780.5271.33940665250.2330.5780.5273.992.1
2.01-2.157.50.360.3352.15002766990.1310.360.3356.8100
2.15-2.327.50.2320.2163.34664862350.0850.2320.2169.9100
2.32-2.557.50.1730.1614.54312157560.0630.1730.16112.3100
2.55-2.857.50.1240.1156.33894051980.0450.1240.11515.6100
2.85-3.297.50.0910.0858.43457346180.0330.0910.08520.2100
3.29-4.027.50.0710.0669.92907439020.0260.0710.06628.499.9
4.02-5.697.30.0570.05311.72215830390.0210.0570.05331.2100
5.69-46.4817.30.0420.03912.81254517170.0150.0420.03930.899.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-IceIcedata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YUC

1yuc


Resolution: 1.8→43.67 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.1894 / WRfactor Rwork: 0.1458 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8936 / SU B: 2.416 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1211 / SU Rfree: 0.1208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2023 2487 5.1 %RANDOM
Rwork0.1558 ---
all0.1581 49124 --
obs0.1581 49124 94.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.13 Å2 / Biso mean: 19.7988 Å2 / Biso min: 5.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.16 Å2
2---0.28 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 131 352 4591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194523
X-RAY DIFFRACTIONr_bond_other_d0.0010.024462
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.9916112
X-RAY DIFFRACTIONr_angle_other_deg0.916310295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3285555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.90225.359209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25315826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5441518
X-RAY DIFFRACTIONr_chiral_restr0.1170.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025123
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021039
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 135 -
Rwork0.247 2439 -
all-2574 -
obs--67.61 %

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