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- PDB-3oap: Crystal structure of human Retinoid X Receptor alpha-ligand bindi... -

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Basic information

Entry
Database: PDB / ID: 3oap
TitleCrystal structure of human Retinoid X Receptor alpha-ligand binding domain complex with 9-cis retinoic acid and the coactivator peptide GRIP-1
Components
  • Nuclear receptor coactivator 2
  • Retinoic acid receptor RXR-alpha
KeywordsTRANSCRIPTION / antiparallel sandwich / ligand binding / coactivator binding / dimerization / activation function
Function / homology
Function and homology information


positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine shuttle / retinoic acid binding / TGFBR3 expression ...positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine shuttle / retinoic acid binding / TGFBR3 expression / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / DNA binding domain binding / nuclear steroid receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain 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 / positive regulation of cholesterol efflux / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / retinoic acid receptor signaling pathway / positive regulation of bone mineralization / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / response to retinoic acid / Recycling of bile acids and salts / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / transcription coregulator binding / response to progesterone / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / peptide binding / SUMOylation of intracellular receptors / 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 / Nuclear Receptor transcription pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / HATs acetylate histones / double-stranded DNA binding / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription regulator complex / transcription coactivator activity / cell differentiation / receptor complex / transcription cis-regulatory region binding / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / 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/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / 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
(9cis)-retinoic acid / Retinoic acid receptor RXR-alpha / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsXia, G. / Smith, C.D. / Muccio, D.D.
CitationJournal: Biochemistry / Year: 2011
Title: Structure, Energetics and Dynamics of Binding Coactivator Peptide to Human Retinoid X Receptor Alpha Ligand Binding Domain Complex with 9-cis-Retinoic Acid.
Authors: Xia, G. / Boerma, L.J. / Cox, B.D. / Qiu, C. / Kang, S. / Smith, C.D. / Renfrow, M.B. / Muccio, D.D.
History
DepositionAug 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Nov 16, 2016Group: Non-polymer description
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Aug 17, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinoic acid receptor RXR-alpha
B: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6033
Polymers27,3032
Non-polymers3001
Water2,594144
1
A: Retinoic acid receptor RXR-alpha
B: Nuclear receptor coactivator 2
hetero molecules

A: Retinoic acid receptor RXR-alpha
B: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2066
Polymers54,6054
Non-polymers6012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Unit cell
Length a, b, c (Å)65.831, 65.831, 111.856
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Retinoic acid receptor RXR-alpha / Retinoid X receptor alpha / Nuclear receptor subfamily 2 group B member 1


Mass: 25897.021 Da / Num. of mol.: 1 / Fragment: hRXRalpha-LBD, UNP residues 228-458
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19793
#2: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Transcriptional intermediary factor 2 / hTIF2 / Class E basic helix-loop-helix protein 75 ...NCoA-2 / Transcriptional intermediary factor 2 / hTIF2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / glucocorticoid receptor interacting protein-1 (GRIP-1)


Mass: 1405.710 Da / Num. of mol.: 1 / Fragment: GRIP-1, UNP residues 686-696 / Source method: obtained synthetically / Source: (synth.) homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-9CR / (9cis)-retinoic acid


Mass: 300.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O2 / Comment: anticancer, antineoplastic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 45.7 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4-20% PEG4000, 4-16% glycerol, 0.1M Bis-Tris, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.5418 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2009
RadiationMonochromator: water cooled Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 20159 / % possible obs: 99.9 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.075 / Χ2: 1.424 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.979.60.65619710.918199.5
1.97-2.0512.90.46919620.9341100
2.05-2.1414.10.31319640.9641100
2.14-2.2514.50.22719741.0031100
2.25-2.3914.50.15719841.0861100
2.39-2.5814.40.12620021.1241100
2.58-2.8414.40.0920081.3171100
2.84-3.2514.30.07120301.6941100
3.25-4.0913.80.05820602.6761100
4.09-5012.90.03922042.286199.6

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Phasing

Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.37-5014.2160.95616
5.05-6.379.7120.947565
4.42-5.0510.2390.955562
4.01-4.429.6510.956555
3.72-4.0110.6220.938540
3.51-3.727.9630.949545
3.33-3.518.7690.92534
3.18-3.337.1280.939541
3.06-3.185.8940.95543
2.96-3.065.6750.921520
2.86-2.966.1930.905522
2.78-2.864.6720.94528
2.71-2.784.9810.944528
2.64-2.714.8680.917498
2.58-2.645.2060.896518
2.53-2.584.5740.907514
2.48-2.533.5720.942523
2.43-2.484.1960.931491
2.39-2.433.0720.959511
2.35-2.393.7690.937509
2.31-2.353.7720.914503
2.27-2.313.2490.951501
2.24-2.273.740.914513
2.21-2.243.6860.898490
2.18-2.213.6780.905503
2.15-2.182.7270.946502
2.12-2.152.8090.924478
2.1-2.123.0530.919509
2.07-2.12.6450.924479
2.05-2.072.3150.935502

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8623 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2436 1532 9.5 %
Rwork0.2038 --
all-16087 -
obs-15643 97.2 %
Solvent computationBsol: 66.6597 Å2
Displacement parametersBiso max: 69.08 Å2 / Biso mean: 30.854 Å2 / Biso min: 14.82 Å2
Baniso -1Baniso -2Baniso -3
1-2.934 Å20 Å20 Å2
2--2.934 Å20 Å2
3----5.868 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 22 144 1955
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.00571.5
X-RAY DIFFRACTIONc_angle_deg1.1352
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.05-2.070.2349450.1955457502
2.07-2.10.2642590.2061420479
2.1-2.120.2548610.2169448509
2.12-2.150.2841500.1981428478
2.15-2.180.2376520.1895450502
2.18-2.210.2989520.2144451503
2.21-2.240.3234400.2147450490
2.24-2.270.2815550.2105458513
2.27-2.310.2224510.1899450501
2.31-2.350.2779480.1984455503
2.35-2.390.2189510.1926458509
2.39-2.430.2005480.182463511
2.43-2.480.2494430.222448491
2.48-2.530.2462570.1893466523
2.53-2.580.2604560.2158458514
2.58-2.640.2843540.2176464518
2.64-2.710.2926470.2067451498
2.71-2.780.2294400.2148488528
2.78-2.860.2546500.1946478528
2.86-2.960.28450.2184477522
2.96-3.060.2823430.2207477520
3.06-3.180.2078540.1988489543
3.18-3.330.2397580.2043483541
3.33-3.510.3123570.2159477534
3.51-3.720.2023460.1844499545
3.72-4.010.2472510.1695489540
4.01-4.420.2006530.1836502555
4.42-5.050.2006490.2002513562
5.05-6.370.2296530.2255512565
6.37-500.2392640.2308552616
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2DRGCNS-1FBY-A.PAR
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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