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- PDB-2p1v: Crystal structure of the ligand binding domain of the retinoid X ... -

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Basic information

Entry
Database: PDB / ID: 2p1v
TitleCrystal structure of the ligand binding domain of the retinoid X receptor alpha in complex with 3-(2'-propoxy)-tetrahydronaphtyl cinnamic acid and a fragment of the coactivator TIF-2
Components
  • Nuclear receptor coactivator 2 peptide
  • Retinoic acid receptor RXR-alpha
KeywordsHORMONE RECEPTOR / protein-ligand complex
Function / homology
Function and homology information


retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / 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 ...retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / 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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / DNA binding domain binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / locomotor rhythm / aryl hydrocarbon receptor binding / nuclear steroid receptor activity / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / positive regulation of bone mineralization / cellular response to hormone stimulus / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / transcription regulator inhibitor activity / retinoic acid receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / hormone-mediated signaling pathway / : / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / peptide binding / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / nuclear receptor binding / transcription coregulator binding / negative regulation of smoothened signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear receptor activity / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / : / nervous system development / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / double-stranded DNA binding / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription coactivator activity / receptor complex / transcription cis-regulatory region binding / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
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 / Nuclear receptor coactivators bHLH domain / 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 / Double treble clef zinc finger, C4 type / 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-5TN / Retinoic acid receptor RXR-alpha / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBourguet, W. / Nahoum, V.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Modulators of the structural dynamics of the retinoid X receptor to reveal receptor function.
Authors: Nahoum, V. / Perez, E. / Germain, P. / Rodriguez-Barrios, F. / Manzo, F. / Kammerer, S. / Lemaire, G. / Hirsch, O. / Royer, C.A. / Gronemeyer, H. / de Lera, A.R. / Bourguet, W.
History
DepositionMar 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,8443
Polymers28,4362
Non-polymers4091
Water1,33374
1
A: Retinoic acid receptor RXR-alpha
B: Nuclear receptor coactivator 2 peptide
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)57,6896
Polymers56,8724
Non-polymers8172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)64.148, 64.148, 113.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a homodimer generated from the monomer in the asymmetric unit by the transformation matrix: 0.0 -1.0 0.0 -1.0 0.0 0.0 0.0 0.0 -1.0 0.0 0.0 0.5

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Components

#1: Protein Retinoic acid receptor RXR-alpha / Retinoid X receptor alpha


Mass: 26856.039 Da / Num. of mol.: 1 / Fragment: ligand binding domain (residues 223-462)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19793
#2: Protein/peptide Nuclear receptor coactivator 2 peptide / NCoA-2 / Transcriptional intermediary factor 2


Mass: 1579.866 Da / Num. of mol.: 1
Fragment: nuclear receptor interaction motif 2 (residues 686-698)
Source method: obtained synthetically
Details: This sequence occurs naturally in humans. The peptide has been synthesized by automatic chemical synthesis.
References: UniProt: Q15596
#3: Chemical ChemComp-5TN / (2E)-3-[4-HYDROXY-3-(5,5,8,8-TETRAMETHYL-3-PROPOXY-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)PHENYL]ACRYLIC ACID


Mass: 408.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H32O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.05 Å3/Da / Density % sol: 39.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 24% PEG 4000, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.975
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2006 / Details: Toroidal mirror
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.2→35.4 Å / Num. all: 12643 / Num. obs: 11503 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Biso Wilson estimate: 32.18 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 5.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 2.9 / Num. measured all: 16418 / Num. unique all: 1549 / Rsym value: 0.235 / % possible all: 87.1

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
DNAdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1mvc

1mvc


Resolution: 2.2→35.4 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.922 / SU B: 11.235 / SU ML: 0.135 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.329 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 561 4.9 %RANDOM
Rwork0.196 ---
all0.198 11502 --
obs0.198 11502 90.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.102 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 30 74 1855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221817
X-RAY DIFFRACTIONr_angle_refined_deg1.1992.0042459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4445218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63523.50677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42815327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8971513
X-RAY DIFFRACTIONr_chiral_restr0.0810.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021334
X-RAY DIFFRACTIONr_nbd_refined0.1940.2835
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21258
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0370.24
X-RAY DIFFRACTIONr_mcbond_it0.5351.51142
X-RAY DIFFRACTIONr_mcangle_it0.91621774
X-RAY DIFFRACTIONr_scbond_it1.3923767
X-RAY DIFFRACTIONr_scangle_it2.1524.5685
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 46 -
Rwork0.18 741 -
obs-787 86.39 %

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