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- PDB-4zo1: Crystal Structure of the T3-bound TR-beta Ligand-binding Domain i... -

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Basic information

Entry
Database: PDB / ID: 4zo1
TitleCrystal Structure of the T3-bound TR-beta Ligand-binding Domain in complex with RXR-alpha
Components
  • Nuclear receptor coactivator 2
  • Retinoic acid receptor RXR-alpha
  • Thyroid hormone receptor beta
KeywordsPROTEIN BINDING / Nuclear receptor / transcription factor / ligand binding / protein-ligand complex
Function / homology
Function and homology information


retinal cone cell apoptotic process / negative regulation of female receptivity / female courtship behavior / retinal cone cell development / thyroid hormone mediated signaling pathway / 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 ...retinal cone cell apoptotic process / negative regulation of female receptivity / female courtship behavior / retinal cone cell development / thyroid hormone mediated signaling pathway / 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 mediated signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / anatomical structure development / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex / retinoic acid binding / cellular response to thyroid hormone stimulus / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / regulation of heart contraction / Signaling by Retinoic Acid / DNA binding domain binding / nuclear steroid receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / type I pneumocyte differentiation / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / thyroid hormone binding / locomotor rhythm / aryl hydrocarbon receptor binding / positive regulation of cholesterol efflux / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / retinoic acid receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of bone mineralization / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / response to progesterone / transcription coregulator binding / nuclear receptor binding / sensory perception of sound / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / circadian regulation of gene expression / 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 / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / HATs acetylate histones / double-stranded DNA binding / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / cell differentiation / transcription coactivator activity / protein dimerization activity / nuclear body / receptor complex / 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 / DNA-templated transcription / chromatin binding / chromatin / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II
Similarity search - Function
Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Thyroid hormone receptor / 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 / Thyroid hormone receptor / 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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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
3,5,3'TRIIODOTHYRONINE / Thyroid hormone receptor beta / Retinoic acid receptor RXR-alpha / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.221 Å
AuthorsBruning, J.B. / Kojetin, D.J. / Matta-Camacho, E. / Hughes, T.S. / Srinivasan, S. / Nwachukwu, J.C. / Cavett, V. / Nowak, J. / Chalmers, M.J. / Marciano, D.P. ...Bruning, J.B. / Kojetin, D.J. / Matta-Camacho, E. / Hughes, T.S. / Srinivasan, S. / Nwachukwu, J.C. / Cavett, V. / Nowak, J. / Chalmers, M.J. / Marciano, D.P. / Kamenecka, T.M. / Rance, M. / Shulman, A.I. / Mangelsdorf, D.J. / Griffin, P.R. / Nettles, K.W.
CitationJournal: Nat Commun / Year: 2015
Title: Structural mechanism for signal transduction in RXR nuclear receptor heterodimers.
Authors: Kojetin, D.J. / Matta-Camacho, E. / Hughes, T.S. / Srinivasan, S. / Nwachukwu, J.C. / Cavett, V. / Nowak, J. / Chalmers, M.J. / Marciano, D.P. / Kamenecka, T.M. / Shulman, A.I. / Rance, M. / ...Authors: Kojetin, D.J. / Matta-Camacho, E. / Hughes, T.S. / Srinivasan, S. / Nwachukwu, J.C. / Cavett, V. / Nowak, J. / Chalmers, M.J. / Marciano, D.P. / Kamenecka, T.M. / Shulman, A.I. / Rance, M. / Griffin, P.R. / Bruning, J.B. / Nettles, K.W.
History
DepositionMay 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,5634
Polymers54,9123
Non-polymers6511
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-19 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.252, 63.252, 225.806
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Thyroid hormone receptor beta / / Nuclear receptor subfamily 1 group A member 2 / c-erbA-2 / c-erbA-beta


Mass: 28525.033 Da / Num. of mol.: 1 / Fragment: ligand binding domain unp residues 210-461
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THRB, ERBA2, NR1A2, THR1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10828
#2: Protein/peptide Nuclear receptor coactivator 2 / / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1162.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596*PLUS
#3: Protein Retinoic acid receptor RXR-alpha / Nuclear receptor subfamily 2 group B member 1 / Retinoid X receptor alpha


Mass: 25224.316 Da / Num. of mol.: 1 / Fragment: ligand binding domain, unp residues 231-455 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P19793
#4: Chemical ChemComp-T3 / 3,5,3'TRIIODOTHYRONINE / T3 / THYROID HORMONE / LIOTHYRONINE / Triiodothyronine


Mass: 650.973 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12I3NO4 / Comment: hormone*YM

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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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 3350, 100 mM Tris pH 8.0, 0.1 M ammonium acetate, and 1 mM Methoprene acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2007
RadiationMonochromator: Side scattering bent cube i-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 8950 / % possible obs: 96.3 % / Redundancy: 11.1 % / Biso Wilson estimate: 93.2 Å2 / Rmerge(I) obs: 0.09 / Χ2: 1.793 / Net I/av σ(I): 31.121 / Net I/σ(I): 10.5 / Num. measured all: 99578
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
3.2-3.314.97981.17386.8
3.31-3.456.78001.30390.80.74
3.45-3.68.28751.36998.10.591
3.6-3.799.88981.40698.10.397
3.79-4.0312.48931.39798.70.382
4.03-4.34149061.49798.70.247
4.34-4.7814.29121.6299.20.15
4.78-5.4713.99291.82999.10.126
5.47-6.8913.59552.27999.10.104
6.89-5011.89843.04294.60.042

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.6_289refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.221→14.925 Å / FOM work R set: 0.771 / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2813 367 5.36 %
Rwork0.2364 6477 -
obs0.2386 6844 76.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.569 Å2 / ksol: 0.232 e/Å3
Displacement parametersBiso max: 348.81 Å2 / Biso mean: 133.27 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--10.4514 Å20 Å2-0 Å2
2---10.4514 Å20 Å2
3----6.2822 Å2
Refinement stepCycle: final / Resolution: 3.221→14.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 23 0 3244
Biso mean--96.13 --
Num. residues----449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043313
X-RAY DIFFRACTIONf_angle_d0.6484523
X-RAY DIFFRACTIONf_chiral_restr0.039537
X-RAY DIFFRACTIONf_plane_restr0.002585
X-RAY DIFFRACTIONf_dihedral_angle_d10.4441098
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2212-3.68120.354520.332280385529
3.6812-4.61510.28531550.27042751290699
4.6151-14.92470.26591600.20642923308399

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