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- PDB-4udb: MR in complex with desisobutyrylciclesonide -

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Basic information

Entry
Database: PDB / ID: 4udb
TitleMR in complex with desisobutyrylciclesonide
Components
  • MINERALOCORTICOID RECEPTOR
  • NUCLEAR RECEPTOR COACTIVATOR 1
KeywordsSIGNALING PROTEIN / NUCLEAR HORMONE RECEPTOR / LIGAND COMPLEX / PEPTIDE COMPLEX
Function / homology
Function and homology information


labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / male mating behavior / hypothalamus development / nuclear steroid receptor activity / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts ...labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / male mating behavior / hypothalamus development / nuclear steroid receptor activity / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / progesterone receptor signaling pathway / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / response to retinoic acid / estrous cycle / nuclear retinoid X receptor binding / histone acetyltransferase activity / cellular response to hormone stimulus / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone acetyltransferase / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / estrogen receptor signaling pathway / lactation / steroid binding / : / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / TBP-class protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cerebellum development / nuclear estrogen receptor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Heme signaling / positive regulation of non-canonical NF-kappaB signal transduction / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / sequence-specific double-stranded DNA binding / : / response to estradiol / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / receptor complex / protein dimerization activity / positive regulation of apoptotic process / DNA-binding transcription factor activity / chromatin binding / regulation of transcription by RNA polymerase II / endoplasmic reticulum membrane / chromatin / positive regulation of DNA-templated transcription / protein-containing complex binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Nuclear receptor coactivator 1 / 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 / : ...Nuclear receptor coactivator 1 / 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 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
DESISOBUYTYRYL CICLESONIDE / Mineralocorticoid receptor / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsEdman, K. / Hogner, A. / Hussein, A. / Aagaard, A. / Backstrom, S. / Bodin, C. / Wissler, L. / JellesmarkJensen, T. / Cavallin, A. / Nilsson, E. ...Edman, K. / Hogner, A. / Hussein, A. / Aagaard, A. / Backstrom, S. / Bodin, C. / Wissler, L. / JellesmarkJensen, T. / Cavallin, A. / Nilsson, E. / Lepisto, M. / Guallar, V.
CitationJournal: Structure / Year: 2015
Title: Ligand Binding Mechanism in Steroid Receptors: From Conserved Plasticity to Differential Evolutionary Constraints.
Authors: Edman, K. / Hosseini, A. / Bjursell, M.K. / Aagaard, A. / Wissler, L. / Gunnarsson, A. / Kaminski, T. / Kohler, C. / Backstrom, S. / Jensen, T.J. / Cavallin, A. / Karlsson, U. / Nilsson, E. ...Authors: Edman, K. / Hosseini, A. / Bjursell, M.K. / Aagaard, A. / Wissler, L. / Gunnarsson, A. / Kaminski, T. / Kohler, C. / Backstrom, S. / Jensen, T.J. / Cavallin, A. / Karlsson, U. / Nilsson, E. / Lecina, D. / Takahashi, R. / Grebner, C. / Geschwindner, S. / Lepisto, M. / Hogner, A.C. / Guallar, V.
History
DepositionDec 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: MINERALOCORTICOID RECEPTOR
B: NUCLEAR RECEPTOR COACTIVATOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2026
Polymers33,4652
Non-polymers7374
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-25.8 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.919, 75.919, 116.996
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein MINERALOCORTICOID RECEPTOR / MR / NUCLEAR RECEPTOR SUBFAMILY 3 GROUP C MEMBER 2


Mass: 31739.393 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 735-984 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P08235
#2: Protein/peptide NUCLEAR RECEPTOR COACTIVATOR 1 / NCOA-1 / CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 74 / BHLHE74 / PROTEIN HIN-2 / RIP160 / RENAL ...NCOA-1 / CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 74 / BHLHE74 / PROTEIN HIN-2 / RIP160 / RENAL CARCINOMA ANTIGEN NY-REN-52 / STEROID RECEPTOR COACTIVATOR 1 / SRC-1 / NCOA1 PEPTIDE


Mass: 1725.958 Da / Num. of mol.: 1 / Fragment: RESIDUES 1427-1441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q15788, histone acetyltransferase

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Non-polymers , 5 types, 64 molecules

#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CV7 / DESISOBUYTYRYL CICLESONIDE


Mass: 470.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H38O6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.83 Å3/Da / Density % sol: 56.5 % / Description: NONE
Crystal growpH: 8.5
Details: 18% PEG4K, 0.14M LISO4, 85MM TRIS PH 8.5, 15% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.977
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.36→50 Å / Num. obs: 14723 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.6 % / Biso Wilson estimate: 52.01 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.1
Reflection shellResolution: 2.36→2.44 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AA2

2aa2


Resolution: 2.36→48.79 Å / Cor.coef. Fo:Fc: 0.9494 / Cor.coef. Fo:Fc free: 0.9399 / SU R Cruickshank DPI: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.28 / SU Rfree Blow DPI: 0.202 / SU Rfree Cruickshank DPI: 0.2
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 739 5.04 %RANDOM
Rwork0.1819 ---
obs0.1837 14672 99.98 %-
Displacement parametersBiso mean: 53.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.4451 Å20 Å20 Å2
2--0.4451 Å20 Å2
3----0.8902 Å2
Refine analyzeLuzzati coordinate error obs: 0.244 Å
Refinement stepCycle: LAST / Resolution: 2.36→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2103 0 49 60 2212
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012218HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.043007HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d776SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes304HARMONIC5
X-RAY DIFFRACTIONt_it2218HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion17.16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion283SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2609SEMIHARMONIC4
LS refinement shellResolution: 2.36→2.55 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2446 146 4.96 %
Rwork0.2017 2800 -
all0.2038 2946 -
obs--99.98 %

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