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- PDB-4uda: MR in complex with dexamethasone -

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Basic information

Entry
Database: PDB / ID: 4uda
TitleMR in complex with dexamethasone
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 / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / hypothalamus development / nuclear steroid receptor activity / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / estrous cycle / cellular response to Thyroglobulin triiodothyronine ...labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / hypothalamus development / nuclear steroid receptor activity / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / estrous cycle / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / Endogenous sterols / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / intracellular steroid hormone receptor signaling pathway / response to retinoic acid / histone acetyltransferase activity / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / histone acetyltransferase / cellular response to hormone stimulus / positive regulation of adipose tissue development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / RORA activates gene expression / TBP-class protein binding / lactation / Regulation of lipid metabolism by PPARalpha / steroid binding / cerebellum development / 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 / nuclear estrogen receptor binding / nuclear receptor binding / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / positive regulation of non-canonical NF-kappaB signal transduction / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / response to estradiol / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / transcription coactivator activity / protein dimerization activity / receptor complex / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / DNA-binding transcription factor activity / chromatin binding / chromatin / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / 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 / Steroid 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 / 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 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
DEXAMETHASONE / Mineralocorticoid receptor / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsEdman, K. / Hogner, A. / Hussein, A. / Bjursell, M. / Aagaard, A. / Backstrom, S. / Bodin, C. / Wissler, L. / Jellesmark-Jensen, T. / Cavallin, A. ...Edman, K. / Hogner, A. / Hussein, A. / Bjursell, M. / Aagaard, A. / Backstrom, S. / Bodin, C. / Wissler, L. / Jellesmark-Jensen, T. / Cavallin, A. / Karlsson, U. / Nilsson, E. / Lecina, D. / Takahashi, R. / Grebner, C. / 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 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 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)31,3704
Polymers30,8862
Non-polymers4852
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-11.8 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.000, 81.400, 45.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 29159.680 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DEX / DEXAMETHASONE / 9A-FLUORO-16BETA-METHYLPREDNISOLONE / Dexamethasone


Mass: 392.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H29FO5 / Comment: medication, antibiotic*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.29 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 7.5 / Details: 30% PEG4000, 0.1M NACL, 0.2M PIPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54
DetectorType: RIGAKU R-AXIS HTC / Date: Nov 4, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.03→40.7 Å / Num. obs: 15085 / % possible obs: 83.9 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 27.44 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.9
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.3 / % possible all: 83.7

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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: 2.03→40.7 Å / Cor.coef. Fo:Fc: 0.9306 / Cor.coef. Fo:Fc free: 0.8687 / SU R Cruickshank DPI: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.248 / SU Rfree Blow DPI: 0.199 / SU Rfree Cruickshank DPI: 0.198
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2401 762 5.05 %RANDOM
Rwork0.1847 ---
obs0.1872 15085 83.73 %-
Displacement parametersBiso mean: 30.86 Å2
Baniso -1Baniso -2Baniso -3
1--5.771 Å20 Å20 Å2
2--9.4843 Å20 Å2
3----3.7134 Å2
Refine analyzeLuzzati coordinate error obs: 0.238 Å
Refinement stepCycle: LAST / Resolution: 2.03→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 34 101 2204
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012163HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.012929HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d763SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes299HARMONIC5
X-RAY DIFFRACTIONt_it2163HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.48
X-RAY DIFFRACTIONt_other_torsion17.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion277SEMIHARMONIC5
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_contact2643SEMIHARMONIC4
LS refinement shellResolution: 2.03→2.17 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.266 87 4.81 %
Rwork0.2098 1721 -
all0.2125 1808 -
obs--83.73 %

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