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- PDB-2a3i: Structural and Biochemical Mechanisms for the Specificity of Horm... -

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Basic information

Entry
Database: PDB / ID: 2a3i
TitleStructural and Biochemical Mechanisms for the Specificity of Hormone Binding and Coactivator Assembly by Mineralocorticoid Receptor
Components
  • Mineralocorticoid receptor
  • Nuclear receptor coactivator 1, residues 1430-1441
KeywordsTRANSFERASE / transcription factor
Function / homology
Function and homology information


labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / male mating behavior / hypothalamus development / nuclear steroid receptor activity / progesterone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine ...labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / male mating behavior / hypothalamus development / nuclear steroid receptor activity / progesterone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / nuclear receptor-mediated steroid hormone 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 / response to retinoic acid / protein-lysine-acetyltransferase activity / estrous cycle / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Recycling of bile acids and salts / histone acetyltransferase / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cellular response to hormone stimulus / estrogen receptor signaling pathway / steroid binding / Regulation of lipid metabolism by PPARalpha / lactation / peroxisome proliferator activated receptor signaling pathway / response to progesterone / positive regulation of adipose tissue development / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / positive regulation of neuron differentiation / SUMOylation of transcription cofactors / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Activation of gene expression by SREBF (SREBP) / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / TBP-class protein binding / cerebellum development / nuclear estrogen receptor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / hippocampus development / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / Nuclear Receptor transcription pathway / positive regulation of non-canonical NF-kappaB signal transduction / Transcriptional regulation of white adipocyte differentiation / cerebral cortex development / mRNA transcription by RNA polymerase II / male gonad development / nuclear receptor activity / RNA polymerase II transcription regulator complex / 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 / signaling 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 / positive regulation of DNA-templated transcription / chromatin / 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
CORTICOSTERONE / Mineralocorticoid receptor / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLi, Y. / Suino, K. / Daugherty, J. / Xu, H.E.
CitationJournal: Mol.Cell / Year: 2005
Title: Structural and biochemical mechanisms for the specificity of hormone binding and coactivator assembly by mineralocorticoid receptor
Authors: Li, Y. / Suino, K. / Daugherty, J. / Xu, H.E.
History
DepositionJun 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mineralocorticoid receptor
B: Nuclear receptor coactivator 1, residues 1430-1441
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2363
Polymers30,8902
Non-polymers3461
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-7 kcal/mol
Surface area12530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.647, 72.259, 81.226
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


Mass: 29460.119 Da / Num. of mol.: 1 / Fragment: Mineralocoricoid receptor / Mutation: C808S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C2, MCR, MLR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08235
#2: Protein/peptide Nuclear receptor coactivator 1, residues 1430-1441 / NCoA-1 / Steroid receptor coactivator-1 / SRC-1 / RIP160 / Hin-2 protein


Mass: 1429.637 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Homo sapiens (humans).
References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-C0R / CORTICOSTERONE / (11-BETA)-11,21-DIHYDROXY-PREGN-4-ENE-3,20-DIONE


Mass: 346.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.2 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.9
Details: PEG mme5K, Sodium Acetate, 1-6 Hexanediol, pH 7.9, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.99998 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 20, 2004
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 20111 / Num. obs: 19665 / % possible obs: 99.5 % / Observed criterion σ(F): 32 / Observed criterion σ(I): 11165 / Biso Wilson estimate: 21.2 Å2
Reflection shellResolution: 1.95→2.02 Å / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→50 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1612758.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1540 7.8 %RANDOM
Rwork0.222 ---
all0.222 20111 --
obs0.222 19661 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.8584 Å2 / ksol: 0.372723 e/Å3
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1-12.07 Å20 Å20 Å2
2--2.41 Å20 Å2
3----14.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-6 Å
Luzzati sigma a0.24 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 0 25 160 2349
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 239 7.6 %
Rwork0.308 2903 -
obs--97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3cor.parcor.top

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