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- PDB-2abi: Crystal structure of the human mineralocorticoid receptor ligand-... -

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Basic information

Entry
Database: PDB / ID: 2abi
TitleCrystal structure of the human mineralocorticoid receptor ligand-binding domain bound to deoxycorticosterone
ComponentsMineralocorticoid receptor
KeywordsTRANSCRIPTION REGULATOR / MINERALOCORTICOID RECEPTOR / STEROID RECEPTO / NUCLEAR RECEPT / TRANSCRIPTION REGULATION / ACTIVATING MUTATION / HYPERTENSION
Function / homology
Function and homology information


nuclear steroid receptor activity / estrogen response element binding / intracellular steroid hormone receptor signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / TBP-class protein binding / steroid binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / positive regulation of non-canonical NF-kappaB signal transduction / nuclear receptor activity ...nuclear steroid receptor activity / estrogen response element binding / intracellular steroid hormone receptor signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / TBP-class protein binding / steroid binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / positive regulation of non-canonical NF-kappaB signal transduction / nuclear receptor activity / sequence-specific double-stranded DNA binding / receptor complex / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / chromatin / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / signal transduction / zinc ion binding / nucleoplasm / cytosol
Similarity search - Function
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 ...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
DESOXYCORTICOSTERONE / Mineralocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsHuyet, J. / Pinon, G.-M. / Rochel, M. / Mayer, C. / Rafestin-Oblin, M.-E. / Fagart, J.
CitationJournal: To be published
Title: Crystal structure of the human mineralocorticoid receptor ligand-binding domain bound to deoxycorticosterone
Authors: Huyet, J. / Pinon, G.-M. / Rochel, M. / Mayer, C. / Rafestin-Oblin, M.-E. / Fagart, J.
History
DepositionJul 15, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 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 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mineralocorticoid receptor
B: Mineralocorticoid receptor
C: Mineralocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0176
Polymers89,0263
Non-polymers9913
Water6,864381
1
A: Mineralocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0062
Polymers29,6751
Non-polymers3301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mineralocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0062
Polymers29,6751
Non-polymers3301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mineralocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0062
Polymers29,6751
Non-polymers3301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.770, 119.770, 41.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Mineralocorticoid receptor / / MR


Mass: 29675.332 Da / Num. of mol.: 3 / Fragment: LIGAND-BINDING DOMAIN / Mutation: C910A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: UV20HL21-27 / Gene: NR3C2, MCR, MLR / Plasmid: PGEX / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON PLUS (DE3) RIL / References: UniProt: P08235
#2: Chemical ChemComp-1CA / DESOXYCORTICOSTERONE / 4-PREGNEN-21-OL-3,20-DIONE / DOC / 21-HYDROXYPROGESTERONE / 11-Deoxycorticosterone


Mass: 330.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30O3 / Comment: hormone*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.02 Å3/Da / Density % sol: 19.9 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: PEG4000, HEPES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 69 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97987 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 8, 2004 / Details: MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97987 Å / Relative weight: 1
ReflectionResolution: 2.33→39.2 Å / Num. all: 28454 / Num. obs: 27439 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.192 % / Rmerge(I) obs: 0.147 / Rsym value: 0.08 / Net I/σ(I): 10.52
Reflection shellResolution: 1.96→2.07 Å / Redundancy: 2.03 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 1.7 / Num. unique all: 3846 / Rsym value: 0.636 / % possible all: 86.4

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
BEASTmodel building
CNS1.1refinement
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1Y9R

1y9r


Resolution: 2.33→39.2 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 385944.39 / 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
Rfree0.2639 2519 10.1 %RANDOM
Rwork0.2074 ---
all0.228 28659 --
obs0.2074 24920 87.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 77.5321 Å2 / ksol: 0.361975 e/Å3
Displacement parametersBiso mean: 44.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.45 Å22.29 Å20 Å2
2---2.45 Å20 Å2
3---4.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.33→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5622 0 72 381 6075
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.792
X-RAY DIFFRACTIONc_scbond_it1.582
X-RAY DIFFRACTIONc_scangle_it2.352.5
LS refinement shellResolution: 2.33→2.48 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 394 9.7 %
Rwork0.367 3664 -
obs--85.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ligand.paramligand.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top

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