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- PDB-4tnt: Structure of the human mineralocorticoid receptor in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 4tnt
TitleStructure of the human mineralocorticoid receptor in complex with DNA
Components
  • DNA (5'-D(*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3')
  • DNA (5'-D(*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3')
  • Mineralocorticoid receptor
KeywordsDNA Binding Protein/DNA / DNA binding protein / DNA Binding Protein-DNA complex
Function / homology
Function and homology information


nuclear steroid receptor activity / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / TBP-class protein 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 / nuclear receptor-mediated steroid hormone signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / TBP-class protein 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 / endoplasmic reticulum membrane / chromatin / regulation of transcription by RNA polymerase II / signal transduction / zinc ion binding / nucleoplasm / cytosol
Similarity search - Function
Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / : / 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 ...Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / : / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Mineralocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3938 Å
AuthorsHudson, W.H. / Ortlund, E.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK095750 United States
American Heart Association13PRE16920012 United States
CitationJournal: Plos One / Year: 2014
Title: Crystal structure of the mineralocorticoid receptor DNA binding domain in complex with DNA.
Authors: Hudson, W.H. / Youn, C. / Ortlund, E.A.
History
DepositionJun 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mineralocorticoid receptor
B: Mineralocorticoid receptor
C: DNA (5'-D(*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3')
D: DNA (5'-D(*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2478
Polymers32,9864
Non-polymers2624
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-30 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.090, 115.136, 81.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Mineralocorticoid receptor / MR / Nuclear receptor subfamily 3 group C member 2


Mass: 11285.915 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C2, MCR, MLR / Plasmid: pMCSG7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P08235
#2: DNA chain DNA (5'-D(*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3')


Mass: 5162.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3')


Mass: 5251.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium malonate, 12 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 14459 / % possible obs: 90.4 % / Redundancy: 5.6 % / Biso Wilson estimate: 68.85 Å2 / Rmerge(I) obs: 0.084 / Χ2: 2.009 / Net I/av σ(I): 27.919 / Net I/σ(I): 17.5 / Num. measured all: 80946
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.383.10.4389481.72360.1
2.38-2.483.30.38611041.57570.3
2.48-2.593.70.41212871.42482.6
2.59-2.734.40.26314691.58692.3
2.73-2.95.20.22115521.798
2.9-3.1260.16415971.80599.6
3.12-3.4470.08815841.998100
3.44-3.937.30.07916081.954100
3.93-4.957.20.06416142.146100
4.95-506.60.07416962.93899.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data scaling
SERGUIdata collection
RefinementResolution: 2.3938→33.231 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 1327 10 %
Rwork0.2086 --
obs0.2136 13268 94.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: final / Resolution: 2.3938→33.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1080 691 695 4 2470
Biso mean--85.89 60.14 -
Num. residues----144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121882
X-RAY DIFFRACTIONf_angle_d1.2432671
X-RAY DIFFRACTIONf_dihedral_angle_d25.17744
X-RAY DIFFRACTIONf_chiral_restr0.05292
X-RAY DIFFRACTIONf_plane_restr0.006224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3938-2.48960.42281110.36681001X-RAY DIFFRACTION72
2.4896-2.60290.37841290.35181164X-RAY DIFFRACTION85
2.6029-2.74010.40281460.32321312X-RAY DIFFRACTION94
2.7401-2.91160.35091520.31261371X-RAY DIFFRACTION99
2.9116-3.13630.33281550.30241402X-RAY DIFFRACTION100
3.1363-3.45160.30341540.2571380X-RAY DIFFRACTION99
3.4516-3.95040.28221560.22111404X-RAY DIFFRACTION100
3.9504-4.97440.2251580.18251424X-RAY DIFFRACTION100
4.9744-33.23450.19721660.14511483X-RAY DIFFRACTION99

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