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- PDB-6ggg: Mineralocorticoid receptor in complex with (s)-13 -

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Basic information

Entry
Database: PDB / ID: 6ggg
TitleMineralocorticoid receptor in complex with (s)-13
Components
  • Mineralocorticoid receptor
  • NCOA1 peptide
KeywordsTRANSCRIPTION / Mineralocorticoid receptor / nuclear hormone receptor / steroid receptor / ligand complex / peptide complex / signaling protein
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
: / 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 ...: / 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
Chem-EYN / Mineralocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsEdman, K. / Aagaard, A. / Tangefjord, S.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Identification of Mineralocorticoid Receptor Modulators with Low Impact on Electrolyte Homeostasis but Maintained Organ Protection.
Authors: Granberg, K.L. / Yuan, Z.Q. / Lindmark, B. / Edman, K. / Kajanus, J. / Hogner, A. / Malmgren, M. / O'Mahony, G. / Nordqvist, A. / Lindberg, J. / Tangefjord, S. / Kossenjans, M. / Lofberg, C. ...Authors: Granberg, K.L. / Yuan, Z.Q. / Lindmark, B. / Edman, K. / Kajanus, J. / Hogner, A. / Malmgren, M. / O'Mahony, G. / Nordqvist, A. / Lindberg, J. / Tangefjord, S. / Kossenjans, M. / Lofberg, C. / Branalt, J. / Liu, D. / Selmi, N. / Nikitidis, G. / Nordberg, P. / Hayen, A. / Aagaard, A. / Hansson, E. / Hermansson, M. / Ivarsson, I. / Jansson-Lofmark, R. / Karlsson, U. / Johansson, U. / William-Olsson, L. / Hartleib-Geschwindner, J. / Bamberg, K.
History
DepositionMay 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.year / _citation_author.name
Revision 1.2Apr 24, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mineralocorticoid receptor
B: NCOA1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0504
Polymers36,5592
Non-polymers4912
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-16 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.729, 75.729, 121.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 34832.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C2, MCR, MLR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08235
#2: Protein/peptide NCOA1 peptide


Mass: 1725.958 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EYN / 2-[(3~{S})-7-fluoranyl-6-(2-methylpropyl)-4-[(3-oxidanylidene-4~{H}-1,4-benzoxazin-6-yl)carbonyl]-2,3-dihydro-1,4-benzoxazin-3-yl]-~{N}-methyl-ethanamide


Mass: 455.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26FN3O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Condition C2 of the morpheus screen (Molecular Dimension).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.985 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.985 Å / Relative weight: 1
ReflectionResolution: 1.71→121.24 Å / Num. obs: 38653 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 36.27 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.031 / Rrim(I) all: 0.109 / Net I/σ(I): 13.1
Reflection shellResolution: 1.71→1.88 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.434 / Mean I/σ(I) obs: 1.8 / Rpim(I) all: 0.431 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4uda

4uda


Resolution: 1.71→64.23 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.09 / SU Rfree Blow DPI: 0.082 / SU Rfree Cruickshank DPI: 0.08
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1930 5 %RANDOM
Rwork0.18 ---
obs0.181 38579 99.3 %-
Displacement parametersBiso mean: 43.62 Å2
Baniso -1Baniso -2Baniso -3
1--3.2406 Å20 Å20 Å2
2---3.2406 Å20 Å2
3---6.4812 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: 1 / Resolution: 1.71→64.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 0 34 174 2227
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012179HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.932958HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d774SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes316HARMONIC5
X-RAY DIFFRACTIONt_it2179HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion15.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion271SEMIHARMONIC5
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_contact2705SEMIHARMONIC4
LS refinement shellResolution: 1.71→1.76 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2847 133 4.96 %
Rwork0.2532 2546 -
all0.2548 2679 -
obs--90.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6384-0.4385-0.53331.64351.062.1923-0.02710.0122-0.0027-0.07940.1197-0.0999-0.01930.0521-0.0926-0.0518-0.01040.0277-0.09360.0049-0.0698-22.961411.08575.2241
26.0799-1.0792-1.53644.9074-1.19486.3585-0.06460.4481-0.1651-0.06930.2184-0.2433-0.52160.3064-0.15390.068-0.12610.0387-0.045-0.0286-0.0552-15.74479.1015-15.8629
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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