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- PDB-6x6e: Glucocorticoid Receptor DNA binding domain in complex with methyl... -

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Basic information

Entry
Database: PDB / ID: 6x6e
TitleGlucocorticoid Receptor DNA binding domain in complex with methylated precursor for a modern recognition element (methylated pre-GBS)
Components
  • DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*GP*GP*AP*GP*(5CM)P*GP*TP*TP*CP*TP*G)-3')
  • DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*GP*CP*TP*CP*(5CM)P*GP*TP*TP*CP*TP*G)-3')
  • Glucocorticoid receptor
KeywordsDNA BINDING PROTEIN / GR / pre-GBS
Function / homology
Function and homology information


Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / glucocorticoid metabolic process / neuroinflammatory response / mammary gland duct morphogenesis / microglia differentiation / astrocyte differentiation ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / glucocorticoid metabolic process / neuroinflammatory response / mammary gland duct morphogenesis / microglia differentiation / astrocyte differentiation / maternal behavior / cellular response to glucocorticoid stimulus / motor behavior / adrenal gland development / regulation of gluconeogenesis / cellular response to steroid hormone stimulus / estrogen response element binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / nuclear receptor-mediated steroid hormone signaling pathway / core promoter sequence-specific DNA binding / cellular response to transforming growth factor beta stimulus / steroid binding / TBP-class protein binding / cellular response to dexamethasone stimulus / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / synaptic transmission, glutamatergic / RNA polymerase II transcription regulatory region sequence-specific DNA binding / chromosome segregation / SUMOylation of intracellular receptors / Hsp90 protein binding / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / spindle / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear receptor activity / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of neuron apoptotic process / : / chromatin organization / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / Potential therapeutics for SARS / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / mitochondrial matrix / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / cell division / negative regulation of DNA-templated transcription / apoptotic process / centrosome / synapse / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Glucocorticoid receptor / Glucocorticoid receptor / : / Nuclear hormone receptor / 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 ...Glucocorticoid receptor / Glucocorticoid receptor / : / Nuclear hormone receptor / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / Glucocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, X. / Ortlund, E.A.
Funding support United States, 2items
OrganizationGrant numberCountry
American Heart Association17POST33660110 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK095750 United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural basis for glucocorticoid receptor recognition of both unmodified and methylated binding sites, precursors of a modern recognition element.
Authors: Liu, X. / Weikum, E.R. / Tilo, D. / Vinson, C. / Ortlund, E.A.
History
DepositionMay 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 22, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 18, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,0978
Polymers27,8354
Non-polymers2624
Water54030
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.385, 39.089, 97.371
Angle α, β, γ (deg.)90.000, 118.618, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Glucocorticoid receptor / GR / Nuclear receptor subfamily 3 group C member 1


Mass: 8398.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C1, GRL / Production host: Escherichia coli (E. coli) / References: UniProt: P04150
#2: DNA chain DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*GP*GP*AP*GP*(5CM)P*GP*TP*TP*CP*TP*G)-3')


Mass: 5555.619 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*GP*CP*TP*CP*(5CM)P*GP*TP*TP*CP*TP*G)-3')


Mass: 5481.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#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.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.91 Å3/Da / Density % sol: 68.56 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM sodium cacodylate pH 6.5, 80 mM calcium chloride, 1 % glycerol, and 7 % PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→36.991 Å / Num. obs: 29271 / % possible obs: 98.69 % / Redundancy: 6.7 % / Biso Wilson estimate: 45.1 Å2 / Rpim(I) all: 0.076 / Rrim(I) all: 0.194 / Net I/σ(I): 16.5
Reflection shellResolution: 2.001→2.072 Å / Redundancy: 4 % / Num. unique obs: 2652 / CC1/2: 0.692 / % possible all: 90.22

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FYL

3fyl


Resolution: 2→36.99 Å / SU ML: 0.1928 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1084
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2122 1993 6.83 %
Rwork0.1811 27203 -
obs0.1832 29196 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.3 Å2
Refinement stepCycle: LAST / Resolution: 2→36.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1112 732 4 30 1878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681945
X-RAY DIFFRACTIONf_angle_d0.882762
X-RAY DIFFRACTIONf_chiral_restr0.0481300
X-RAY DIFFRACTIONf_plane_restr0.0041231
X-RAY DIFFRACTIONf_dihedral_angle_d27.4689501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.33181240.31891691X-RAY DIFFRACTION87.22
2.05-2.110.29981410.28091924X-RAY DIFFRACTION98.85
2.11-2.170.25761410.24451944X-RAY DIFFRACTION99.81
2.17-2.240.28921430.22991940X-RAY DIFFRACTION99.76
2.24-2.320.281440.21931950X-RAY DIFFRACTION99.95
2.32-2.410.24861410.19991947X-RAY DIFFRACTION100
2.41-2.520.25441450.21131964X-RAY DIFFRACTION99.86
2.52-2.650.23841430.21941949X-RAY DIFFRACTION99.86
2.65-2.820.21871440.20151975X-RAY DIFFRACTION99.95
2.82-3.040.20341430.21851960X-RAY DIFFRACTION100
3.04-3.340.29191400.20591925X-RAY DIFFRACTION98.19
3.34-3.830.2161460.17751968X-RAY DIFFRACTION98.6
3.83-4.820.18161460.14852005X-RAY DIFFRACTION99.95
4.82-36.990.17021520.14992061X-RAY DIFFRACTION99.82
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)
18.59966954751.882920874351.246957545315.639811421690.1299362165914.11287107650.09397924356870.00286568234102-0.928108205589-0.142544635168-0.1187123382280.4869942972410.204142558488-0.7659295203390.06499980842550.3188398108130.00876464509398-0.007047270136010.410994219723-0.03105736662380.50606412092717.8512781989-18.3245344492-1.58291354346
27.664451619211.021378508593.366131588384.86221393085-2.3588299207810.1486081275-0.108189267694-0.429640636203-0.0456041689229-0.0280853853825-0.0873608108894-0.0373480899124-0.244658755774-0.1408292536450.1592930004890.3145926830050.01135452389210.0008898007399660.286266654775-0.03796783824070.38289251584427.5719274738-15.08969690850.565753819111
39.428959101352.66858629185-1.388606412065.303590555550.1465948963674.739874655440.162994285668-2.189761786670.04228927057861.17040550672-0.143665017769-0.540992069092-0.5066669325230.225968082117-0.04639730651090.7014923767740.00647404285648-0.1575911696930.9134613907090.007916528323620.4650712733341.4519749088-17.294048754825.5876594117
47.97165634463-3.150880820430.8859107520527.68657354017-2.195782235140.625162122603-1.504921225320.11898171547-0.99803150239-1.898230263470.514047622049-1.532638405511.558807758610.02967944430820.8262528665021.47861423692-0.2238821741580.5012763280561.247051977270.1705045700971.6200612900331.5547565955-30.586765532919.9800883756
55.96546142771-0.1602505771370.4991067586284.822644998952.744698387088.33414297441-0.0673539450617-0.834924739631-0.07658378970550.673769309614-0.0345952426318-0.5798859622620.09706662360870.03273915377020.1287682687660.4074580317040.0181518081446-0.07789410797670.408691049990.04718241976690.39188901259540.3933836057-21.493157141315.2961209414
610.15136503813.86510284968-1.723889525588.587405671290.9350450733552.070532081150.7652524193870.0570696769132-1.91852405870.226795676239-0.18757649244-0.941922461216-0.00110575084659-0.654667803123-0.6670729415980.4635152514360.0349351368125-0.1377554460640.5800649839260.03153182894720.9100645494757.21496466695-14.41499859360.754058572628
71.952562540271.862109917251.863984094842.039762084721.774642498929.83658915557-0.956184747086-2.04914559354-1.129323190922.179354236420.7957835136210.750971201343-1.37735590428-0.9970106878610.03781981673570.6233118534080.05291785952880.09430605601751.388764695990.2669325639040.78318335031813.4339364458-19.211160094517.1781708259
83.124484723062.05475755016-0.8167989883732.47041253426-0.004851634347482.47440657934-0.171026567092-1.78572567892-0.09282144180211.000533870520.4522618668990.087896608657-1.55377385944-1.05655909386-0.2479830768171.097653509950.334659223553-0.1953584250351.46759822915-0.1368361452160.52444671365130.2924102135-14.302915388430.8785327748
94.86707305466-3.56046739891-1.483645522835.99221829431-1.027049040565.45350340111-1.09209802991-1.85457312002-0.0885989643903-0.6705909438730.6280779387250.222180934006-1.355635235920.1362250752450.3924635180051.1847150109-0.0353043765307-0.2324711506851.537157891360.04978870052640.55044259996537.0654436344-19.158140716836.6136370412
103.06953386762-2.102107171091.237650849864.2498201259-1.297597128877.77918049171-0.25457073354-2.28331802151-0.5856525796090.728570107250.4914094855890.453551039354-0.420716001574-0.803953498247-0.2608398651210.4718567080710.07164154192960.03584951392851.084204859280.09117634041790.58448520775115.1371478233-16.757321088615.8322027085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 419 through 450 )
2X-RAY DIFFRACTION2chain 'A' and (resid 451 through 491 )
3X-RAY DIFFRACTION3chain 'B' and (resid 419 through 449 )
4X-RAY DIFFRACTION4chain 'B' and (resid 450 through 454 )
5X-RAY DIFFRACTION5chain 'B' and (resid 455 through 489 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 5 )
7X-RAY DIFFRACTION7chain 'C' and (resid 6 through 10 )
8X-RAY DIFFRACTION8chain 'C' and (resid 11 through 18 )
9X-RAY DIFFRACTION9chain 'D' and (resid 19 through 23 )
10X-RAY DIFFRACTION10chain 'D' and (resid 24 through 36 )

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