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- PDB-6x6d: Glucocorticoid Receptor DNA binding domain in complex with unmodi... -

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Basic information

Entry
Database: PDB / ID: 6x6d
TitleGlucocorticoid Receptor DNA binding domain in complex with unmodified precursor for a modern recognition element (pre-GBS)
Components
  • DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*GP*GP*AP*GP*CP*GP*TP*TP*CP*TP*G)-3')
  • DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*GP*CP*TP*CP*CP*GP*TP*TP*CP*TP*G)-3')
  • Glucocorticoid receptor
KeywordsDNA/DNA BINDING PROTEIN / GR / pre-GBS / DNA BINDING PROTEIN / DNA-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / glucocorticoid metabolic process / response to cortisol / PTK6 Expression / neuroinflammatory response / mammary gland duct morphogenesis / microglia differentiation ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / glucocorticoid metabolic process / response to cortisol / PTK6 Expression / neuroinflammatory response / mammary gland duct morphogenesis / microglia differentiation / maternal behavior / astrocyte differentiation / adrenal gland development / regulation of gluconeogenesis / cellular response to glucocorticoid stimulus / cellular response to steroid hormone stimulus / motor behavior / estrogen response element binding / cellular response to dexamethasone stimulus / nuclear receptor-mediated steroid hormone signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cellular response to transforming growth factor beta stimulus / core promoter sequence-specific DNA binding / steroid binding / TBP-class protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / RNA polymerase II transcription regulatory region sequence-specific DNA binding / chromosome segregation / synaptic transmission, glutamatergic / SUMOylation of intracellular receptors / promoter-specific chromatin binding / Hsp90 protein binding / Nuclear Receptor transcription pathway / response to wounding / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / spindle / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / mitochondrial matrix / DNA-binding transcription factor activity / cell division / negative regulation of DNA-templated transcription / apoptotic process / synapse / centrosome / 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 / cytoplasm / cytosol
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
CACODYLATE ION / DNA / DNA (> 10) / Glucocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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*CP*GP*TP*TP*CP*TP*G)-3')
D: DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*GP*CP*TP*CP*CP*GP*TP*TP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8919
Polymers27,4934
Non-polymers3995
Water23413
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)130.426, 39.000, 96.791
Angle α, β, γ (deg.)90.000, 118.710, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-204-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 8241.719 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

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*GP*GP*AP*GP*CP*GP*TP*TP*CP*TP*G)-3')


Mass: 5541.592 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*CP*GP*TP*TP*CP*TP*G)-3')


Mass: 5467.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 18 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.93 Å3/Da / Density % sol: 68.68 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM Sodium cacodylate pH 6.5, 80 mM Calcium chloride, 1 % glycerol, and 8.5% 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 MX300-HS / Detector: CCD / Date: Aug 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→39.456 Å / Num. obs: 15307 / % possible obs: 98.56 % / Redundancy: 3.1 % / Biso Wilson estimate: 57.66 Å2 / Rpim(I) all: 0.079 / Rrim(I) all: 0.148 / Net I/σ(I): 14.05
Reflection shellResolution: 2.48→2.57 Å / Num. unique obs: 1508 / CC1/2: 0.705

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FYL

3fyl


Resolution: 2.48→39.456 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2113 768 5.02 %
Rwork0.1903 14539 -
obs0.1913 15307 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.89 Å2 / Biso mean: 71.8805 Å2 / Biso min: 30.99 Å2
Refinement stepCycle: final / Resolution: 2.48→39.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1127 730 9 13 1879
Biso mean--90.81 65.2 -
Num. residues----183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051965
X-RAY DIFFRACTIONf_angle_d0.6622791
X-RAY DIFFRACTIONf_chiral_restr0.034306
X-RAY DIFFRACTIONf_plane_restr0.004234
X-RAY DIFFRACTIONf_dihedral_angle_d22.5981060
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4801-2.67150.29311500.2826284698
2.6715-2.94030.2711520.2473288599
2.9403-3.36560.23511520.2259288498
3.3656-4.23950.20851550.1724292399
4.2395-39.4560.18121590.1664300199
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)
14.04450.15621.66285.515-0.46639.42070.42740.0958-2.7891-0.2914-0.15310.47891.4185-0.7403-0.330.6108-0.00210.08380.5209-0.09460.982918.7455-26.5024-4.7829
23.48771.04131.64584.4819-2.66027.76220.0919-0.30730.07920.612-0.13960.8359-0.1383-0.7080.03820.44480.03850.05490.3934-0.05310.633317.1518-14.9225-0.1429
32.4445-2.86353.19224.1219-3.96284.2247-0.4389-1.23982.11061.5956-0.68020.3081-1.0519-0.94390.49230.97330.1172-0.40680.9511-0.19111.194527.3807-6.00886.2154
42.02332.33622.7958.67790.77569.19440.0481-0.0325-0.74450.2713-0.0738-1.7352-0.14080.94250.26760.4757-0.0007-0.00270.63010.04930.724936.7065-17.41471.7658
51.8478-0.6432.92395.73630.4927.98740.9056-1.1735-1.2279-0.6546-0.29020.02081.4282-0.1844-0.10070.60970.0271-0.0450.57460.1210.830227.9541-23.9895.3411
68.4497-0.56964.47053.9705-1.98068.8226-0.37790.37370.2649-0.4002-0.1775-0.43890.16880.20560.22410.3692-0.00110.0350.4317-0.0440.543427.7584-14.3473-1.6473
70.3882-1.8364-0.34859.74460.7342.99240.16630.25641.0268-1.2727-0.38462.1777-0.835-0.68340.13280.64760.0903-0.07370.4248-0.00740.944516.9976-9.6177-6.6422
86.2429-0.2766-0.11853.28242.49842.5107-0.0892-1.07870.78551.2740.1239-0.4544-1.41890.6303-0.00471.07050.0099-0.13641.0067-0.10640.746245.105-14.012125.6194
97.3811-0.95040.75934.51563.54213.1410.356-1.1787-0.51760.7846-0.47590.48291.1503-0.57890.26120.9201-0.0535-0.02490.82390.08680.597735.7103-22.644225.273
101.0326-0.45410.03190.2073-0.016-0.003-1.5509-0.996-1.14512.0944-0.78280.83773.9403-1.96790.09841.5368-0.32810.14640.98320.15211.188932.2299-30.416618.0312
114.1991-1.11590.89843.31772.46752.8904-0.1821-0.14760.0101-0.0856-0.2556-0.0772-0.1403-0.29430.0440.54660.04860.01680.5370.01230.582240.5843-22.1947.0582
126.7858-0.69940.70463.63480.50152.1472-0.8573-0.58590.8765-0.6015-0.6511-0.1487-1.9498-0.6050.39640.95960.1024-0.14270.6738-0.03440.661636.8433-13.515913.6793
136.4849-1.4932.28923.05331.92393.1554-0.3221-0.33170.33760.3874-0.0141-1.02730.58540.5172-0.08710.69040.022-0.12980.6260.14130.648742.412-23.848117.1472
145.2972-1.30381.28922.62611.72752.77040.2732-1.9151-1.61091.89430.51890.09132.07510.7139-0.12131.33940.14050.01381.15380.12660.948644.1468-27.449529.4136
153.10080.17863.60252.7661-2.4687.62950.2213-0.1963-1.0063-0.14740.0159-0.349-0.573-0.31470.03140.52550.0777-0.02090.8841-0.11210.89737.254-14.34450.7338
168.6968-0.05415.53633.7455-1.34738.7825-1.1397-1.2643-1.13972.5260.65870.0688-1.4344-0.7006-0.46970.87230.0193-0.00811.35390.140.887613.5557-18.97617.0765
173.46160.683.48732.3141-1.09517.92270.9483-1.6794-0.72760.246-0.4297-0.6836-0.9106-1.8457-0.09860.9720.0254-0.16271.1236-0.08140.681629.7637-14.346124.5721
186.7326-5.00214.6455.7761-5.51325.2856-0.5623-2.1457-0.15222.19361.17830.4109-1.23-2.19241.93031.58070.3449-0.24292.1494-0.24320.510531.9444-12.754940.7921
197.9995-3.09015.58513.42970.06468.7577-1.0595-1.1906-0.8278-1.31360.63930.6252-1.2844-0.0453-0.24961.1763-0.1218-0.22061.62070.05270.689437.0792-18.747136.3867
209.9117-1.53586.32314.34510.53058.66530.3216-2.5384-0.53210.86530.66261.1315-0.5737-1.52170.18411.03060.2506-0.09761.6946-0.11910.754322.554-13.151726.4755
218.5048-1.72854.30863.89861.24539.8004-0.3092-1.3056-1.0731-0.68940.13840.2274-0.8554-0.5489-0.27430.6212-0.0174-0.0350.68330.04120.613416.4318-19.767710.0802
228.545-1.13855.06454.4354-1.12928.76890.115-0.6817-1.17620.89110.55431.9925-0.4227-1.0415-0.05670.53240.05420.01140.9227-0.03150.98921.3303-16.82546.6905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 417 through 429 )A417 - 429
2X-RAY DIFFRACTION2chain 'A' and (resid 430 through 450 )A430 - 450
3X-RAY DIFFRACTION3chain 'A' and (resid 451 through 455 )A451 - 455
4X-RAY DIFFRACTION4chain 'A' and (resid 456 through 465 )A456 - 465
5X-RAY DIFFRACTION5chain 'A' and (resid 466 through 473 )A466 - 473
6X-RAY DIFFRACTION6chain 'A' and (resid 474 through 483 )A474 - 483
7X-RAY DIFFRACTION7chain 'A' and (resid 484 through 490 )A484 - 490
8X-RAY DIFFRACTION8chain 'B' and (resid 418 through 438 )B418 - 438
9X-RAY DIFFRACTION9chain 'B' and (resid 439 through 450 )B439 - 450
10X-RAY DIFFRACTION10chain 'B' and (resid 451 through 455 )B451 - 455
11X-RAY DIFFRACTION11chain 'B' and (resid 456 through 465 )B456 - 465
12X-RAY DIFFRACTION12chain 'B' and (resid 466 through 473 )B466 - 473
13X-RAY DIFFRACTION13chain 'B' and (resid 474 through 484 )B474 - 484
14X-RAY DIFFRACTION14chain 'B' and (resid 485 through 490 )B485 - 490
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 5 )C1 - 5
16X-RAY DIFFRACTION16chain 'C' and (resid 6 through 10 )C6 - 10
17X-RAY DIFFRACTION17chain 'C' and (resid 11 through 15 )C11 - 15
18X-RAY DIFFRACTION18chain 'C' and (resid 16 through 18 )C16 - 18
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 5 )D1 - 5
20X-RAY DIFFRACTION20chain 'D' and (resid 6 through 10 )D6 - 10
21X-RAY DIFFRACTION21chain 'D' and (resid 11 through 15 )D11 - 15
22X-RAY DIFFRACTION22chain 'D' and (resid 16 through 18 )D16 - 18

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