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- PDB-6bqu: Human GR (418-507) in complex with monomeric DNA binding site -

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Basic information

Entry
Database: PDB / ID: 6bqu
TitleHuman GR (418-507) in complex with monomeric DNA binding site
Components
  • DNA (5'-D(P*AP*AP*GP*CP*TP*AP*GP*TP*AP*CP*AP*TP*TP*TP*GP*C)-3')
  • DNA (5'-D(P*TP*GP*CP*AP*AP*AP*TP*GP*TP*AP*CP*TP*AP*GP*CP*T)-3')
  • Glucocorticoid receptor
KeywordsDNA BINDING PROTEIN/DNA / Glucocorticoid receptor Monomeric binding site / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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 / neuroinflammatory response / glucocorticoid metabolic process / microglia differentiation / mammary gland duct morphogenesis / maternal behavior ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / neuroinflammatory response / glucocorticoid metabolic process / microglia differentiation / mammary gland duct morphogenesis / maternal behavior / astrocyte differentiation / cellular response to glucocorticoid stimulus / motor behavior / regulation of gluconeogenesis / adrenal gland development / 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 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / TBP-class protein binding / steroid binding / cellular response to dexamethasone stimulus / synaptic transmission, glutamatergic / chromosome segregation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / SUMOylation of intracellular receptors / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / spindle / Regulation of RUNX2 expression and activity / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of neuron apoptotic process / Circadian Clock / chromatin organization / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 / centrosome / apoptotic process / synapse / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / 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 / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Glucocorticoid receptor / Glucocorticoid receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear hormone 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 ...Glucocorticoid receptor / Glucocorticoid receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear hormone 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Glucocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPufall, M.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CAREER grant 1552862 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)K99/R00 CA149088 United States
CitationJournal: To Be Published
Title: General and sequence-specific roles for DNA in glucocorticoid receptor DNA-binding stoichiometry
Authors: Pufall, M.A.
History
DepositionNov 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
B: Glucocorticoid receptor
C: DNA (5'-D(P*TP*GP*CP*AP*AP*AP*TP*GP*TP*AP*CP*TP*AP*GP*CP*T)-3')
D: DNA (5'-D(P*AP*AP*GP*CP*TP*AP*GP*TP*AP*CP*AP*TP*TP*TP*GP*C)-3')
A: Glucocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2058
Polymers25,9434
Non-polymers2624
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-27 kcal/mol
Surface area12650 Å2
Unit cell
Length a, b, c (Å)38.231, 88.235, 103.905
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 8074.493 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) / Strain (production host): BL21 / Variant (production host): Gold / References: UniProt: P04150
#2: DNA chain DNA (5'-D(P*TP*GP*CP*AP*AP*AP*TP*GP*TP*AP*CP*TP*AP*GP*CP*T)-3')


Mass: 4897.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*AP*GP*CP*TP*AP*GP*TP*AP*CP*AP*TP*TP*TP*GP*C)-3')


Mass: 4897.203 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.: 10 / 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: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.005 M Magnesium sulfate heptahydrate, 0.05 M MES monohydrate, pH 6.0, 5 percent w/v, Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→51.952 Å / Num. obs: 12750 / % possible obs: 99.66 % / Redundancy: 6.8 % / Biso Wilson estimate: 40.405 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06019 / Net I/σ(I): 16.2
Reflection shellResolution: 2.5→2.75 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.8355 / Num. unique all: 1246 / Num. unique obs: 3122 / CC1/2: 0.821 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G99

3g99


Resolution: 2.5→51.952 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2
RfactorNum. reflection% reflection
Rfree0.2487 591 4.64 %
Rwork0.2134 --
obs0.215 12724 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→51.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 656 4 10 1773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051853
X-RAY DIFFRACTIONf_angle_d0.6872621
X-RAY DIFFRACTIONf_dihedral_angle_d19.692999
X-RAY DIFFRACTIONf_chiral_restr0.043285
X-RAY DIFFRACTIONf_plane_restr0.003227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.75160.36491400.30242982X-RAY DIFFRACTION100
2.7516-3.14970.32611380.28382992X-RAY DIFFRACTION100
3.1497-3.96810.24361400.22412995X-RAY DIFFRACTION99
3.9681-51.96370.21791730.17333164X-RAY DIFFRACTION100
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)
18.0169-1.07661.27798.45255.07286.8748-0.4913-1.0243-1.37980.77270.20430.60331.1717-0.64720.43170.7397-0.07460.07140.49170.05070.7633-53.9302-77.9767205.1607
26.1706-4.1856-3.4094.31994.67596.62180.24930.52280.04340.0189-0.1154-0.4908-0.01560.1061-0.24620.67380.0387-0.03440.6299-0.00170.6196-44.0975-68.4282211.0752
36.2901-2.46470.30883.5721-1.86192.6836-0.30140.88520.0071-0.84090.0076-0.0197-0.050.68430.27870.6239-0.07270.02710.5556-0.01560.5561-51.507-71.2534200.5143
40.83980.31210.37377.0853-1.27328.28350.1597-0.5298-0.03491.18770.36490.31690.4219-0.6621-0.37950.81340.0978-0.0570.67120.11050.6199-46.3864-73.8918234.1086
53.73460.57612.06727.4264-4.32678.2216-0.10.01080.05520.0370.20970.08250.0396-0.3933-0.15660.49140.0723-0.02490.4338-0.01270.5183-43.5038-69.6692220.4227
62.8178-0.4564-1.9694.95792.51323.77960.3163-0.04010.20580.5607-0.5433-0.7259-0.70390.77010.24050.6567-0.0225-0.05950.51830.06750.5219-39.3015-68.8222231.4862
77.04-4.2797-1.02994.40663.22864.3021.7356-0.4006-1.9122-0.11170.1113-1.36113.1186-0.7481-1.89142.16360.225-0.39211.0375-0.16730.9867-42.2983-93.3268213.4659
82.4521-2.0320.18185.3017-5.67919.40620.1343-0.2959-0.3905-0.13240.39020.20540.5602-0.7609-0.64210.8784-0.1122-0.12720.65290.11170.7388-46.6983-85.8712236.3192
98.09783.6691-0.53249.0381-5.32964.56170.4259-1.63051.61682.60032.3303-1.1164-1.35370.2283-1.60141.31730.11740.110.9497-0.17020.931-43.7141-81.0262255.7455
104.8988-5.2815-3.30257.59452.43814.33280.32520.275-0.14870.51181.45451.13921.4428-3.6397-1.71711.33760.0485-0.03211.47010.4270.8131-52.0495-81.767251.2602
111.9553-1.44092.74896.6859-1.31373.86080.80880.2667-0.4639-0.57120.42840.15041.5007-0.4996-1.09020.99-0.0909-0.15550.8060.05520.758-45.6219-86.9788226.1189
122.2873-2.7044-2.12543.99330.78736.0188-0.06080.4297-0.5292-0.96180.8737-1.44920.63150.9593-0.83530.6901-0.07820.09280.6763-0.19830.8126-42.0588-76.6362196.3865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 439 through 455 )
2X-RAY DIFFRACTION2chain 'A' and (resid 456 through 473 )
3X-RAY DIFFRACTION3chain 'A' and (resid 474 through 489 )
4X-RAY DIFFRACTION4chain 'B' and (resid 419 through 450 )
5X-RAY DIFFRACTION5chain 'B' and (resid 451 through 473 )
6X-RAY DIFFRACTION6chain 'B' and (resid 474 through 490 )
7X-RAY DIFFRACTION7chain 'C' and (resid 0 through 4 )
8X-RAY DIFFRACTION8chain 'C' and (resid 5 through 14 )
9X-RAY DIFFRACTION9chain 'C' and (resid 15 through 15 )
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 5 )
11X-RAY DIFFRACTION11chain 'D' and (resid 6 through 16 )
12X-RAY DIFFRACTION12chain 'A' and (resid 419 through 438 )

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