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

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Basic information

Entry
Database: PDB / ID: 6bsf
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 complex
Function / homology
Function and homology information


Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / response to cortisol / steroid hormone binding / glucocorticoid metabolic process / PTK6 Expression / neuroinflammatory response / mammary gland duct morphogenesis / microglia differentiation ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / response to cortisol / steroid hormone binding / glucocorticoid metabolic process / PTK6 Expression / neuroinflammatory response / mammary gland duct morphogenesis / microglia differentiation / astrocyte differentiation / maternal behavior / cellular response to glucocorticoid stimulus / motor behavior / regulation of gluconeogenesis / adrenal gland development / cellular response to steroid hormone stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / 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 / RNA polymerase II transcription regulatory region sequence-specific DNA binding / synaptic transmission, glutamatergic / chromosome segregation / SUMOylation of intracellular receptors / promoter-specific chromatin binding / Hsp90 protein binding / Nuclear Receptor transcription pathway / positive regulation of miRNA transcription / response to wounding / 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 / chromosome / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / sequence-specific DNA binding / 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 / 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 / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
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 / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. ...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 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Glucocorticoid receptor / Glucocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 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
DepositionDec 2, 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 1.2Aug 18, 2021Group: Database references / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)30,4128
Polymers30,1514
Non-polymers2624
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-26 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.345, 87.907, 103.702
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: 10178.069 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C1, GRL / Cell line (production host): Gold / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P04150, UniProt: P79269*PLUS
#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.: 13 / 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: 2.93 Å3/Da / Density % sol: 58.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.05 M MES monohydrate pH 6.0 0.005 M Magnesium sulfate heptahydrate 5% 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: 2.4→33.528 Å / Num. obs: 14303 / % possible obs: 99.62 % / Redundancy: 6.7 % / Biso Wilson estimate: 58.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07266 / Rpim(I) all: 0.03007 / Rrim(I) all: 0.07879 / Net I/σ(I): 17.8
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.354 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 1373 / CC1/2: 0.681 / Rpim(I) all: 0.628 / Rrim(I) all: 1.497 / % possible all: 99.85

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.4→33.528 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2334 715 5.01 %
Rwork0.2061 --
obs0.2075 14270 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→33.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1099 652 4 14 1769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141847
X-RAY DIFFRACTIONf_angle_d1.4742615
X-RAY DIFFRACTIONf_dihedral_angle_d19.936998
X-RAY DIFFRACTIONf_chiral_restr0.064288
X-RAY DIFFRACTIONf_plane_restr0.007226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.58530.34661400.32052649X-RAY DIFFRACTION100
2.5853-2.84540.32741560.28382638X-RAY DIFFRACTION100
2.8454-3.25680.31391200.26142714X-RAY DIFFRACTION100
3.2568-4.10210.22221430.20242696X-RAY DIFFRACTION99
4.1021-33.53140.19151560.16492858X-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)
14.8772-1.89852.54418.5977-1.72332.89030.1581-0.88620.15481.33460.42950.37760.5957-0.7117-0.5280.82180.0996-0.00090.76310.11720.4928-65.9272-73.2393233.7511
28.84333.04010.43427.8131-2.03369.2154-0.1548-0.0035-0.53810.4203-0.148-0.40770.68250.76930.43440.49390.09850.00910.4964-0.08030.3627-57.4324-69.1849219.9544
37.06732.2959-1.83128.3136-2.30839.66070.4087-0.05680.2330.6836-0.0876-0.019-0.54490.0808-0.2190.52820.11170.01290.35220.01560.4273-62.7334-69.1491227.1599
45.1531-2.58472.26738.015-0.48672.19841.38150.1983-2.2594-0.16831.247-1.39713.9618-0.5634-2.40562.24680.1033-0.37971.2534-0.29860.9522-61.265-92.831213.4318
56.7669-0.1088-0.57228.8984-6.84155.75450.0393-0.4771-0.282-0.00040.5770.4420.9152-1.3371-0.66360.6109-0.0585-0.10.54230.06780.5227-65.9377-84.9452237.6936
66.3643-2.29022.88756.25992.22045.9835-0.0121-0.3485-0.65250.24220.48220.8350.3632-1.6299-0.46811.0341-0.0242-0.04950.91440.24030.6621-67.0685-83.9986243.4527
77.6227-3.99774.10739.5699-6.48545.36530.92311.001-0.8563-0.81550.45250.28072.1112-1.3426-1.38641.3-0.1367-0.32310.94190.03660.6635-67.108-86.2178217.1166
80.19640.2335-0.50744.69840.73734.18490.06330.5515-0.8992-1.05550.953-1.38710.57561.7915-0.61430.6238-0.04060.08060.6294-0.24990.6769-61.5826-76.5316196.0488
93.0661-4.6382-2.5157.12874.4326.53770.383-0.6425-1.3410.6113-0.13730.32841.00060.1207-0.29630.9062-0.00530.1030.4512-0.01980.7466-71.0147-79.4382202.6851
101.64551.85793.42912.85834.35957.9132-1.098-2.1195-0.4631-0.87030.27482.93190.4073-1.52630.76880.5694-0.0659-0.01891.0092-0.04470.8642-77.7675-73.631209.5377
119.5668-4.079-5.06547.74442.0718.5055-0.2296-0.06960.58870.02270.01540.0363-1.19130.05910.18290.64270.0889-0.03040.39090.03630.5024-66.2637-63.6218211.4754
121.6877-1.1729-1.38197.20844.12667.44870.2365-0.0894-0.74970.80050.1652-0.99540.49951.7354-0.49690.63320.1398-0.08070.727-0.0250.6129-59.8794-72.8044209.9044
137.8432-5.2625-1.1128.6004-2.26769.451-0.3690.2683-0.0879-0.8820.1844-0.2905-0.86550.11590.20140.4804-0.08760.02020.4316-0.03760.4248-70.5506-70.8606200.61
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 419 through 449 )
2X-RAY DIFFRACTION2chain 'B' and (resid 450 through 464 )
3X-RAY DIFFRACTION3chain 'B' and (resid 465 through 489 )
4X-RAY DIFFRACTION4chain 'C' and (resid 0 through 4 )
5X-RAY DIFFRACTION5chain 'C' and (resid 5 through 15 )
6X-RAY DIFFRACTION6chain 'D' and (resid 1 through 10 )
7X-RAY DIFFRACTION7chain 'D' and (resid 11 through 16 )
8X-RAY DIFFRACTION8chain 'A' and (resid 419 through 438 )
9X-RAY DIFFRACTION9chain 'A' and (resid 439 through 450 )
10X-RAY DIFFRACTION10chain 'A' and (resid 451 through 455 )
11X-RAY DIFFRACTION11chain 'A' and (resid 456 through 465 )
12X-RAY DIFFRACTION12chain 'A' and (resid 466 through 473 )
13X-RAY DIFFRACTION13chain 'A' and (resid 474 through 489 )

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