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- PDB-6bse: Glucocorticoid receptor bound to high cooperativity monomer sequence -

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Basic information

Entry
Database: PDB / ID: 6bse
TitleGlucocorticoid receptor bound to high cooperativity monomer sequence
Components
  • DNA (5'-D(P*AP*CP*CP*AP*CP*GP*TP*GP*TP*AP*CP*TP*TP*TP*TP*T)-3')
  • DNA (5'-D(P*TP*AP*AP*AP*AP*AP*GP*TP*AP*CP*AP*CP*GP*TP*GP*G)-3')
  • Glucocorticoid receptor
KeywordsGENE REGULATION / glucocorticoid receptor gene expression protein:DNA binding
Function / homology
Function and homology information


nuclear glucocorticoid receptor activity / steroid hormone binding / cellular response to glucocorticoid stimulus / microtubule organizing center / cellular response to steroid hormone stimulus / steroid binding / spindle / nuclear receptor activity / chromatin organization / sequence-specific DNA binding ...nuclear glucocorticoid receptor activity / steroid hormone binding / cellular response to glucocorticoid stimulus / microtubule organizing center / cellular response to steroid hormone stimulus / steroid binding / spindle / nuclear receptor activity / chromatin organization / sequence-specific DNA binding / nuclear speck / DNA-binding transcription factor activity / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleus / 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 / 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 speciesSaguinus oedipus (cotton-top tamarin)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsPufall, M.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 1552862 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)K99/R00 CO149088 United States
Carver Charitable Trust01-224 United States
CitationJournal: To Be Published
Title: General and sequence-specific roles for DNA in glucocorticoid receptor DNA-binding stoichiometry
Authors: Pufall, M.A. / Zhang, L.
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 1.2Oct 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
A: Glucocorticoid receptor
B: Glucocorticoid receptor
C: DNA (5'-D(P*TP*AP*AP*AP*AP*AP*GP*TP*AP*CP*AP*CP*GP*TP*GP*G)-3')
D: DNA (5'-D(P*AP*CP*CP*AP*CP*GP*TP*GP*TP*AP*CP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4128
Polymers30,1514
Non-polymers2624
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-23 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.447, 95.172, 104.719
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.) Saguinus oedipus (cotton-top tamarin) / Gene: NR3C1, GRL / Cell line (production host): Gold / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P79269
#2: DNA chain DNA (5'-D(P*TP*AP*AP*AP*AP*AP*GP*TP*AP*CP*AP*CP*GP*TP*GP*G)-3')


Mass: 4955.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*CP*CP*AP*CP*GP*TP*GP*TP*AP*CP*TP*TP*TP*TP*T)-3')


Mass: 4839.151 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: isolated from a natural source / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.26 Å3/Da / Density % sol: 62.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.08 M KCl 0.04 M Sodium cacodylate trihydrate 60% v/v (+/-)-2-Methyl-2,4-pentanediol 0.012 M Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→16.71 Å / Num. obs: 17036 / % possible obs: 98.68 % / Redundancy: 2 % / Biso Wilson estimate: 37.64 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.04967 / Rpim(I) all: 0.04967 / Rrim(I) all: 0.07025 / Net I/σ(I): 15.25
Reflection shellResolution: 2.35→2.434 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3246 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 1678 / CC1/2: 0.796 / Rpim(I) all: 0.3246 / Rrim(I) all: 0.4591 / % possible all: 99.88

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G99

3g99


Resolution: 2.35→16.75 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 789 4.67 %
Rwork0.1922 --
obs0.194 16883 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→16.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 653 4 104 1867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121858
X-RAY DIFFRACTIONf_angle_d1.2932628
X-RAY DIFFRACTIONf_dihedral_angle_d19.7141006
X-RAY DIFFRACTIONf_chiral_restr0.06289
X-RAY DIFFRACTIONf_plane_restr0.007227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.49680.30341220.24862658X-RAY DIFFRACTION100
2.4968-2.68890.27831320.23422645X-RAY DIFFRACTION100
2.6889-2.95810.23831170.23122690X-RAY DIFFRACTION100
2.9581-3.38310.25711310.20852687X-RAY DIFFRACTION99
3.3831-4.25080.27431340.19982583X-RAY DIFFRACTION95
4.2508-16.75050.15711530.14022831X-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)
16.02814.14464.96839.94326.55355.4856-0.11610.40450.5242-0.75820.05680.8199-0.646-1.15030.45680.04170.02050.02720.72480.19170.2678-19.079829.4266-13.1642
29.3485-0.42694.96466.01580.52937.656-0.11670.92480.6543-0.39670.2239-0.1462-0.6546-0.0013-0.16680.35850.01120.06560.36720.05830.2255-7.37533.7799-12.0884
30.3407-0.8747-0.89912.2432.30312.3647-0.4362-2.52431.56160.9541-1.4892-3.5798-0.78010.36861.67330.8028-0.3647-0.2811.28430.22441.08031.178233.38530.5407
47.55170.10280.64996.3789-0.6846.47470.07770.19130.37750.08910.00460.0734-0.067-0.09210.01480.28440.08280.06070.4350.00820.1917-13.206126.5752.0062
53.9222-1.7711-1.64272.60991.5226.4997-0.0435-0.6913-0.06560.0461-0.39870.41120.1115-0.72130.47280.14380.0104-0.00290.3346-0.00980.2309-6.817625.5929-5.2534
66.50494.5643-3.80573.4732-3.22343.36260.26771.21830.3587-0.0248-0.2795-1.6007-1.63660.0123-0.11340.4614-0.0710.15340.47120.08160.3999-1.297829.5372-15.835
71.3108-0.96581.92142.5345-1.95452.97690.0865-1.09530.40921.41220.3235-0.6332-0.05580.9478-0.29910.6447-0.0781-0.08280.5996-0.09150.3886-6.709735.369925.8442
83.8585-0.1444-2.0338.28821.20185.60150.09760.69350.5302-0.3198-0.73851.3088-1.0322-1.14030.54690.6550.19740.03430.5665-0.24660.594-17.91139.986917.6832
98.12741.0233-0.21142.2983.73748.497-0.1256-0.1755-0.41990.02930.09360.41630.2249-0.5205-0.01780.2606-0.0154-0.00460.32680.03010.2104-16.039825.033210.1172
106.7262-2.34550.18836.55932.83832.82920.0498-0.85570.24740.1191-0.2436-0.2032-0.43850.06430.1460.2962-0.0817-0.03270.3461-0.07320.2544-11.736430.670115.3513
119.1209-2.38640.94860.6428-0.4632.692-0.4271-1.97840.3861.17840.52050.5215-0.3832-0.4899-0.06731.2825-0.09040.34790.8097-0.17420.4236-19.436836.440628.5481
122.2444-1.97172.87564.3304-5.85838.1350.67630.2459-0.1601-0.71310.69781.6189-0.78690.2064-1.29520.88130.0389-0.02830.88210.16230.565-13.727141.6895-29.1669
132.91952.4518-1.43162.431-2.32446.79291.0840.43320.2620.9073-0.374-0.0298-0.22840.0392-1.00960.6478-0.0057-0.03560.58630.08820.5248-5.856845.6448-14.0189
147.51344.975-2.91154.0389-0.13345.47470.8796-0.72190.5731.5802-0.39871.0186-2.428-0.9053-0.41321.07160.13430.13240.5524-0.05440.5106-13.837246.21333.8596
152.2505-0.65762.66453.3499-3.4987.07250.68510.6048-0.532-0.14460.3080.1162-0.95750.0501-0.65591.2418-0.13050.05470.3899-0.07980.5179-7.334943.367114.1605
162.13570.4115-1.78028.70895.40587.66680.77540.3360.995-0.93240.2733-1.042-1.6442-0.9637-0.77831.3724-0.0035-0.08930.6291-0.08240.6611-6.78551.24419.4527
173.37771.109-2.082.5674-3.08047.1738-0.10930.60120.5929-0.0660.68030.2037-0.8572-0.9266-0.65050.7035-0.02230.09680.35330.10570.4612-9.927844.4768-13.9855
184.0838-3.67913.46193.4919-4.13318.73060.96210.0037-1.74660.68263.7284-1.6623-0.37822.2338-4.59890.8060.1718-0.08491.1861-0.16480.928-5.349538.2059-31.8496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 417 through 429 )
2X-RAY DIFFRACTION2chain 'A' and (resid 430 through 450 )
3X-RAY DIFFRACTION3chain 'A' and (resid 451 through 455 )
4X-RAY DIFFRACTION4chain 'A' and (resid 456 through 473 )
5X-RAY DIFFRACTION5chain 'A' and (resid 474 through 484 )
6X-RAY DIFFRACTION6chain 'A' and (resid 485 through 489 )
7X-RAY DIFFRACTION7chain 'B' and (resid 419 through 438 )
8X-RAY DIFFRACTION8chain 'B' and (resid 439 through 454 )
9X-RAY DIFFRACTION9chain 'B' and (resid 455 through 464 )
10X-RAY DIFFRACTION10chain 'B' and (resid 465 through 483 )
11X-RAY DIFFRACTION11chain 'B' and (resid 484 through 490 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 5 )
13X-RAY DIFFRACTION13chain 'C' and (resid 6 through 10 )
14X-RAY DIFFRACTION14chain 'C' and (resid 11 through 15 )
15X-RAY DIFFRACTION15chain 'C' and (resid 16 through 16 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 5 )
17X-RAY DIFFRACTION17chain 'D' and (resid 6 through 15 )
18X-RAY DIFFRACTION18chain 'D' and (resid 16 through 16 )

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