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- PDB-5cby: AncGR2 DNA Binding Domain - (+)GRE Complex -

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Basic information

Entry
Database: PDB / ID: 5cby
TitleAncGR2 DNA Binding Domain - (+)GRE Complex
Components
  • AncGR2 DNA Binding Domain
  • DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3')
  • DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3')
Keywordsdna binding protein/dna / DNA binding proteins / 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 / glucocorticoid metabolic process / neuroinflammatory response / microglia differentiation / maternal behavior / mammary gland duct morphogenesis ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / glucocorticoid metabolic process / neuroinflammatory response / microglia differentiation / maternal behavior / mammary gland duct morphogenesis / nucleus localization / 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 / intracellular steroid hormone receptor 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 / spindle / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / Regulation of RUNX2 expression and activity / positive regulation of neuron apoptotic process / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / gene expression / chromatin organization / DNA-binding transcription activator activity, RNA polymerase II-specific / Potential therapeutics for SARS / DNA-binding transcription factor activity, RNA polymerase II-specific / mitochondrial matrix / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / cell division / centrosome / negative regulation of DNA-templated transcription / synapse / apoptotic process / chromatin / regulation of DNA-templated transcription / 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 / membrane / identical protein binding / nucleus / 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 / 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 speciesUNCLASSIFIED (unknown)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.997 Å
AuthorsHudson, W.H. / Ortlund, E.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK095750 United States
American Heart Association14GRNT20460124 United States
American Heart Association13PRE16920012 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space.
Authors: Hudson, W.H. / Kossmann, B.R. / de Vera, I.M. / Chuo, S.W. / Weikum, E.R. / Eick, G.N. / Thornton, J.W. / Ivanov, I.N. / Kojetin, D.J. / Ortlund, E.A.
History
DepositionJul 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: AncGR2 DNA Binding Domain
B: AncGR2 DNA Binding Domain
C: DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3')
D: DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8088
Polymers34,5464
Non-polymers2624
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-32 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.644, 38.798, 98.250
Angle α, β, γ (deg.)90.00, 119.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein AncGR2 DNA Binding Domain / GR / Nuclear receptor subfamily 3 group C member 1


Mass: 11769.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) UNCLASSIFIED (unknown) / Production host: Escherichia coli (E. coli) / References: UniProt: P04150*PLUS
#2: DNA chain DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3')


Mass: 5540.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3')


Mass: 5466.553 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 / Water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE WAS GENERATED FROM ANCESTRAL SEQUENCE RECONSTRUCTION

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES (pH 7.5) and 15% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 27141 / % possible obs: 91.3 % / Redundancy: 4.8 % / Net I/σ(I): 20.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SERGUIdata collection
HKL-2000data reduction
PHASERphasing
RefinementResolution: 1.997→36.743 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 1999 7.37 %
Rwork0.1821 --
obs0.1847 27116 90.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.997→36.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1140 730 4 138 2012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011999
X-RAY DIFFRACTIONf_angle_d1.2022837
X-RAY DIFFRACTIONf_dihedral_angle_d23.862802
X-RAY DIFFRACTIONf_chiral_restr0.052307
X-RAY DIFFRACTIONf_plane_restr0.009239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9967-2.04660.254890.23391108X-RAY DIFFRACTION57
2.0466-2.1020.21361060.21141342X-RAY DIFFRACTION69
2.102-2.16380.21281230.18971541X-RAY DIFFRACTION78
2.1638-2.23360.22441310.1951653X-RAY DIFFRACTION85
2.2336-2.31350.24391420.19431774X-RAY DIFFRACTION92
2.3135-2.40610.20621500.19331894X-RAY DIFFRACTION96
2.4061-2.51550.23461520.19581905X-RAY DIFFRACTION98
2.5155-2.64810.25481550.19851960X-RAY DIFFRACTION99
2.6481-2.8140.25991550.19651952X-RAY DIFFRACTION100
2.814-3.03120.22331580.19981979X-RAY DIFFRACTION100
3.0312-3.3360.23621550.18961943X-RAY DIFFRACTION99
3.336-3.81830.21961600.18522001X-RAY DIFFRACTION100
3.8183-4.8090.19521590.15652003X-RAY DIFFRACTION100
4.809-36.74890.18161640.15682062X-RAY DIFFRACTION100

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