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- PDB-5va7: Glucocorticoid Receptor DNA Binding Domain - IL11 AP-1 recognitio... -

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Basic information

Entry
Database: PDB / ID: 5va7
TitleGlucocorticoid Receptor DNA Binding Domain - IL11 AP-1 recognition element Complex
Components
  • DNA (5'-D(*AP*GP*GP*GP*TP*GP*AP*GP*TP*CP*AP*GP*GP*AP*TP*G)-3')
  • DNA (5'-D(*CP*AP*TP*CP*CP*TP*GP*AP*CP*TP*CP*AP*CP*CP*CP*T)-3')
  • Glucocorticoid receptor
Keywordstranscription/dna / Nuclear Receptor / Transcription Factor / DNA Binding / Development / Protein-DNA complex / transcription-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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.153 Å
AuthorsWeikum, E.R. / Ortlund, E.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F31GM113397-01A1 United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Tethering not required: the glucocorticoid receptor binds directly to activator protein-1 recognition motifs to repress inflammatory genes.
Authors: Weikum, E.R. / de Vera, I.M.S. / Nwachukwu, J.C. / Hudson, W.H. / Nettles, K.W. / Kojetin, D.J. / Ortlund, E.A.
History
DepositionMar 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,7548
Polymers25,4924
Non-polymers2624
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, NMR studies also conform monomeric protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-22 kcal/mol
Surface area13620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.143, 96.855, 104.554
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 7847.297 Da / Num. of mol.: 2 / Fragment: unp residues 89-158
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
#2: DNA chain DNA (5'-D(*AP*GP*GP*GP*TP*GP*AP*GP*TP*CP*AP*GP*GP*AP*TP*G)-3')


Mass: 5043.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*AP*TP*CP*CP*TP*GP*AP*CP*TP*CP*AP*CP*CP*CP*T)-3')


Mass: 4754.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#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.: 47 / 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: 3.89 Å3/Da / Density % sol: 68.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium Nitratie, 15 % PEG 3350, 1 % glycerol

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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: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 21954 / % possible obs: 99.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 42.85 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.04 / Rrim(I) all: 0.094 / Χ2: 0.79 / Net I/σ(I): 10.6 / Num. measured all: 117427
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.18-2.263.50.57520600.7490.340.6720.73896.4
2.26-2.354.60.41721830.8740.2170.4720.91599.9
2.35-2.465.30.31821550.9410.1510.3530.716100
2.46-2.585.80.27421610.9560.1240.3020.805100
2.58-2.7560.2121780.980.0930.230.871100
2.75-2.9660.15321830.9880.0680.1680.866100
2.96-3.265.90.10522010.9970.0470.1160.795100
3.26-3.735.70.07122120.9980.0320.0780.78100
3.73-4.75.60.06822420.9950.0320.0750.753100
4.7-504.90.06423790.9930.0320.0720.63399.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
Cootmodel building
RefinementResolution: 2.153→32.793 Å / SU ML: 0.23 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 23.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 1531 7 %
Rwork0.2009 20327 -
obs0.2027 21858 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.36 Å2 / Biso mean: 53.6848 Å2 / Biso min: 27.01 Å2
Refinement stepCycle: final / Resolution: 2.153→32.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1078 650 4 47 1779
Biso mean--37.81 48.17 -
Num. residues----172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091820
X-RAY DIFFRACTIONf_angle_d1.0582576
X-RAY DIFFRACTIONf_chiral_restr0.045282
X-RAY DIFFRACTIONf_plane_restr0.005220
X-RAY DIFFRACTIONf_dihedral_angle_d22.641728
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1533-2.22280.29491160.28671498161481
2.2228-2.30220.36531300.343518621992100
2.3022-2.39440.25651320.236218291961100
2.3944-2.50330.24591550.225818632018100
2.5033-2.63520.25451350.229318601995100
2.6352-2.80030.26081410.221718712012100
2.8003-3.01630.2611420.229818672009100
3.0163-3.31960.2251420.21781842198499
3.3196-3.79940.26811410.20471882202399
3.7994-4.78440.17861440.16619322076100
4.7844-32.79670.19251530.167120212174100

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