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- PDB-5emq: Transcription factor GRDBD and GRE complex -

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Basic information

Entry
Database: PDB / ID: 5emq
TitleTranscription factor GRDBD and GRE complex
Components
  • DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*CP*AP*TP*GP*TP*TP*CP*TP*G)-3')
  • DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*GP*AP*TP*GP*TP*TP*CP*TP*G)-3')
  • Glucocorticoid receptor
KeywordsTRANSCRIPTION/DNA / Transcription factor / complex / DNA / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsLian, T. / Jin, J. / Su, X.
CitationJournal: To Be Published
Title: The effects of cytosine methylation on general transcription factors
Authors: Lian, T. / Jin, J. / Su, X.
History
DepositionNov 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 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
C: DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*GP*AP*TP*GP*TP*TP*CP*TP*G)-3')
D: DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*CP*AP*TP*GP*TP*TP*CP*TP*G)-3')
A: Glucocorticoid receptor
B: Glucocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9958
Polymers31,7344
Non-polymers2624
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-33 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.032, 100.384, 111.897
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: DNA chain DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*GP*AP*TP*GP*TP*TP*CP*TP*G)-3')


Mass: 5515.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*CP*AP*TP*GP*TP*TP*CP*TP*G)-3')


Mass: 5475.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Glucocorticoid receptor / GR / Nuclear receptor subfamily 3 group C member 1


Mass: 10371.312 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 411-500
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C1, GRL
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpHIS4 (others)
References: UniProt: P04150
#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.: 35 / 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: 3.45 Å3/Da / Density % sol: 69.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50mM Na Cacodylate, 2.25mM Spermine, 18mM MgCl2, 9% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→45.796 Å / Num. obs: 19855 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 40.73 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.079 / Χ2: 1.006 / Net I/σ(I): 10.99 / Num. measured all: 56936
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.50.8120.4532.6712925438143550.5599.4
2.5-30.9560.2035.2518081657864450.24998
3-3.50.9990.06612.29904336333050.0898.3
3.5-40.9970.04619.365478190718760.05698.4
4-60.9970.03423.757252278626890.04296.5
6-100.9980.03126.9526019709190.03794.7
100.9990.02728.56952952660.03390.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata processing
Cootmodel building
RefinementResolution: 2.3→37.361 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2243 1014 5.12 %
Rwork0.1999 18800 -
obs0.2011 19814 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.54 Å2 / Biso mean: 49.1019 Å2 / Biso min: 17.38 Å2
Refinement stepCycle: final / Resolution: 2.3→37.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1068 729 4 35 1836
Biso mean--34.61 39.18 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091899
X-RAY DIFFRACTIONf_angle_d1.1412701
X-RAY DIFFRACTIONf_chiral_restr0.05300
X-RAY DIFFRACTIONf_plane_restr0.005220
X-RAY DIFFRACTIONf_dihedral_angle_d25.791757
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.42130.29051450.2612671281699
2.4213-2.5730.2931480.25912660280898
2.573-2.77160.26851650.25362634279998
2.7716-3.05030.29061410.24172653279498
3.0503-3.49150.22961310.22022683281498
3.4915-4.39780.20181520.16942719287198
4.3978-37.3660.17271320.16292780291295
Refinement TLS params.Method: refined / Origin x: -11.1083 Å / Origin y: 11.9619 Å / Origin z: -6.9796 Å
111213212223313233
T0.3013 Å20.0006 Å20.0106 Å2-0.2795 Å20.002 Å2--0.2814 Å2
L1.3816 °2-0.1434 °20.5663 °2-1.4724 °20.1692 °2--3.1584 °2
S0.0427 Å °0.0732 Å °-0.2628 Å °-0.2062 Å °0.0504 Å °0.0015 Å °0.6086 Å °-0.0712 Å °-0.0769 Å °
Refinement TLS groupSelection details: ALL

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