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- PDB-5emc: Transcription factor GRDBD and smGRE complex -

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Basic information

Entry
Database: PDB / ID: 5emc
TitleTranscription factor GRDBD and smGRE complex
Components
  • DNA (5'-D(*CP*CP*AP*GP*AP*AP*(5CM)P*AP*TP*CP*AP*TP*GP*TP*TP*(5CM)P*TP*G)-3')
  • DNA (5'-D(*CP*CP*AP*GP*AP*AP*(5CM)P*AP*TP*GP*AP*TP*GP*TP*TP*(5CM)P*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 / 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 / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / 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 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsSu, X.D. / Lian, T. / Jin, J.
CitationJournal: To Be Published
Title: The effects of cytosine methylation on general transcription factors
Authors: Jin, J. / Lian, T. / SU, X.D.
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 / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id

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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*(5CM)P*AP*TP*CP*AP*TP*GP*TP*TP*(5CM)P*TP*G)-3')
A: Glucocorticoid receptor
B: Glucocorticoid receptor
D: DNA (5'-D(*CP*CP*AP*GP*AP*AP*(5CM)P*AP*TP*GP*AP*TP*GP*TP*TP*(5CM)P*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0528
Polymers31,7904
Non-polymers2624
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-10 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.942, 99.643, 112.229
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*(5CM)P*AP*TP*CP*AP*TP*GP*TP*TP*(5CM)P*TP*G)-3')


Mass: 5503.622 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: 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
#3: DNA chain DNA (5'-D(*CP*CP*AP*GP*AP*AP*(5CM)P*AP*TP*GP*AP*TP*GP*TP*TP*(5CM)P*TP*G)-3')


Mass: 5543.646 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.: 184 / 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: 3.42 Å3/Da / Density % sol: 69.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 50mM HEPES, 100mM KCl, 10mM MgCl2, 5% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→37.256 Å / Num. obs: 19780 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 33.17 Å2 / Rmerge F obs: 0.991 / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.154 / Χ2: 0.888 / Net I/σ(I): 5.45 / Num. measured all: 57041
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.50.7210.5192.0513083434243010.6399.1
2.5-2.80.8760.333.0713066443843630.40198.3
2.8-30.9410.2264.225969207420160.27497.2
3-40.9910.1037.3614456521949940.12395.7
4-50.9870.08210.125076190618040.09894.6
5-60.990.0769.9522548517970.09293.7
6-100.9930.07410.5824779648810.08991.4
10-500.9930.06211.446602892420.07683.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata processing
MOLREPphasing
Cootmodel building
RefinementResolution: 2.3→37.256 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 1005 5.08 %Random
Rwork0.2248 18775 --
obs0.2266 19398 98.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.42 Å2 / Biso mean: 41.5606 Å2 / Biso min: 16.97 Å2
Refinement stepCycle: final / Resolution: 2.3→37.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 731 4 184 1973
Biso mean--28.19 44.75 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061887
X-RAY DIFFRACTIONf_angle_d0.8922692
X-RAY DIFFRACTIONf_chiral_restr0.035295
X-RAY DIFFRACTIONf_plane_restr0.004220
X-RAY DIFFRACTIONf_dihedral_angle_d23.482718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.42130.3231550.27882662X-RAY DIFFRACTION100
2.4213-2.5730.29291320.26322660X-RAY DIFFRACTION99
2.573-2.77160.32271560.24292674X-RAY DIFFRACTION99
2.7716-3.05040.26211450.24262651X-RAY DIFFRACTION99
3.0504-3.49150.29391410.22382648X-RAY DIFFRACTION97
3.4915-4.39780.20731400.19662672X-RAY DIFFRACTION97
4.3978-37.26110.24831360.21462808X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 11.1622 Å / Origin y: -11.7974 Å / Origin z: -6.8315 Å
111213212223313233
T0.3075 Å2-0.0136 Å2-0.0109 Å2-0.2618 Å20.0346 Å2--0.2856 Å2
L0.8173 °2-0.1957 °2-0.2918 °2-0.9677 °2-0.2531 °2--1.4678 °2
S0.0005 Å °0.058 Å °0.1798 Å °-0.1856 Å °0.0914 Å °-0.0094 Å °-0.4316 Å °0.0873 Å °-0.0617 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allC1 - 18
2X-RAY DIFFRACTION1allA438 - 527
3X-RAY DIFFRACTION1allB437 - 527
4X-RAY DIFFRACTION1allD27 - 44
5X-RAY DIFFRACTION1allS1 - 190
6X-RAY DIFFRACTION1allS191 - 195

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