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- PDB-5cc0: AncSR2 - TSLP nGRE complex -

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Basic information

Entry
Database: PDB / ID: 5cc0
TitleAncSR2 - TSLP nGRE complex
Components
  • AncSR2 DNA Binding Domain
  • DNA (5'-D(*AP*GP*CP*TP*CP*TP*CP*CP*CP*GP*GP*AP*GP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*CP*TP*CP*CP*GP*GP*GP*AP*GP*AP*GP*CP*T)-3')
Keywordsdna binding protein/DNA / DNA binding proteins / dna binding protein-DNA complex
Function / homology
Function and homology information


glandular epithelial cell maturation / tertiary branching involved in mammary gland duct morphogenesis / ovulation from ovarian follicle / negative regulation of phosphorylation / paracrine signaling / maintenance of protein location in nucleus / regulation of epithelial cell proliferation / nuclear steroid receptor activity / lung alveolus development / progesterone receptor signaling pathway ...glandular epithelial cell maturation / tertiary branching involved in mammary gland duct morphogenesis / ovulation from ovarian follicle / negative regulation of phosphorylation / paracrine signaling / maintenance of protein location in nucleus / regulation of epithelial cell proliferation / nuclear steroid receptor activity / lung alveolus development / progesterone receptor signaling pathway / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / G protein-coupled receptor activity / SUMOylation of intracellular receptors / transcription coactivator binding / Nuclear Receptor transcription pathway / nuclear receptor activity / cell-cell signaling / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / mitochondrial outer membrane / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / signaling receptor binding / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Progesterone receptor / Progesterone 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. ...Progesterone receptor / Progesterone 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) / Progesterone receptor
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.405 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: AncSR2 DNA Binding Domain
C: DNA (5'-D(*CP*GP*CP*CP*TP*CP*CP*GP*GP*GP*AP*GP*AP*GP*CP*T)-3')
D: DNA (5'-D(*AP*GP*CP*TP*CP*TP*CP*CP*CP*GP*GP*AP*GP*GP*CP*G)-3')
B: AncSR2 DNA Binding Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6808
Polymers28,4184
Non-polymers2624
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-24 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.334, 72.507, 104.942
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 AncSR2 DNA Binding Domain


Mass: 9309.050 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: UniProt: P06401*PLUS
#2: DNA chain DNA (5'-D(*CP*GP*CP*CP*TP*CP*CP*GP*GP*GP*AP*GP*AP*GP*CP*T)-3')


Mass: 4900.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*GP*CP*TP*CP*TP*CP*CP*CP*GP*GP*AP*GP*GP*CP*G)-3')


Mass: 4900.167 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.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: in 0.1 M HEPES (pH 7.5), 10% PEG 20000, 5% glycerol, 5% ethanol

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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: Mar 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→45 Å / Num. obs: 15335 / % possible obs: 99.8 % / Redundancy: 8.3 % / Net I/σ(I): 34.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SERGUIdata collection
PHASERphasing
HKL-2000data reduction
RefinementResolution: 2.405→38.469 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2372 1534 10.01 %
Rwork0.2143 --
obs0.2166 15332 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.405→38.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1095 650 4 2 1751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131851
X-RAY DIFFRACTIONf_angle_d1.6192619
X-RAY DIFFRACTIONf_dihedral_angle_d24.176733
X-RAY DIFFRACTIONf_chiral_restr0.064287
X-RAY DIFFRACTIONf_plane_restr0.007223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4048-2.48240.39961300.3461164X-RAY DIFFRACTION95
2.4824-2.57110.35371370.33111236X-RAY DIFFRACTION99
2.5711-2.6740.33531390.30441250X-RAY DIFFRACTION100
2.674-2.79570.35321400.31091260X-RAY DIFFRACTION100
2.7957-2.94310.32471370.30631233X-RAY DIFFRACTION100
2.9431-3.12740.32571400.29331253X-RAY DIFFRACTION99
3.1274-3.36870.29481360.27581212X-RAY DIFFRACTION96
3.3687-3.70750.23841350.23861242X-RAY DIFFRACTION99
3.7075-4.24340.25931430.20411280X-RAY DIFFRACTION100
4.2434-5.34390.23281440.1891296X-RAY DIFFRACTION100
5.3439-38.47430.16491530.16281372X-RAY DIFFRACTION100

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