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- PDB-5dui: Identification of a new FoxO1 binding site that precludes CREB bi... -

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Basic information

Entry
Database: PDB / ID: 5dui
TitleIdentification of a new FoxO1 binding site that precludes CREB binding at the glucose-6-phosphatase catalytic subunit gene promoter
Components
  • DNA (5'-D(*AP*TP*GP*AP*TP*TP*TP*AP*CP*GP*TP*AP*AP*AP*AP*TP*AP*GP*AP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*TP*CP*TP*AP*TP*TP*TP*TP*AP*CP*GP*TP*AP*AP*AP*TP*CP*A)-3')
  • Forkhead box protein O1
KeywordsTRANSCRIPTION/dna / transcription factor / winged helix / DNA binding / protein-DNA complex / diabetes / transcription regulation / TRANSCRIPTION-dna complex
Function / homology
Function and homology information


cellular response to hyperoxia / regulation of transcription initiation by RNA polymerase II / AKT-mediated inactivation of FOXO1A / FOXO-mediated transcription of cell cycle genes / AKT phosphorylates targets in the nucleus / positive regulation of smooth muscle cell apoptotic process / neuronal stem cell population maintenance / regulation of neural precursor cell proliferation / response to fatty acid / negative regulation of stress-activated MAPK cascade ...cellular response to hyperoxia / regulation of transcription initiation by RNA polymerase II / AKT-mediated inactivation of FOXO1A / FOXO-mediated transcription of cell cycle genes / AKT phosphorylates targets in the nucleus / positive regulation of smooth muscle cell apoptotic process / neuronal stem cell population maintenance / regulation of neural precursor cell proliferation / response to fatty acid / negative regulation of stress-activated MAPK cascade / Regulation of FOXO transcriptional activity by acetylation / regulation of reactive oxygen species metabolic process / negative regulation of cardiac muscle hypertrophy in response to stress / cellular response to cold / temperature homeostasis / negative regulation of fat cell differentiation / FOXO-mediated transcription of cell death genes / blood vessel development / protein acetylation / fat cell differentiation / Constitutive Signaling by AKT1 E17K in Cancer / intracellular glucose homeostasis / Regulation of gene expression in beta cells / Regulation of localization of FOXO transcription factors / canonical Wnt signaling pathway / negative regulation of insulin secretion / cellular response to nitric oxide / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of autophagy / energy homeostasis / positive regulation of gluconeogenesis / cellular response to starvation / protein phosphatase 2A binding / promoter-specific chromatin binding / negative regulation of canonical Wnt signaling pathway / MAPK6/MAPK4 signaling / chromatin DNA binding / beta-catenin binding / autophagy / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to insulin stimulus / positive regulation of protein catabolic process / insulin receptor signaling pathway / cellular response to oxidative stress / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / sequence-specific DNA binding / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / chromatin binding / ubiquitin protein ligase binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / FOXO protein, KIX-binding domain / KIX-binding domain of forkhead box O, CR2 / FOXO protein, transactivation domain / Transactivation domain of FOXO protein family / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 ...: / FOXO protein, KIX-binding domain / KIX-binding domain of forkhead box O, CR2 / FOXO protein, transactivation domain / Transactivation domain of FOXO protein family / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Forkhead box protein O1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.306 Å
AuthorsSingh, P. / Endrizzi, J.A. / Chi, Y.-I.
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Crystal structures reveal a new and novel FoxO1 binding site within the human glucose-6-phosphatase catalytic subunit 1 gene promoter.
Authors: Singh, P. / Han, E.H. / Endrizzi, J.A. / O'Brien, R.M. / Chi, Y.I.
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Forkhead box protein O1
B: Forkhead box protein O1
C: DNA (5'-D(*TP*TP*TP*TP*CP*TP*AP*TP*TP*TP*TP*AP*CP*GP*TP*AP*AP*AP*TP*CP*A)-3')
D: DNA (5'-D(*AP*TP*GP*AP*TP*TP*TP*AP*CP*GP*TP*AP*AP*AP*AP*TP*AP*GP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)37,7714
Polymers37,7714
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-33 kcal/mol
Surface area16610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.610, 79.026, 48.266
Angle α, β, γ (deg.)90.000, 90.790, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Forkhead box protein O1 / / Forkhead box protein O1A / Forkhead in rhabdomyosarcoma


Mass: 12445.928 Da / Num. of mol.: 2 / Fragment: unp residues 151-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXO1, FKHR, FOXO1A / Production host: Escherichia coli (E. coli) / References: UniProt: Q12778
#2: DNA chain DNA (5'-D(*TP*TP*TP*TP*CP*TP*AP*TP*TP*TP*TP*AP*CP*GP*TP*AP*AP*AP*TP*CP*A)-3')


Mass: 6377.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*TP*GP*AP*TP*TP*TP*AP*CP*GP*TP*AP*AP*AP*AP*TP*AP*GP*AP*AP*A)-3')


Mass: 6502.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 14-18% PEG 8000 0.1M Ammonium sulfate 20mM Magnesium chloride 50mM MES pH 5.6 10% 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: Mar 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 14596 / % possible obs: 94.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 41.13 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1.007 / Net I/av σ(I): 16.574 / Net I/σ(I): 22.2 / Num. measured all: 65246
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.342.60.4656620.81785.5
2.34-2.382.70.4256550.7887.4
2.38-2.432.80.416830.81989.9
2.43-2.482.90.4047150.85591.9
2.48-2.533.20.3347300.84593.6
2.53-2.593.40.2927160.87694
2.59-2.663.50.2777140.93293.8
2.66-2.733.80.2297270.94194.7
2.73-2.813.90.1987411.01896
2.81-2.94.10.177371.00496.6
2.9-34.50.1427470.95497
3-3.124.80.1297581.1397.9
3.12-3.2650.1087341.05295
3.26-3.445.40.0937371.03896.2
3.44-3.655.70.0857641.0897.4
3.65-3.9360.0897561.24198.4
3.93-4.336.20.0867641.24798.1
4.33-4.956.10.0767621.05898.8
4.95-6.246.20.0697720.93299
6.24-505.80.0677220.77988.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CO6

3co6


Resolution: 2.306→40.144 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 28.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2452 605 4.96 %
Rwork0.2083 11586 -
obs0.2102 12191 78.68 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.576 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 189.95 Å2 / Biso mean: 69.4285 Å2 / Biso min: 23.49 Å2
Baniso -1Baniso -2Baniso -3
1-1.9587 Å20 Å2-3.9023 Å2
2---1.4792 Å20 Å2
3----0.4796 Å2
Refinement stepCycle: final / Resolution: 2.306→40.144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1368 855 0 51 2274
Biso mean---45.24 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022360
X-RAY DIFFRACTIONf_angle_d0.7583362
X-RAY DIFFRACTIONf_chiral_restr0.045359
X-RAY DIFFRACTIONf_plane_restr0.001276
X-RAY DIFFRACTIONf_dihedral_angle_d21.452923
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3061-2.53820.2849650.25911448151339
2.5382-2.90540.35331500.2783009315982
2.9054-3.66010.25931900.21743537372796
3.6601-40.15040.21162000.1823592379297
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2232-0.03680.47477.95951.00474.92150.0483-0.1826-0.12520.40480.1915-0.70970.46510.4976-0.16620.34470.10670.18530.07890.02190.5235-9.255-14.2928.101
23.8506-2.2481-0.18776.67480.04741.8956-0.1012-0.44620.46470.44850.1193-0.3328-0.15970.1019-0.06530.5141-0.01090.28020.1694-0.12340.455626.75115.14-9.566
32.3423-0.3231-2.7130.04810.3893.2017-0.0633-0.18180.0649-0.24420.0194-0.16090.12390.5239-0.10920.4767-0.05850.56240.4223-0.10160.56496.5390.3916.869
45.97550.6318-4.32420.063-0.46323.1756-0.1736-0.0691-0.0788-0.24480.1311-0.26260.22750.47170.30590.6546-0.03220.54370.4634-0.05580.72774.4950.4318.655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 160:245 )A160 - 245
2X-RAY DIFFRACTION2( CHAIN B AND RESID 161:245 )B161 - 245
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1:21 )C1 - 21
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1:21 )D1 - 21

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