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- PDB-2uzk: Crystal structure of the human FOXO3a-DBD bound to DNA -

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Basic information

Entry
Database: PDB / ID: 2uzk
TitleCrystal structure of the human FOXO3a-DBD bound to DNA
Components
  • 5'-D(*CP*TP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*C)-3'
  • 5'-D(*GP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*AP*G)-3'
  • FORKHEAD BOX PROTEIN O3AFOX proteins
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION / CHROMOSOMAL REARRANGEMENT / ACTIVATOR / APOPTOSIS / DNA-BINDING / WINGED HELIX / PROTO-ONCOGENE / FORKHEAD TRANSCRIPTION FACTORS / NUCLEAR PROTEIN / PHOSPHORYLATION / DNA-BINDING DOMAIN
Function / homology
Function and homology information


positive regulation of muscle atrophy / initiation of primordial ovarian follicle growth / positive regulation of hydrogen peroxide-mediated programmed cell death / RNA polymerase II transcription repressor complex / mitochondrial transcription factor activity / RUNX3 regulates BCL2L11 (BIM) transcription / cellular response to corticosterone stimulus / FOXO-mediated transcription of cell cycle genes / AKT phosphorylates targets in the nucleus / ovulation from ovarian follicle ...positive regulation of muscle atrophy / initiation of primordial ovarian follicle growth / positive regulation of hydrogen peroxide-mediated programmed cell death / RNA polymerase II transcription repressor complex / mitochondrial transcription factor activity / RUNX3 regulates BCL2L11 (BIM) transcription / cellular response to corticosterone stimulus / FOXO-mediated transcription of cell cycle genes / AKT phosphorylates targets in the nucleus / ovulation from ovarian follicle / response to water-immersion restraint stress / neuronal stem cell population maintenance / mitochondrial transcription / regulation of neural precursor cell proliferation / response to fatty acid / Signaling by NODAL / positive regulation of regulatory T cell differentiation / brain morphogenesis / positive regulation of endothelial cell apoptotic process / oocyte maturation / Regulation of FOXO transcriptional activity by acetylation / positive regulation of reactive oxygen species biosynthetic process / FOXO-mediated transcription of cell death genes / antral ovarian follicle growth / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / response to dexamethasone / response to starvation / Constitutive Signaling by AKT1 E17K in Cancer / Regulation of localization of FOXO transcription factors / DNA damage response, signal transduction by p53 class mediator / negative regulation of neuron differentiation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / canonical Wnt signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cellular response to glucose starvation / positive regulation of autophagy / extrinsic apoptotic signaling pathway in absence of ligand / tumor necrosis factor-mediated signaling pathway / FLT3 Signaling / negative regulation of cell migration / cellular response to nerve growth factor stimulus / positive regulation of erythrocyte differentiation / transcription coregulator binding / cellular response to glucose stimulus / MAPK6/MAPK4 signaling / negative regulation of canonical Wnt signaling pathway / chromatin DNA binding / beta-catenin binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / regulation of translation / cellular response to oxidative stress / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / mitochondrial outer membrane / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / 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 / Fork head domain signature 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 O3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTsai, K.-L. / Sun, Y.-J. / Huang, C.-Y. / Yang, J.-Y. / Hung, M.-C. / Hsiao, C.-D.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Crystal Structure of the Human Foxo3A-Dbd/DNA Complex Suggests the Effects of Post-Translational Modification.
Authors: Tsai, K.-L. / Sun, Y.-J. / Huang, C.-Y. / Yang, J.-Y. / Hung, M.-C. / Hsiao, C.-D.
History
DepositionApr 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FORKHEAD BOX PROTEIN O3A
B: 5'-D(*CP*TP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*C)-3'
C: FORKHEAD BOX PROTEIN O3A
D: 5'-D(*CP*TP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*C)-3'
E: 5'-D(*GP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*AP*G)-3'
F: 5'-D(*GP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*AP*G)-3'


Theoretical massNumber of molelcules
Total (without water)37,9196
Polymers37,9196
Non-polymers00
Water3,765209
1
A: FORKHEAD BOX PROTEIN O3A
B: 5'-D(*CP*TP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*C)-3'
E: 5'-D(*GP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*AP*G)-3'


Theoretical massNumber of molelcules
Total (without water)18,9603
Polymers18,9603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-23.2 kcal/mol
Surface area10450 Å2
MethodPISA
2
C: FORKHEAD BOX PROTEIN O3A
D: 5'-D(*CP*TP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*C)-3'
F: 5'-D(*GP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*AP*G)-3'


Theoretical massNumber of molelcules
Total (without water)18,9603
Polymers18,9603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-17.4 kcal/mol
Surface area10210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.964, 41.964, 354.817
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein FORKHEAD BOX PROTEIN O3A / FOX proteins / FORKHEAD IN RHABDOMYOSARCOMA-LIKE 1 / AF6Q21 PROTEIN


Mass: 11019.484 Da / Num. of mol.: 2 / Fragment: DNA-BINDING DOMAIN, RESIDUES 158-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O43524
#2: DNA chain 5'-D(*CP*TP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*C)-3' / FOXO CONSENSUS BINDING SEQUENCE


Mass: 3943.613 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#3: DNA chain 5'-D(*GP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*AP*G)-3' / FOXO CONSENSUS BINDING SEQUENCE


Mass: 3996.619 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.32 Å3/Da / Density % sol: 46.5 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 9491 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 40.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.5 / % possible all: 97.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C6Y

2c6y


Resolution: 2.7→24.13 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 25787.54 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: RESIDUES 157 AND 1157 ARE MET AND ALA, RESPECTIVELY. THESE TWO RESIDUES ARE GENERATED FORM VECTOR, NOT THE WILD TYPE FOXO3A AMINO ACIDS. THE SIDE CHAINS OF THESE RESIDUES 1242, 1243, 1245, ...Details: RESIDUES 157 AND 1157 ARE MET AND ALA, RESPECTIVELY. THESE TWO RESIDUES ARE GENERATED FORM VECTOR, NOT THE WILD TYPE FOXO3A AMINO ACIDS. THE SIDE CHAINS OF THESE RESIDUES 1242, 1243, 1245, 1246, AND 1247 IN CHAIN D ARE DISAPPEARED. GLY RESIDUES ARE SUBSTITUTED FOR THESE RESIDUES IN THIS MODEL. RESIDUES 1248-1253 IN CHAIN D ARE DISORDERED, AND NOT DETERMINED IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 488 5.3 %RANDOM
Rwork0.242 ---
obs0.242 9125 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 247.326 Å2 / ksol: 0.283777 e/Å3
Displacement parametersBiso mean: 18.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å22.68 Å20 Å2
2--1.57 Å20 Å2
3----3.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.7→24.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1478 1054 0 209 2741
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d32.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.45
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.011.5
X-RAY DIFFRACTIONc_mcangle_it3.412
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it2.942.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 69 5.1 %
Rwork0.324 1273 -
obs--84.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3DNA-RNA_REP.PARAMDNA-RNA_REP.TOP

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