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- PDB-3l2c: Crystal Structure of the DNA Binding Domain of FOXO4 Bound to DNA -

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Basic information

Entry
Database: PDB / ID: 3l2c
TitleCrystal Structure of the DNA Binding Domain of FOXO4 Bound to DNA
Components
  • FOXO consensus binding sequence, minus strand
  • FOXO consensus binding sequence, plus strand
  • Forkhead box protein O4FOX proteins
KeywordsTRANSCRIPTION/DNA / forkhead / forkhead box / winged helix / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


negative regulation of smooth muscle cell differentiation / FOXO-mediated transcription of cell cycle genes / AKT phosphorylates targets in the nucleus / response to water-immersion restraint stress / negative regulation of G0 to G1 transition / Cardiogenesis / muscle organ development / Regulation of FOXO transcriptional activity by acetylation / FOXO-mediated transcription of cell death genes / positive regulation of smooth muscle cell migration ...negative regulation of smooth muscle cell differentiation / FOXO-mediated transcription of cell cycle genes / AKT phosphorylates targets in the nucleus / response to water-immersion restraint stress / negative regulation of G0 to G1 transition / Cardiogenesis / muscle organ development / Regulation of FOXO transcriptional activity by acetylation / FOXO-mediated transcription of cell death genes / positive regulation of smooth muscle cell migration / Constitutive Signaling by AKT1 E17K in Cancer / mitotic G2 DNA damage checkpoint signaling / Regulation of localization of FOXO transcription factors / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of angiogenesis / response to nutrient levels / promoter-specific chromatin binding / stem cell differentiation / beta-catenin binding / sequence-specific double-stranded DNA binding / insulin receptor signaling pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / response to oxidative stress / sequence-specific DNA binding / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / 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 ...: / 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 O4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.868 Å
AuthorsBoura, E. / Silhan, J. / Sulc, M. / Brynda, J. / Obsilova, V. / Obsil, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structure of the human FOXO4-DBD-DNA complex at 1.9 A resolution reveals new details of FOXO binding to the DNA
Authors: Boura, E. / Rezabkova, L. / Brynda, J. / Obsilova, V. / Obsil, T.
History
DepositionDec 15, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionDec 29, 2009ID: 3BPY
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: FOXO consensus binding sequence, plus strand
C: FOXO consensus binding sequence, minus strand
A: Forkhead box protein O4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2665
Polymers20,2173
Non-polymers492
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-20 kcal/mol
Surface area8650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.810, 71.700, 131.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: DNA chain FOXO consensus binding sequence, plus strand


Mass: 3943.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA
#2: DNA chain FOXO consensus binding sequence, minus strand


Mass: 3996.619 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA
#3: Protein Forkhead box protein O4 / FOX proteins / Forkhead transcription factor FOXO4 / Fork head domain transcription factor AFX1


Mass: 12276.740 Da / Num. of mol.: 1 / Fragment: DNA binding domain, UNP residues 86-187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AFX, AFX1, FOXO4, MLLT7 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P98177
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: HEPES, MgCl2, PEG MME, pH 7.3, vapor diffusion, hanging drop, temperature 292K, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2MgCl211
3PEG MME11
4HEPES12
5MgCl212
6PEG MME12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 5, 2007
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.868→65.938 Å / Num. all: 16689 / Num. obs: 16135 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 12.2
Reflection shellResolution: 1.868→1.96 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3 / Num. measured all: 12693 / Num. unique all: 1953 / Rsym value: 0.251 / % possible all: 81.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.04 Å35.47 Å
Translation2.04 Å35.47 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
MAR345dtbdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UZK

2uzk


Resolution: 1.868→19 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.524 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 807 5 %RANDOM
Rwork0.193 ---
obs0.195 16083 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.875 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2--0.17 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.868→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms697 527 2 163 1389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211306
X-RAY DIFFRACTIONr_angle_refined_deg1.9242.4311874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.592584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.78423.42935
X-RAY DIFFRACTIONr_dihedral_angle_3_deg6.8715126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.219155
X-RAY DIFFRACTIONr_chiral_restr0.1090.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02807
X-RAY DIFFRACTIONr_nbd_refined0.1850.2478
X-RAY DIFFRACTIONr_nbtor_refined0.30.2820
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2140
X-RAY DIFFRACTIONr_metal_ion_refined0.0390.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.211
X-RAY DIFFRACTIONr_mcbond_it1.2341.5437
X-RAY DIFFRACTIONr_mcangle_it1.8742675
X-RAY DIFFRACTIONr_scbond_it2.00931164
X-RAY DIFFRACTIONr_scangle_it2.8294.51199
LS refinement shellResolution: 1.868→1.916 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 45 -
Rwork0.235 997 -
all-1042 -
obs--89.21 %

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