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- PDB-6o3t: Structural basis of FOXC2 and DNA interactions -

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Basic information

Entry
Database: PDB / ID: 6o3t
TitleStructural basis of FOXC2 and DNA interactions
Components
  • DNA (5'-D(*AP*AP*AP*TP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*GP*CP*CP*CP*G)-3')
  • DNA (5'-D(*TP*TP*CP*GP*GP*GP*CP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*AP*T)-3')
  • Forkhead box protein C2
KeywordsGENE REGULATION/DNA / Forkhead Transcription Factor DNA binding / GENE REGULATION / GENE REGULATION-DNA complex
Function / homology
Function and homology information


apoptotic process involved in outflow tract morphogenesis / negative regulation of apoptotic process involved in outflow tract morphogenesis / paraxial mesodermal cell fate commitment / glomerular endothelium development / Formation of intermediate mesoderm / embryonic viscerocranium morphogenesis / positive regulation of vascular wound healing / glomerular mesangial cell development / Formation of the ureteric bud / podocyte differentiation ...apoptotic process involved in outflow tract morphogenesis / negative regulation of apoptotic process involved in outflow tract morphogenesis / paraxial mesodermal cell fate commitment / glomerular endothelium development / Formation of intermediate mesoderm / embryonic viscerocranium morphogenesis / positive regulation of vascular wound healing / glomerular mesangial cell development / Formation of the ureteric bud / podocyte differentiation / lymphangiogenesis / neural crest cell development / regulation of organ growth / metanephros development / embryonic heart tube development / camera-type eye development / collagen fibril organization / positive regulation of cell adhesion mediated by integrin / negative regulation of cold-induced thermogenesis / ventricular cardiac muscle tissue morphogenesis / cardiac muscle cell proliferation / artery morphogenesis / ureteric bud development / DNA-binding transcription activator activity / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / mesoderm development / blood vessel remodeling / anatomical structure morphogenesis / vascular endothelial growth factor receptor signaling pathway / somitogenesis / Notch signaling pathway / positive regulation of endothelial cell migration / blood vessel diameter maintenance / ossification / response to hormone / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / chromatin DNA binding / sequence-specific double-stranded DNA binding / insulin receptor signaling pathway / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / cell differentiation / nuclear body / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / Fork head domain conserved site1 / Fork head domain signature 1. / 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 ...: / Fork head domain conserved site1 / Fork head domain signature 1. / 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 C2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsNam, H.-J. / Li, S.
CitationJournal: Acs Omega / Year: 2019
Title: Crystal Structure of FOXC2 in Complex with DNA Target.
Authors: Li, S. / Pradhan, L. / Ashur, S. / Joshi, A. / Nam, H.J.
History
DepositionFeb 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 C2
C: DNA (5'-D(*AP*AP*AP*TP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*GP*CP*CP*CP*G)-3')
D: DNA (5'-D(*TP*TP*CP*GP*GP*GP*CP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*AP*T)-3')
B: Forkhead box protein C2


Theoretical massNumber of molelcules
Total (without water)35,4164
Polymers35,4164
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-35 kcal/mol
Surface area15120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.365, 41.812, 82.654
Angle α, β, γ (deg.)90.00, 98.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Forkhead box protein C2 / Forkhead-related protein FKHL14 / Mesenchyme fork head protein 1 / MFH-1 protein / Transcription factor FKH-14


Mass: 11266.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXC2, FKHL14, MFH1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99958
#2: DNA chain DNA (5'-D(*AP*AP*AP*TP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*GP*CP*CP*CP*G)-3')


Mass: 6430.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*TP*CP*GP*GP*GP*CP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*AP*T)-3')


Mass: 6452.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 3.1 Å3/Da / Density % sol: 64.62 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG MME 2000, 100 mM sodium acetate pH 4.6, 200 mM ammonium sulfate, 10 mM BME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.05→40 Å / Num. obs: 8013 / % possible obs: 96.8 % / Redundancy: 3 % / Biso Wilson estimate: 73.94 Å2 / Rpim(I) all: 0.065 / Rsym value: 0.097 / Net I/σ(I): 12.9
Reflection shellResolution: 3.05→3.15 Å / Rpim(I) all: 0.233 / Rsym value: 0.356

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X07

5x07


Resolution: 3.06→36.377 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2683 389 4.93 %
Rwork0.2332 --
obs0.2349 7889 93.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.06→36.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1342 855 0 0 2197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112338
X-RAY DIFFRACTIONf_angle_d1.4293337
X-RAY DIFFRACTIONf_dihedral_angle_d21.6321235
X-RAY DIFFRACTIONf_chiral_restr0.074355
X-RAY DIFFRACTIONf_plane_restr0.01278
LS refinement shellResolution: 3.0601→3.169 Å
RfactorNum. reflection% reflection
Rfree0.3619 114 -
Rwork0.2658 2313 -
obs--88 %
Refinement TLS params.Method: refined / Origin x: 17.7311 Å / Origin y: 15.0212 Å / Origin z: 103.7462 Å
111213212223313233
T0.4237 Å2-0.0235 Å20.2387 Å2-0.7044 Å2-0.0032 Å2--1.1286 Å2
L4.5476 °20.0312 °20.4604 °2-2.3091 °2-0.1718 °2--3.068 °2
S-0.2778 Å °1.4765 Å °-0.1193 Å °-0.4496 Å °0.2397 Å °-0.3161 Å °0.113 Å °0.6186 Å °0.0116 Å °
Refinement TLS groupSelection details: all

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