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- PDB-6ako: Crystal Structure of FOXC2 DBD Bound to DBE2 DNA -

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Basic information

Entry
Database: PDB / ID: 6ako
TitleCrystal Structure of FOXC2 DBD Bound to DBE2 DNA
Components
  • DNA (5'-D(CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)-3')
  • DNA (5'-D(TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3')
  • Forkhead box protein C2
KeywordsDNA BINDING PROTEIN/DNA / FOXC / DNA binding domain / DNA recognition / Crystal Structure / Lymphoedema distichiasis syndrome / DNA BINDING PROTEIN-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 / positive regulation of vascular wound healing / Formation of intermediate mesoderm / glomerular endothelium development / embryonic viscerocranium morphogenesis / Formation of the ureteric bud / lymphangiogenesis / podocyte differentiation ...apoptotic process involved in outflow tract morphogenesis / negative regulation of apoptotic process involved in outflow tract morphogenesis / paraxial mesodermal cell fate commitment / positive regulation of vascular wound healing / Formation of intermediate mesoderm / glomerular endothelium development / embryonic viscerocranium morphogenesis / Formation of the ureteric bud / lymphangiogenesis / podocyte differentiation / glomerular mesangial cell development / neural crest cell development / regulation of organ growth / metanephros development / camera-type eye development / embryonic heart tube development / collagen fibril organization / positive regulation of cell adhesion mediated by integrin / positive regulation of cell migration involved in sprouting angiogenesis / artery morphogenesis / negative regulation of cold-induced thermogenesis / ureteric bud development / branching involved in blood vessel morphogenesis / DNA-binding transcription activator activity / ventricular cardiac muscle tissue morphogenesis / mesoderm development / blood vessel remodeling / anatomical structure morphogenesis / vascular endothelial growth factor receptor signaling pathway / cardiac muscle cell proliferation / somitogenesis / response to hormone / Notch signaling pathway / positive regulation of endothelial cell migration / ossification / blood vessel diameter maintenance / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription cis-regulatory region binding / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / chromatin / 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. ...: / : / 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)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.396 Å
AuthorsChen, X. / Wei, H. / Li, J. / Liang, X. / Dai, S. / Jiang, L. / Guo, M. / Chen, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China81372904 China
National Natural Science Foundation of China81570537 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural basis for DNA recognition by FOXC2.
Authors: Chen, X. / Wei, H. / Li, J. / Liang, X. / Dai, S. / Jiang, L. / Guo, M. / Qu, L. / Chen, Z. / Chen, L. / Chen, Y.
History
DepositionSep 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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: DNA (5'-D(CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)-3')
B: DNA (5'-D(TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3')
C: Forkhead box protein C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1474
Polymers22,1233
Non-polymers241
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-36 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.540, 72.924, 99.047
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: DNA chain DNA (5'-D(CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)-3')


Mass: 4932.272 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA (5'-D(TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3')


Mass: 4860.159 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein Forkhead box protein C2 / Forkhead-related protein FKHL14 / Mesenchyme fork head protein 1 / MFH-1 protein / Transcription factor FKH-14


Mass: 12330.169 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXC2, FKHL14, MFH1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99958
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.47 Å3/Da / Density % sol: 64.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 50 mM Bis-Tris propane (pH 6.68), 14% PEG4K, 200 mM NaCl, 10 mM MgCl2, 1 mM TCEP

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Data collection

DiffractionMean temperature: 85 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.587 Å
DetectorType: RIGAKU / Detector: CCD / Date: Mar 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.587 Å / Relative weight: 1
ReflectionResolution: 2.396→40.97 Å / Num. obs: 11726 / % possible obs: 92 % / Redundancy: 12.1 % / CC1/2: 1 / Rmerge(I) obs: 0.04052 / Net I/σ(I): 34.65
Reflection shellResolution: 2.396→2.482 Å / Rmerge(I) obs: 0.3016 / Num. unique obs: 780 / CC1/2: 0.979

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data collection
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X07

5x07


Resolution: 2.396→40.97 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.5
RfactorNum. reflection% reflection
Rfree0.2503 1162 9.99 %
Rwork0.2277 --
obs0.23 11631 91.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.396→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms812 650 1 10 1473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031564
X-RAY DIFFRACTIONf_angle_d0.6112247
X-RAY DIFFRACTIONf_dihedral_angle_d22.676819
X-RAY DIFFRACTIONf_chiral_restr0.035235
X-RAY DIFFRACTIONf_plane_restr0.003180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3963-2.50530.37591010.3423905X-RAY DIFFRACTION65
2.5053-2.63740.34631220.34741108X-RAY DIFFRACTION80
2.6374-2.80260.40941470.34991333X-RAY DIFFRACTION95
2.8026-3.01890.36431540.34471390X-RAY DIFFRACTION99
3.0189-3.32260.30551540.27411371X-RAY DIFFRACTION97
3.3226-3.80310.25691540.23271397X-RAY DIFFRACTION99
3.8031-4.79040.20851600.19771446X-RAY DIFFRACTION100
4.7904-40.97520.19711700.16851519X-RAY DIFFRACTION100
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)
15.7258-0.7520.2898.6502-5.25326.25950.64540.0840.65160.88260.15281.3843-3.39410.8272-0.65591.4645-0.0410.06250.93120.04210.7022-10.29995.6092-8.6848
22.2155-0.3551-1.20152.88420.97312.9438-0.6506-0.52260.36170.04540.4491-0.0126-1.94550.7060.25650.90230.0012-0.03730.7139-0.04380.6054-5.02451.27878.0135
32.2937-1.5533-1.31612.9878-1.44864.86950.7722-1.1970.35340.8613-0.39110.8488-1.03080.6639-0.34961.03560.05490.09670.9866-0.20050.674-16.71481.44522.9517
48.10353.2940.47623.6131.99427.46750.5174-0.4005-1.9574-0.02111.03571.7431-0.04780.2049-0.86631.4784-0.1685-0.04721.64850.08990.9407-18.6559-9.105930.4288
53.3825-0.39431.01343.61131.12796.52180.1423-0.33570.2718-0.12250.2925-0.7079-1.93260.9729-0.25480.9260.13280.05041.17060.00850.603-11.6898-6.2524.0024
61.3599-1.1431-1.11014.26971.20722.94770.1056-0.32460.5669-0.07940.3935-0.0641-1.67290.0865-0.31840.97140.055-0.08040.7561-0.00440.6148-8.34624.20843.1286
72.79124.1508-1.16448.31521.40587.23660.81721.4513-1.766-0.5143-1.20270.7849-1.24390.5922-0.05460.82680.0088-0.31521.723-0.06150.948-10.0827-0.3438-13.8795
83.4064-0.8370.56612.11250.56772.69750.0596-0.5941-0.68390.3718-0.0399-0.13730.07880.0542-0.11950.44690.0076-0.04140.50350.00270.4887-6.4871-16.42328.3281
93.9711-0.0026-0.17133.9623-0.09614.3460.18430.18120.70970.42770.1273-0.7195-0.7010.8179-0.19210.597-0.08220.02410.7269-0.14230.5299-3.3946-8.15812.3321
103.57051.2631-2.85351.89510.69427.30380.1682-0.16350.35220.0036-0.39760.0369-1.1722-0.620.4960.44860.0423-0.09610.73670.07170.7038-18.9685-9.95396.4513
110.9256-0.6491.13373.7245-0.05761.7347-0.5981.02790.01322.23270.3109-0.30330.3463-0.52160.92751.15420.03020.260.75520.07870.631-19.9953-19.069721.3646
122.62010.0312-0.35053.03490.6623.0353-0.09870.5052-0.3497-0.5799-0.1703-0.13580.2344-0.00570.17470.50430.0876-0.03170.8097-0.02360.5364-15.4982-15.67770.5278
136.0962-2.14150.66234.7311-0.093.0585-0.42880.8266-0.3612-0.40410.03420.6743-1.18270.55360.17070.5384-0.1573-0.11950.65120.06890.5497-8.3829-12.9786-6.6413
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 10 )
3X-RAY DIFFRACTION3chain 'A' and (resid 11 through 15 )
4X-RAY DIFFRACTION4chain 'A' and (resid 16 through 16 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 5 )
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 15 )
7X-RAY DIFFRACTION7chain 'B' and (resid 16 through 16 )
8X-RAY DIFFRACTION8chain 'C' and (resid 70 through 105 )
9X-RAY DIFFRACTION9chain 'C' and (resid 106 through 126 )
10X-RAY DIFFRACTION10chain 'C' and (resid 127 through 133 )
11X-RAY DIFFRACTION11chain 'C' and (resid 134 through 144 )
12X-RAY DIFFRACTION12chain 'C' and (resid 145 through 158 )
13X-RAY DIFFRACTION13chain 'C' and (resid 159 through 166 )

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