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- PDB-6akp: Crystal Structural of FOXC2 DNA binding domain bound to PC promoter -

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Basic information

Entry
Database: PDB / ID: 6akp
TitleCrystal Structural of FOXC2 DNA binding domain bound to PC promoter
Components
  • DNA (5'-D(AP*CP*AP*CP*AP*AP*AP*TP*AP*TP*TP*TP*GP*TP*GP*T)-3')
  • Forkhead box protein C2
KeywordsDNA BINDING PROTEIN/DNA / FOXC / DNA binding domain / DNA recognition / Crystal Structural / 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 / cardiac muscle cell proliferation / vascular endothelial growth factor receptor signaling pathway / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.323 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(AP*CP*AP*CP*AP*AP*AP*TP*AP*TP*TP*TP*GP*TP*GP*T)-3')
B: DNA (5'-D(AP*CP*AP*CP*AP*AP*AP*TP*AP*TP*TP*TP*GP*TP*GP*T)-3')
C: Forkhead box protein C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1474
Polymers22,1233
Non-polymers241
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-24 kcal/mol
Surface area11090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.837, 80.214, 101.154
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(AP*CP*AP*CP*AP*AP*AP*TP*AP*TP*TP*TP*GP*TP*GP*T)-3')


Mass: 4896.216 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.84 Å3/Da / Density % sol: 67.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 50mM NaOAc pH4.7, 14%PEG4K, 200mM NaCl, 10mM MgCl2, 0.5mM TCEP

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Data collection

DiffractionMean temperature: 85 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.323→37.29 Å / Num. obs: 15111 / % possible obs: 98 % / Redundancy: 13.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.1289 / Net I/σ(I): 13.97
Reflection shellResolution: 2.323→2.407 Å / Rmerge(I) obs: 0.9166 / Num. unique obs: 1366 / CC1/2: 0.913

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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: 2.323→37.283 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.12
RfactorNum. reflection% reflection
Rfree0.247 1505 10.03 %
Rwork0.2174 --
obs0.2204 15012 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.323→37.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms797 650 1 16 1464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041548
X-RAY DIFFRACTIONf_angle_d0.652224
X-RAY DIFFRACTIONf_dihedral_angle_d22.608805
X-RAY DIFFRACTIONf_chiral_restr0.035233
X-RAY DIFFRACTIONf_plane_restr0.003176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3235-2.39850.41531200.36261095X-RAY DIFFRACTION91
2.3985-2.48420.33331350.33111207X-RAY DIFFRACTION98
2.4842-2.58360.35951360.31311226X-RAY DIFFRACTION99
2.5836-2.70120.32871350.30841207X-RAY DIFFRACTION100
2.7012-2.84350.30471380.29741235X-RAY DIFFRACTION100
2.8435-3.02160.34361370.30271237X-RAY DIFFRACTION100
3.0216-3.25480.29091350.27891209X-RAY DIFFRACTION98
3.2548-3.58210.3151390.23741223X-RAY DIFFRACTION98
3.5821-4.09990.24841390.20671259X-RAY DIFFRACTION99
4.0999-5.16320.17971420.17271278X-RAY DIFFRACTION100
5.1632-37.28810.19461490.15821331X-RAY DIFFRACTION99
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)
10.5063-0.1883-0.77922.7209-0.75992.34310.6968-0.0847-1.4723-0.15410.95080.03372.5221-2.1791-1.67651.7296-0.1176-0.09251.31140.15261.1552-32.141372.628210.7602
25.31770.96271.47772.29830.07122.11840.6611-0.420.74271.4590.6405-2.23360.76670.6058-0.97530.844-0.0658-0.01770.91240.08821.0006-26.357182.840423.8216
31.9748-0.26110.35064.9175-1.9264.34180.273-0.7748-0.41960.65850.74520.0614-0.4074-1.3696-0.40751.1002-0.002-0.00840.9476-0.00510.7449-27.985178.669443.627
44.00083.9283-0.10097.87290.23992.12670.46630.9310.107-0.8732-0.1376-0.4007-3.1174-1.2746-0.10321.50710.1504-0.1541.08570.03510.9234-24.481285.940344.1005
53.0646-1.5837-0.75711.9446-1.50172.13590.44390.4123-0.51870.268-0.021-0.54480.702-0.8879-0.1770.994-0.004-0.08970.85320.05040.7387-28.835978.348719.7119
63.5744-0.21671.44772.429-0.11532.90950.21240.05290.7436-0.2958-0.2222-0.11620.0032-0.25210.00190.45540.01970.0230.3730.06820.4955-39.612994.53892.3863
75.7678-2.4925-0.26557.427-3.6195.6157-0.2534-1.55940.01660.89220.4562-0.288-0.96670.2366-0.49460.5717-0.10920.00230.6824-0.01990.6416-28.6235101.356911.1076
89.0726-1.62992.68463.7052-1.18936.5191-0.2935-0.81531.25880.7116-0.2805-0.0005-0.4723-0.7750.26180.62130.0273-0.01040.6158-0.00140.5335-39.391794.706912.1747
91.3523-1.20651.27325.66310.19462.56980.2515-1.1813-0.92610.8895-0.62440.51620.8377-0.82880.06320.6327-0.09990.03070.8240.14040.7432-48.001890.25049.2385
105.17250.260.31094.4171-0.54832.3230.0106-0.6563-0.53340.17330.06170.00650.9640.2714-0.09820.77470.0482-0.0150.48090.05280.6706-36.03284.45377.9734
118.29492.45685.59327.19511.76863.7860.53560.8449-1.1928-0.73720.0104-0.42120.50120.8073-0.07780.59110.05890.0510.8194-0.04180.7208-24.87590.91993.8281
122.2018-1.2346-1.7180.67110.96851.31580.8052-0.68820.95342.21870.71970.8332-0.11880.7608-1.40151.077-0.0395-0.07591.37120.17591.1601-23.541994.506617.8955
132.84970.00410.14492.6753-0.02931.2356-0.0236-0.1071-0.1514-0.3479-0.1939-0.32660.378-0.16610.04350.5323-0.020.05640.72140.06690.6538-30.249698.1432-0.9593
142.8002-1.3087-1.79796.86671.70213.2417-0.65561.16920.2372-0.64190.9864-1.30941.0993-0.4758-0.08891.0915-0.21340.17431.3139-0.20530.9789-29.928494.0615-10.2621
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 13 )
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 18 )
3X-RAY DIFFRACTION3chain 'A' and (resid 19 through 24 )
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 13 )
5X-RAY DIFFRACTION5chain 'B' and (resid 14 through 24 )
6X-RAY DIFFRACTION6chain 'C' and (resid 70 through 87 )
7X-RAY DIFFRACTION7chain 'C' and (resid 88 through 94 )
8X-RAY DIFFRACTION8chain 'C' and (resid 95 through 105 )
9X-RAY DIFFRACTION9chain 'C' and (resid 106 through 112 )
10X-RAY DIFFRACTION10chain 'C' and (resid 113 through 126 )
11X-RAY DIFFRACTION11chain 'C' and (resid 127 through 133 )
12X-RAY DIFFRACTION12chain 'C' and (resid 134 through 144 )
13X-RAY DIFFRACTION13chain 'C' and (resid 145 through 162 )
14X-RAY DIFFRACTION14chain 'C' and (resid 163 through 168 )

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