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- PDB-6lbm: Crystal Structure of FOXC2-DBD bound to a palindromic DNA sequence -

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Basic information

Entry
Database: PDB / ID: 6lbm
TitleCrystal Structure of FOXC2-DBD bound to a palindromic DNA sequence
Components
  • Forkhead box protein C2FOX proteins
  • IRE0
KeywordsTRANSCRIPTION / Forkhead transcription / DNA binding specificity
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 / Formation of the ureteric bud / glomerular endothelium development / Formation of intermediate mesoderm / positive regulation of vascular wound healing / embryonic viscerocranium morphogenesis / glomerular mesangial cell development / podocyte differentiation ...apoptotic process involved in outflow tract morphogenesis / negative regulation of apoptotic process involved in outflow tract morphogenesis / paraxial mesodermal cell fate commitment / Formation of the ureteric bud / glomerular endothelium development / Formation of intermediate mesoderm / positive regulation of vascular wound healing / embryonic viscerocranium morphogenesis / glomerular mesangial cell development / 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 / cardiac muscle cell proliferation / ureteric bud development / artery morphogenesis / ventricular cardiac muscle tissue morphogenesis / DNA-binding transcription activator activity / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / mesoderm development / anatomical structure morphogenesis / blood vessel remodeling / vascular endothelial growth factor receptor signaling pathway / somitogenesis / Notch signaling pathway / blood vessel diameter maintenance / positive regulation of endothelial cell migration / 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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
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: 2.841 Å
AuthorsLi, J. / Dai, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81372904 China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Mechanism of forkhead transcription factors binding to a novel palindromic DNA site.
Authors: Li, J. / Dai, S. / Chen, X. / Liang, X. / Qu, L. / Jiang, L. / Guo, M. / Zhou, Z. / Wei, H. / Zhang, H. / Chen, Z. / Chen, L. / Chen, Y.
History
DepositionNov 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Forkhead box protein C2
A: IRE0
B: IRE0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6204
Polymers24,5963
Non-polymers241
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, bicare
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-33 kcal/mol
Surface area10210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.521, 42.656, 103.277
Angle α, β, γ (deg.)90.000, 103.160, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Forkhead box protein C2 / FOX proteins / 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
#2: DNA chain IRE0


Mass: 6132.990 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)
#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 / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.21 Å3/Da / Density % sol: 70.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 50 mM HEPES, pH 7.5, 8%-12% PEG4000 (w/v), 250 mM NaCl, 10 mM MgCl2 and 1 mM TCEP.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.84→39.281 Å / Num. obs: 9399 / % possible obs: 94.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 71.1 Å2 / CC1/2: 0.986 / Net I/σ(I): 15.43
Reflection shellResolution: 2.84→2.94 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 547 / CC1/2: 0.718

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
PHENIXphasing
HKL-2000V716.1data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AKO

6ako


Resolution: 2.841→39.281 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.9
RfactorNum. reflection% reflection
Rfree0.2626 414 4.41 %
Rwork0.2327 --
obs0.234 9390 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 185.17 Å2 / Biso mean: 82.1874 Å2 / Biso min: 22.53 Å2
Refinement stepCycle: final / Resolution: 2.841→39.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms790 590 1 12 1393
Biso mean--69.32 66.26 -
Num. residues----124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051476
X-RAY DIFFRACTIONf_angle_d0.7092115
X-RAY DIFFRACTIONf_chiral_restr0.038225
X-RAY DIFFRACTIONf_plane_restr0.004171
X-RAY DIFFRACTIONf_dihedral_angle_d24.336774
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.841-2.940.30761200.3076265185
2.94-4.09580.27811480.24993118100
4.0958-39.2810.24411460.2062320799
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)
15.0022-1.3206-0.21192.17440.24755.95980.0073-0.5350.2320.15930.19850.331-0.5631-0.3749-0.35710.2794-0.00940.02030.40940.02820.277117.4709-6.21875.1432
23.8067-1.6607-2.39035.9382.99286.31110.5058-0.81760.07140.9985-0.1262-2.07390.0994-0.432-0.46350.3384-0.0136-0.13710.5278-0.02910.4898124.6413-10.034811.6036
32.87222.13443.79357.235-2.9392.00090.6946-1.04851.83471.69010.9840.2948-1.62870.06391.72520.7932-0.17330.1160.2354-0.82820.2779117.87722.387613.5757
46.523-1.6312-0.32096.1650.90825.11750.6314-0.6665-0.4920.8244-0.56520.2380.1595-1.1563-0.260.3474-0.1033-0.03090.57020.09680.3796112.7833-13.055513.0713
54.1064-1.67031.18991.3582-0.27080.40640.8071-0.3418-1.47410.4803-0.13411.24150.59691.615-0.36870.97450.0711-0.28211.3950.14160.6806126.4261-23.464918.3199
64.6115-3.4103-3.34998.29450.57583.0852-0.2989-0.0018-1.2554-0.6583-0.23750.7960.7889-0.96680.31350.5671-0.13940.00650.28610.1230.4592119.0971-20.47715.8461
79.5189-4.50114.28062.6138-1.66572.199-0.28881.78270.3132-0.9285-0.23220.836-0.05580.37250.05480.48970.0293-0.2820.4977-0.00951.0524117.6062-13.7639-3.7618
87.9374-4.52940.6247.5747-0.1382.95510.26541.3027-2.0433-2.3980.29051.6106-0.6233-0.3894-0.39250.67650.17260.03530.5777-0.16020.4307117.9489-5.793-4.4542
94.18355.35992.42259.87532.08971.72840.3302-0.0179-0.9947-1.34060.28120.16480.0971-0.03410.32470.3730.35-0.46011.2263-0.59291.1421110.5109-14.044-7.2722
104.1516-0.21330.13913.8719-0.30724.06960.0431-1.6898-1.08241.31230.2407-0.0283-0.5097-0.2424-0.22870.7034-0.02370.0091.27020.21030.8218108.4284-13.239319.6344
113.3866-2.42260.12273.5097-1.57774.8995-0.0783-1.9772-0.26381.01540.69420.9655-0.667-1.004-0.46440.8625-0.1780.00261.53220.11350.8241106.2501-12.028819.7986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 71 through 87 )C71 - 87
2X-RAY DIFFRACTION2chain 'C' and (resid 88 through 105 )C88 - 105
3X-RAY DIFFRACTION3chain 'C' and (resid 106 through 112 )C106 - 112
4X-RAY DIFFRACTION4chain 'C' and (resid 113 through 133 )C113 - 133
5X-RAY DIFFRACTION5chain 'C' and (resid 134 through 144 )C134 - 144
6X-RAY DIFFRACTION6chain 'C' and (resid 145 through 152 )C145 - 152
7X-RAY DIFFRACTION7chain 'C' and (resid 153 through 157 )C153 - 157
8X-RAY DIFFRACTION8chain 'C' and (resid 158 through 162 )C158 - 162
9X-RAY DIFFRACTION9chain 'C' and (resid 163 through 168 )C163 - 168
10X-RAY DIFFRACTION10chain 'A' and (resid 1 through 15 )A1 - 15
11X-RAY DIFFRACTION11chain 'B' and (resid 7 through 20 )B7 - 20

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