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- PDB-7cby: Structure of FOXG1 DNA binding domain bound to DBE2 DNA site -

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Basic information

Entry
Database: PDB / ID: 7cby
TitleStructure of FOXG1 DNA binding domain bound to DBE2 DNA site
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 G1
KeywordsTRANSCRIPTION / FOXG1 / Forkhead box / transcription factors / FOXG1 syndrome / DBE2
Function / homology
Function and homology information


pyramidal neuron migration to cerebral cortex / FOXO-mediated transcription of cell cycle genes / neuron fate determination / dorsal/ventral pattern formation / axon midline choice point recognition / inner ear morphogenesis / positive regulation of neuroblast proliferation / negative regulation of neuron differentiation / Regulation of MECP2 expression and activity / neuroblast proliferation ...pyramidal neuron migration to cerebral cortex / FOXO-mediated transcription of cell cycle genes / neuron fate determination / dorsal/ventral pattern formation / axon midline choice point recognition / inner ear morphogenesis / positive regulation of neuroblast proliferation / negative regulation of neuron differentiation / Regulation of MECP2 expression and activity / neuroblast proliferation / positive regulation of cell cycle / positive regulation of neuron differentiation / regulation of mitotic cell cycle / brain development / sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / 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
DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / Forkhead box protein G1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.646 Å
AuthorsDai, S.Y. / Li, J. / Chen, Y.H.
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structural Basis for DNA Recognition by FOXG1 and the Characterization of Disease-causing FOXG1 Mutations.
Authors: Dai, S. / Li, J. / Zhang, H. / Chen, X. / Guo, M. / Chen, Z. / Chen, Y.
History
DepositionJun 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 29, 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(*TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3')
B: DNA (5'-D(*CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)-3')
C: Forkhead box protein G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3844
Polymers22,2783
Non-polymers1061
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-20 kcal/mol
Surface area10610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.126, 61.446, 73.594
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: 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: obtained synthetically / Details: SF file contains Friedel pairs. / Source: (synth.) Homo sapiens (human)
#2: 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: obtained synthetically / Details: SF file contains Friedel pairs. / Source: (synth.) Homo sapiens (human)
#3: Protein Forkhead box protein G1 / Brain factor 1 / BF1 / Brain factor 2 / hBF-2 / Forkhead box protein G1A / Forkhead box protein G1B ...Brain factor 1 / BF1 / Brain factor 2 / hBF-2 / Forkhead box protein G1A / Forkhead box protein G1B / Forkhead box protein G1C / Forkhead-related protein FKHL1 / HFK1 / Forkhead-related protein FKHL2 / HFK2 / Forkhead-related protein FKHL3 / HFK3


Mass: 12485.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Homo sapiens (human)
Gene: FOXG1, FKH2, FKHL1, FKHL2, FKHL3, FKHL4, FOXG1A, FOXG1B, FOXG1C
Production host: Escherichia coli O103:H2 str. 12009 (bacteria)
References: UniProt: P55316
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 80 mM NaCl, 40 mM Sodium cacodylate, pH 6.0, 45% 2-Methyl-2,4-pentanediol, 12 mM spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.64→22.9 Å / Num. obs: 26897 / % possible obs: 98.9 % / Redundancy: 13.7 % / Rrim(I) all: 0.035 / Net I/σ(I): 20.7
Reflection shellResolution: 1.64→1.7 Å / Num. unique obs: 2635 / Rpim(I) all: 0.312

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Processing

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

6ako


Resolution: 1.646→22.871 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1822 2449 4.88 %
Rwork0.1562 47693 -
obs0.1575 25550 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.4 Å2 / Biso mean: 21.948 Å2 / Biso min: 4.27 Å2
Refinement stepCycle: final / Resolution: 1.646→22.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms825 650 7 351 1833
Biso mean--33.98 34.14 -
Num. residues----132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091603
X-RAY DIFFRACTIONf_angle_d1.1172299
X-RAY DIFFRACTIONf_chiral_restr0.052240
X-RAY DIFFRACTIONf_plane_restr0.009185
X-RAY DIFFRACTIONf_dihedral_angle_d21.7251056
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6462-1.67970.17831370.1676247687
1.6797-1.71630.18441340.1775275496
1.7163-1.75620.18751520.1709281899
1.7562-1.80010.21671580.16942809100
1.8001-1.84870.22361470.16872859100
1.8487-1.90310.20891490.16282870100
1.9031-1.96450.1621210.15442868100
1.9645-2.03470.20061360.16182873100
2.0347-2.11610.19041600.16172820100
2.1161-2.21230.22591210.15772880100
2.2123-2.32880.19911370.15712870100
2.3288-2.47460.1931480.1622855100
2.4746-2.66540.20051340.15932902100
2.6654-2.93310.20281750.17132809100
2.9331-3.35640.1681360.1445284299
3.3564-4.22430.14411540.12892840100
4.2243-100.16391500.1563254890
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)
13.0533-0.6975-0.28150.6484-0.48644.2081-0.17390.05020.16990.05930.02420.174-0.49360.15090.07920.18070.0185-0.03280.11070.01830.0487-9.971-0.54884.4643
20.13170.0865-0.47641.72680.35192.53510.16970.4434-1.2569-0.08430.1003-0.5425-0.06620.8005-0.02520.0840.07670.0330.242-0.00830.20824.5188-9.276810.8523
32.7292-0.7153-0.10355.2221-1.93136.8120.0215-0.29690.14780.6023-0.1048-0.111-0.68840.89480.05050.0792-0.004-0.02110.22220.0650.17919.0377-5.62728.1154
43.0253-2.4305-2.32314.77813.06463.9199-0.0696-0.1286-0.62750.2853-0.04590.70060.27530.01940.01090.25170.0224-0.05490.23690.08890.23311.1759-15.922335.8311
53.01741.22450.790.83511.00142.40080.01230.5792-1.54760.12710.49320.0762-0.00591.4551-0.17080.10.1154-0.05260.35520.0170.283313.086-13.352427.9498
61.9349-0.42870.73280.86331.11764.17530.09780.05620.1366-0.0545-0.144-0.0864-0.4070.42970.0290.08770.00560.00810.13310.05960.13483.1559-2.902918.3381
75.77660.95712.46042.65140.65132.6648-0.03930.4582-0.4709-0.28770.0909-0.19790.03310.5115-0.04830.16880.0210.02380.19580.01380.0828-5.596-5.10670.1936
81.7046-0.836-0.6742.91840.02290.9086-0.0432-0.22870.320.76680.0029-0.6973-0.3520.342-0.03140.2224-0.0323-0.01850.0901-0.00730.1616-4.46574.580831.2394
93.98930.5540.93661.99520.81052.4189-0.077-0.2813-0.18840.0509-0.06750.1670.2047-0.1905-0.04440.0706-0.00670.02720.07150.02210.0833-12.2663-8.445225.52
102.31680.0031-0.32212.57280.58863.55080.06760.10440.0454-0.0441-0.25850.4675-0.071-0.6695-0.03490.05550.01420.01550.136-0.010.1016-17.8153-4.084520.4665
112.5444-1.28350.82743.6118-0.33123.30320.17350.85780.66860.0871-0.4995-0.156-0.85751.1468-0.04670.1370.05480.0603-0.2172-0.04550.1321-8.39015.932425.0969
123.58650.2170.10412.29490.92763.09780.17960.104-0.2586-0.0708-0.1824-0.22250.0914-0.04060.02930.06420.0297-0.00330.05180.02910.0415-6.9716-7.080416.4004
138.0342-1.07722.36452.25780.31583.7150.18850.8185-0.1489-0.818-0.20811.41320.1805-1.0672-0.00480.30410.0072-0.13930.6518-0.05540.4092-23.3044-11.48227.1907
141.9359-0.61722.15240.6746-1.32596.30070.48030.29-1.1204-0.0966-0.16570.84620.9885-0.3586-0.12180.1972-0.08510.07930.02340.08740.2333-13.4335-17.020623.6241
154.47860.3733-0.30863.3056-3.51714.7498-0.1911-0.5613-0.46780.9952-0.1441-0.23960.08840.4049-0.03240.28950.05020.06570.1580.10250.1838-5.3118-14.2433.6932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )A1 - 5
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 10 )A6 - 10
3X-RAY DIFFRACTION3chain 'A' and (resid 11 through 15 )A11 - 15
4X-RAY DIFFRACTION4chain 'A' and (resid 16 through 16 )A16
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 5 )B1 - 5
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 10 )B6 - 10
7X-RAY DIFFRACTION7chain 'B' and (resid 11 through 16 )B11 - 16
8X-RAY DIFFRACTION8chain 'C' and (resid 177 through 185 )C177 - 185
9X-RAY DIFFRACTION9chain 'C' and (resid 186 through 196 )C186 - 196
10X-RAY DIFFRACTION10chain 'C' and (resid 197 through 214 )C197 - 214
11X-RAY DIFFRACTION11chain 'C' and (resid 215 through 221 )C215 - 221
12X-RAY DIFFRACTION12chain 'C' and (resid 222 through 242 )C222 - 242
13X-RAY DIFFRACTION13chain 'C' and (resid 243 through 253 )C243 - 253
14X-RAY DIFFRACTION14chain 'C' and (resid 254 through 266 )C254 - 266
15X-RAY DIFFRACTION15chain 'C' and (resid 267 through 276 )C267 - 276

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