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- PDB-7vou: The crystal structure of human forkhead box protein in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7vou
TitleThe crystal structure of human forkhead box protein in complex with DNA 1
Components
  • DNA (5'-D(*AP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3')
  • DNA (5'-D(*CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*T)-3')
  • Forkhead box protein L2
KeywordsTRANSCRIPTION/DNA / DNA-protein complex / transcription factor / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


granulosa cell differentiation / female somatic sex determination / extraocular skeletal muscle development / cysteine-type endopeptidase regulator activity involved in apoptotic process / oocyte growth / positive regulation of luteinizing hormone secretion / embryonic eye morphogenesis / positive regulation of follicle-stimulating hormone secretion / apoptotic DNA fragmentation / Flemming body ...granulosa cell differentiation / female somatic sex determination / extraocular skeletal muscle development / cysteine-type endopeptidase regulator activity involved in apoptotic process / oocyte growth / positive regulation of luteinizing hormone secretion / embryonic eye morphogenesis / positive regulation of follicle-stimulating hormone secretion / apoptotic DNA fragmentation / Flemming body / ubiquitin conjugating enzyme binding / uterus development / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / SUMOylation of transcription factors / single fertilization / anatomical structure morphogenesis / ovarian follicle development / nuclear estrogen receptor binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / 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
DNA / DNA (> 10) / Forkhead box protein L2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsChoi, Y. / Yoon, H.J. / Lee, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1A2B2008142 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: FOXL2 and FOXA1 cooperatively assemble on the TP53 promoter in alternative dimer configurations.
Authors: Choi, Y. / Luo, Y. / Lee, S. / Jin, H. / Yoon, H.J. / Hahn, Y. / Bae, J. / Lee, H.H.
History
DepositionOct 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 7, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 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
A: DNA (5'-D(*AP*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*T)-3')
C: Forkhead box protein L2


Theoretical massNumber of molelcules
Total (without water)22,6433
Polymers22,6433
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-21 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.987, 47.987, 164.414
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: DNA chain DNA (5'-D(*AP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3')


Mass: 4869.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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*T)-3')


Mass: 4923.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein Forkhead box protein L2


Mass: 12850.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXL2 / Production host: Escherichia coli (E. coli) / References: UniProt: P58012

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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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-tris pH 5.5, 0.15 M NaCl, and 26% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 3950 / % possible obs: 100 % / Redundancy: 21.1 % / Biso Wilson estimate: 84.45 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.02 / Rrim(I) all: 0.093 / Χ2: 0.973 / Net I/σ(I): 9.8 / Num. measured all: 83510
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.1519.50.8581850.9880.1920.880.671100
3.15-3.2119.30.4781910.9970.1110.4910.693100
3.21-3.27200.5581810.990.1260.5720.683100
3.27-3.3418.40.3171920.9950.0750.3260.746100
3.34-3.4118.60.2461910.9960.0580.2530.735100
3.41-3.4920.20.361860.9830.0810.370.751100
3.49-3.58210.2761910.9920.0610.2830.729100
3.58-3.6822.30.2551950.990.0530.260.759100
3.68-3.7821.40.2491890.990.0530.2541.132100
3.78-3.91220.1921860.9930.0410.1961.029100
3.91-4.0423.20.1371960.9960.0280.140.835100
4.04-4.2123.70.11950.9980.0210.1020.864100
4.21-4.423.10.0991930.9950.0210.1010.841100
4.4-4.6321.90.1231900.9960.0260.1262.854100
4.63-4.92210.0722080.9980.0160.0740.989100
4.92-5.323.60.0652030.9990.0130.0660.865100
5.3-5.8322.40.0591970.9990.0120.060.816100
5.83-6.6719.50.0522110.9990.0120.0540.999100
6.67-8.421.90.0462150.9990.010.0470.888100
8.4-50200.0452550.9980.010.0461.36599.6

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CBY

7cby


Resolution: 3.1→46.07 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2802 384 9.97 %
Rwork0.221 3468 -
obs0.2269 3852 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.62 Å2 / Biso mean: 90.479 Å2 / Biso min: 36.57 Å2
Refinement stepCycle: final / Resolution: 3.1→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms706 650 0 0 1356
Num. residues----118
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.550.28631190.25351088120797
3.55-4.470.27791280.23051144127299
4.47-46.070.27961370.20751236137399
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)
17.10540.317-0.42422.294-3.54075.2418-0.2104-0.31460.40220.42350.0473-0.62280.14570.0754-0.11890.51120.0219-0.05850.514-0.04820.5657-0.5944-25.00917.009
24.55450.5250.07182.5063-0.16184.55520.2471-0.4872-0.0545-0.391-0.1049-1.31250.37580.5304-0.0490.510.0505-0.00110.48410.03170.65361.5934-23.76817.5897
38.34741.74381.02884.6109-0.06868.6068-0.17611.06010.5403-0.51080.3364-0.45850.3475-0.1716-0.16120.61370.01460.06340.48980.16160.3995-4.8393-19.42123.3715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 16)A1 - 16
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 16)B1 - 16
3X-RAY DIFFRACTION3(chain 'C' and resid 181 through 266)C181 - 266

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