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

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Basic information

Entry
Database: PDB / ID: 7vov
TitleThe crystal structure of human forkhead box protein in complex with DNA 2
Components
  • DNA (5'-D(P*AP*AP*AP*TP*AP*TP*TP*TP*AP*TP*TP*AP*TP*CP*GP*A)-3')
  • DNA (5'-D(P*TP*CP*GP*AP*TP*AP*AP*TP*AP*AP*AP*TP*AP*TP*T)-3')
  • Forkhead box protein L2
KeywordsTRANSCRIPTION/DNA / transcription factor / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


granulosa cell differentiation / female somatic sex determination / cysteine-type endopeptidase regulator activity involved in apoptotic process / extraocular skeletal muscle development / oocyte growth / embryonic eye morphogenesis / positive regulation of luteinizing hormone secretion / positive regulation of follicle-stimulating hormone secretion / apoptotic DNA fragmentation / Flemming body ...granulosa cell differentiation / female somatic sex determination / cysteine-type endopeptidase regulator activity involved in apoptotic process / extraocular skeletal muscle development / oocyte growth / embryonic eye morphogenesis / positive regulation of luteinizing hormone secretion / positive regulation of follicle-stimulating hormone secretion / apoptotic DNA fragmentation / Flemming body / ubiquitin conjugating enzyme binding / uterus development / SUMOylation of transcription factors / anatomical structure morphogenesis / single fertilization / ovarian follicle development / nuclear estrogen receptor binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / 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 / regulation of transcription by RNA polymerase II / chromatin / 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. ...: / : / 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: 3.15 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 15, 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Forkhead box protein L2
B: Forkhead box protein L2
C: DNA (5'-D(P*AP*AP*AP*TP*AP*TP*TP*TP*AP*TP*TP*AP*TP*CP*GP*A)-3')
D: DNA (5'-D(P*TP*CP*GP*AP*TP*AP*AP*TP*AP*AP*AP*TP*AP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)31,5124
Polymers31,5124
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-23 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.600, 98.600, 64.730
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Forkhead box protein L2


Mass: 11012.628 Da / Num. of mol.: 2
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
#2: DNA chain DNA (5'-D(P*AP*AP*AP*TP*AP*TP*TP*TP*AP*TP*TP*AP*TP*CP*GP*A)-3')


Mass: 4895.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*TP*CP*GP*AP*TP*AP*AP*TP*AP*AP*AP*TP*AP*TP*T)-3')


Mass: 4591.034 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 6% ethylene glycol, 0.1 M Citric acid pH 3.5, and 15% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 3.14→19.766 Å / Num. obs: 6586 / % possible obs: 99.8 % / Redundancy: 19.676 % / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.068 / Χ2: 0.867 / Net I/σ(I): 37.42 / Num. measured all: 129588
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.14-3.3318.530.3766.5419234104510380.9960.38799.3
3.33-3.5619.1770.3648.1188329829820.9850.373100
3.56-3.8421.1490.23513.49195429249240.9940.241100
3.84-4.221.1050.15121.83177498418410.9960.155100
4.2-4.720.4980.08142.03160507837830.9990.083100
4.7-5.4119.9310.06450.89136736866860.9990.066100
5.41-6.6117.8080.04376.07103825835830.9990.044100
6.61-9.2719.3080.026110.81901746746710.027100
9.27-19.76618.1170.023130.99510929028210.02397.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C6Y

2c6y


Resolution: 3.15→19.766 Å / Cross valid method: THROUGHOUT / σ(F): 52 / Phase error: 30.58 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.275 324 4.99 %
Rwork0.2485 6139 -
obs0.2588 6493 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 236.87 Å2 / Biso mean: 89.7719 Å2 / Biso min: 42.17 Å2
Refinement stepCycle: final / Resolution: 3.15→19.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 636 0 0 2135
Num. residues----208
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 95 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1527-3.9650.2861600.257430283188
3.965-17.90680.27861640.257331113275
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)
10.36160.3844-0.15811.0819-0.23830.31060.09940.0128-0.0237-0.07850.18790.02930.04530.05750.08910.1993-0.28640.0069-0.1795-0.00791.163733.6181-32.1617-0.6997
20.40770.46410.08850.76990.17890.030.18440.1083-0.01920.06320.13980.0254-0.0545-0.03310.13440.1484-0.6520.20990.10970.1651.192733.5069-34.0653-3.0351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'C' and resid 0 through 15)C0 - 15
2X-RAY DIFFRACTION2(chain 'D' and resid 3 through 17)D3 - 17

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