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- PDB-6osw: An order-to-disorder structural switch activates the FoxM1 transc... -

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Basic information

Entry
Database: PDB / ID: 6osw
TitleAn order-to-disorder structural switch activates the FoxM1 transcription factor
Components(Forkhead box M1) x 2
KeywordsCELL CYCLE / transcription factor / negative regulatory domain / transactivation domain
Function / homology
Function and homology information


regulation of cell cycle => GO:0051726 / RNA polymerase II transcription regulatory region sequence-specific DNA binding / G2/M transition of mitotic cell cycle / regulation of cell population proliferation / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Forkhead box protein M1 / 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
Biological speciesDanio rerio (zebrafish)
MethodSOLUTION NMR / na
AuthorsMarceau, A.H. / Rubin, S.M. / Nerli, S. / McShane, A.C. / Sgourakis, N.G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA132685 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM124148 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM125034 United States
CitationJournal: Elife / Year: 2019
Title: An order-to-disorder structural switch activates the FoxM1 transcription factor.
Authors: Marceau, A.H. / Brison, C.M. / Nerli, S. / Arsenault, H.E. / McShan, A.C. / Chen, E. / Lee, H.W. / Benanti, J.A. / Sgourakis, N.G. / Rubin, S.M.
History
DepositionMay 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Forkhead box M1
B: Forkhead box M1


Theoretical massNumber of molelcules
Total (without water)16,4662
Polymers16,4662
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1090 Å2
ΔGint-9 kcal/mol
Surface area5500 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1target function

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Components

#1: Protein Forkhead box M1 / Forkhead box M1-like


Mass: 10515.116 Da / Num. of mol.: 1 / Fragment: residues 1-106 / Mutation: L19A, L104A, C87A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: foxm1, foxm1l / Production host: Escherichia coli (E. coli) / References: UniProt: Q7T2G3
#2: Protein Forkhead box M1 / Forkhead box M1-like


Mass: 5950.556 Da / Num. of mol.: 1 / Fragment: residues 569-623 / Mutation: L569A, V571A, L622A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: foxm1, foxm1l / Production host: Escherichia coli (E. coli) / References: UniProt: Q7T2G3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
114isotropic1TROSY-HNCO
124isotropic1TROSY-HN(CA)CO
134isotropic1TROSY-HNCA
144isotropic1TROSY-HN(CO)CA
154isotropic1TROSY-HNCB
1134isotropic1TROSY-HN(COCA)CB
1125isotropic1HMQC
1115isotropic1methyl-HSQC
1105isotropic1NOESY HN-NHN
195isotropic1NOESY N-NHN
185isotropic1NOESY HNHAro-CMHM
175isotropic1NOESY CM-NHN
1145isotropic1NOESY HM-CMHM
1155isotropic1NOESY CM-CMHM
163isotropic1isotopomer-selective TOCSY
1164isotropic1TROSY-HSQC
1174isotropic2Dnh (NH)
1184isotropic2DNC (NCO)

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution4270 uM [U-13C; U-15N] FoxM1 NRD, 270 uM [U-13C] FoxM1 TAD, 20 mM sodium phosphate, 100 mM potassium chloride, 95% H2O/5% D2ON15_C13_D2O95% H2O/5% D2O
solution5270 uM [U-13C; U-15N; U-2H] FoxM1 NRD, 270 uM [U-13C; U-15N; U-2H] FoxM1 TAD, 20 mM sodium phosphate, 100 mM potassium chloride, 95% H2O/5% D2ON15_C13ILV_D2095% H2O/5% D2O
solution3270 uM [U-13C; U-15N; U-2H] FoxM1 NRD, 270 uM [U-13C; U-15N; U-2H] FoxM1 TAD, 20 mM sodium phosphate, 100 mM potassium chloride, 95% H2O/5% D2O15N_13C_D2_Iso_sample95% H2O/5% D2Olabeled with N15, 13C glucose (1H,13C-glucose), and deuterated media
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
270 uMFoxM1 NRD[U-13C; U-15N]4
270 uMFoxM1 TAD[U-13C]4
20 mMsodium phosphatenatural abundance4
100 mMpotassium chloridenatural abundance4
270 uMFoxM1 NRD[U-13C; U-15N; U-2H]5
270 uMFoxM1 TAD[U-13C; U-15N; U-2H]5
20 mMsodium phosphatenatural abundance5
100 mMpotassium chloridenatural abundance5
270 uMFoxM1 NRD[U-13C; U-15N; U-2H]3
270 uMFoxM1 TAD[U-13C; U-15N; U-2H]3
20 mMsodium phosphatenatural abundance3
100 mMpotassium chloridenatural abundance3
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6.3 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD8001
Varian INOVA600VarianINOVA6006002

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Processing

NMR software
NameDeveloperClassification
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
RefinementMethod: na / Software ordinal: 1
Details: The authors state that refinement was performed using the RASREC-Rosetta protocol. The ensemble structures were selected based on rosetta energies, minimum number of NOE violations and good ...Details: The authors state that refinement was performed using the RASREC-Rosetta protocol. The ensemble structures were selected based on rosetta energies, minimum number of NOE violations and good fit to RDC measurements. The best representative conformer (model 1) was selected based upon rosetta energies.
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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