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- PDB-3g73: Structure of the FOXM1 DNA binding -

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Basic information

Entry
Database: PDB / ID: 3g73
TitleStructure of the FOXM1 DNA binding
Components
  • DNA (5'-D(P*AP*AP*AP*TP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*GP*CP*CP*CP*G)-3')
  • DNA (5'-D(P*TP*TP*CP*GP*GP*GP*CP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*AP*T)-3')
  • Forkhead box protein M1
KeywordsTRANSCRIPTION/DNA / DNA-Binding domain / Forkhead transcription factors / FOXM1 / Winged helix / Forkhead / Transcription regulation / TRANSCRIPTION-DNA COMPLEX / Activator / DNA-binding / Nucleus / Phosphoprotein / Transcription
Function / homology
Function and homology information


regulation of Ras protein signal transduction / Polo-like kinase mediated events / positive regulation of double-strand break repair / regulation of reactive oxygen species metabolic process / negative regulation of stress-activated MAPK cascade / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Cyclin A/B1/B2 associated events during G2/M transition / regulation of cell growth / RNA polymerase II transcription regulatory region sequence-specific DNA binding / G2/M transition of mitotic cell cycle ...regulation of Ras protein signal transduction / Polo-like kinase mediated events / positive regulation of double-strand break repair / regulation of reactive oxygen species metabolic process / negative regulation of stress-activated MAPK cascade / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Cyclin A/B1/B2 associated events during G2/M transition / regulation of cell growth / 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, RNA polymerase II-specific / regulation of cell cycle / DNA-binding transcription factor activity / DNA repair / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / 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. ...: / 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-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Forkhead box protein M1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsLittler, D.R. / Perrakis, A. / Hibbert, R.G. / Medema, R.H.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Structure of the FoxM1 DNA-recognition domain bound to a promoter sequence
Authors: Littler, D.R. / Alvarez-Fernandez, M. / Stein, A. / Hibbert, R.G. / Heidebrecht, T. / Aloy, P. / Medema, R.H. / Perrakis, A.
History
DepositionFeb 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Forkhead box protein M1
B: Forkhead box protein M1
C: DNA (5'-D(P*AP*AP*AP*TP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*GP*CP*CP*CP*G)-3')
D: DNA (5'-D(P*TP*TP*CP*GP*GP*GP*CP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1336
Polymers46,0844
Non-polymers492
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-64 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.070, 119.750, 152.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Forkhead box protein M1 / Forkhead-related protein FKHL16 / Hepatocyte nuclear factor 3 forkhead homolog 11 / HNF-3/fork-head ...Forkhead-related protein FKHL16 / Hepatocyte nuclear factor 3 forkhead homolog 11 / HNF-3/fork-head homolog 11 / HFH-11 / Winged-helix factor from INS-1 cells / M-phase phosphoprotein 2 / MPM-2 reactive phosphoprotein 2 / Transcription factor Trident


Mass: 16600.861 Da / Num. of mol.: 2 / Fragment: DNA-binding domain, UNP residues 222-360
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKHL16, FOXM1, HFH11, MPP2, WIN / Plasmid: pET28-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q08050
#2: DNA chain DNA (5'-D(P*AP*AP*AP*TP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*GP*CP*CP*CP*G)-3')


Mass: 6430.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA oligo
#3: DNA chain DNA (5'-D(P*TP*TP*CP*GP*GP*GP*CP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*AP*T)-3')


Mass: 6452.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA oligo
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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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: 3.1 Å3/Da / Density % sol: 60.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 24% PEG3350, 0.2M Sodium Malonate, pH7.5, 3uL Protein at 12g/L mixed with DNA at 0.5mM added tO 3uL of reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG335011
2Sodium Malonate11
3HOH11
4PEG335012
5Sodium Malonate12
6HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Nov 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.2→76 Å / Num. obs: 27165 / % possible obs: 91.4 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 48.1 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.1 / % possible all: 59.4

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Processing

Software
NameVersionClassification
DNAdata collection
AMoREphasing
REFMAC5.5.0063refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C6Y

2c6y


Resolution: 2.21→32.94 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 9.275 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23425 1389 5.2 %RANDOM
Rwork0.204 ---
obs0.20557 25545 91.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.23 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2--0.23 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.21→32.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1560 861 2 163 2586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212582
X-RAY DIFFRACTIONr_bond_other_d0.0010.021510
X-RAY DIFFRACTIONr_angle_refined_deg1.4462.3543676
X-RAY DIFFRACTIONr_angle_other_deg0.92233694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8315185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.39522.37580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63915276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8121512
X-RAY DIFFRACTIONr_chiral_restr0.0660.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212201
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0592933
X-RAY DIFFRACTIONr_mcbond_other0.2112362
X-RAY DIFFRACTIONr_mcangle_it1.78231523
X-RAY DIFFRACTIONr_scbond_it0.96521649
X-RAY DIFFRACTIONr_scangle_it1.54532152
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.21→2.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 69 -
Rwork0.331 1117 -
obs--54.88 %
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)
13.8974-1.9459-0.75144.93820.92014.1264-0.1242-0.0764-0.09770.35350.1006-0.30560.17590.20090.02370.02930.0188-0.01870.14330.0410.049210.297429.182212.9834
28.95711.7863-0.33564.39130.55347.6112-0.34970.8179-0.3373-0.25950.14240.05230.1524-0.0090.20730.04360.01020.02260.1841-0.01880.041410.262523.7499-2.3788
33.48030.0694-0.76813.8758-1.74329.72470.22540.0460.09790.26330.07840.277-0.1218-0.9885-0.30380.05550.05570.0220.21980.01970.0253-4.467136.216325.5536
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 21
2X-RAY DIFFRACTION1D1 - 21
3X-RAY DIFFRACTION2A232 - 321
4X-RAY DIFFRACTION3B235 - 327

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