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- PDB-3f27: Structure of Sox17 Bound to DNA -

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Basic information

Entry
Database: PDB / ID: 3f27
TitleStructure of Sox17 Bound to DNA
Components
  • DNA (5'-D(*DCP*DCP*DAP*DGP*DGP*DAP*DCP*DAP*DAP*DTP*DAP*DGP*DAP*DGP*DAP*DC)-3')
  • DNA (5'-D(*DGP*DTP*DCP*DTP*DCP*DTP*DAP*DTP*DTP*DGP*DTP*DCP*DCP*DTP*DGP*DG)-3')
  • Transcription factor SOX-17
KeywordsTranscription/dna / protein-DNA complex / HMG domain / endodermal / Activator / DNA-binding / Nucleus / Transcription / Transcription regulation / Transcription-dna COMPLEX
Function / homology
Function and homology information


endodermal cell fate determination / common bile duct development / stem cell fate specification / cardiogenic plate morphogenesis / regulation of cardiac cell fate specification / inner cell mass cellular morphogenesis / endocardium formation / endodermal digestive tract morphogenesis / ureter development / gallbladder development ...endodermal cell fate determination / common bile duct development / stem cell fate specification / cardiogenic plate morphogenesis / regulation of cardiac cell fate specification / inner cell mass cellular morphogenesis / endocardium formation / endodermal digestive tract morphogenesis / ureter development / gallbladder development / endoderm formation / cardiac cell fate determination / embryonic foregut morphogenesis / cell migration involved in gastrulation / endoderm development / regulation of stem cell division / endodermal cell fate specification / regulation of stem cell proliferation / rostrocaudal neural tube patterning / endocardial cell differentiation / Deactivation of the beta-catenin transactivating complex / metanephros development / embryonic heart tube development / cellular response to leukemia inhibitory factor / embryonic heart tube morphogenesis / signal transduction involved in regulation of gene expression / response to alkaloid / embryonic organ development / heart looping / outflow tract morphogenesis / vasculogenesis / regulation of cell differentiation / negative regulation of Wnt signaling pathway / gastrulation / stem cell differentiation / regulation of embryonic development / positive regulation of cell differentiation / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / protein destabilization / negative regulation of cell growth / beta-catenin binding / heart development / sequence-specific double-stranded DNA binding / positive regulation of protein catabolic process / transcription regulator complex / angiogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein stabilization / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of gene expression / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / DNA-templated transcription / nucleoplasm / nucleus
Similarity search - Function
Sox, C-terminal / Sox 7/17/18, central domain / Sox 17/18 central domain / Sox C-terminal domain profile. / : / High mobility group box domain / DNA Binding (I), subunit A / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group ...Sox, C-terminal / Sox 7/17/18, central domain / Sox 17/18 central domain / Sox C-terminal domain profile. / : / High mobility group box domain / DNA Binding (I), subunit A / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor SOX-17
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsPalasingam, P. / Jauch, R. / Ng, C.K.L. / Kolatkar, P.R.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: The Structure of Sox17 Bound to DNA Reveals a Conserved Bending Topology but Selective Protein Interaction Platforms
Authors: Palasingam, P. / Jauch, R. / Ng, C.K.L. / Kolatkar, P.R.
History
DepositionOct 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 14, 2023Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 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

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Assembly

Deposited unit
A: DNA (5'-D(*DGP*DTP*DCP*DTP*DCP*DTP*DAP*DTP*DTP*DGP*DTP*DCP*DCP*DTP*DGP*DG)-3')
B: DNA (5'-D(*DCP*DCP*DAP*DGP*DGP*DAP*DCP*DAP*DAP*DTP*DAP*DGP*DAP*DGP*DAP*DC)-3')
D: Transcription factor SOX-17


Theoretical massNumber of molelcules
Total (without water)19,8813
Polymers19,8813
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-10 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.753, 68.753, 66.329
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: DNA chain DNA (5'-D(*DGP*DTP*DCP*DTP*DCP*DTP*DAP*DTP*DTP*DGP*DTP*DCP*DCP*DTP*DGP*DG)-3')


Mass: 4871.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Lama1 / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*DCP*DCP*DAP*DGP*DGP*DAP*DCP*DAP*DAP*DTP*DAP*DGP*DAP*DGP*DAP*DC)-3')


Mass: 4925.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Lama1 / Source: (synth.) synthetic construct (others)
#3: Protein Transcription factor SOX-17


Mass: 10084.687 Da / Num. of mol.: 1 / Fragment: HMG box, residues 66-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sox-17, Sox17 / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q61473

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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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 30% PEG 3350, 0.2M MGCL2, pH 7.4, vapor diffusion, hanging drop, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2MgCl211
3PEG 335012
4MgCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Details: Platinum
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→66.33 Å / Num. obs: 4970 / % possible obs: 99.9 % / Redundancy: 9.86 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 22.75
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3.75

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GT0

1gt0


Resolution: 2.75→20.73 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 1 / SU B: 32.153 / SU ML: 0.305 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 228 4.6 %RANDOM
Rwork0.242 ---
obs0.243 4703 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.14 Å2 / Biso mean: 25.696 Å2 / Biso min: 9.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å21.13 Å20 Å2
2--2.25 Å20 Å2
3----3.38 Å2
Refinement stepCycle: LAST / Resolution: 2.75→20.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms633 650 0 0 1283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211376
X-RAY DIFFRACTIONr_angle_refined_deg1.8612.5421988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.808573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73521.94436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.17315128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.491510
X-RAY DIFFRACTIONr_chiral_restr0.0910.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02826
X-RAY DIFFRACTIONr_nbd_refined0.2460.2492
X-RAY DIFFRACTIONr_nbtor_refined0.310.2847
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.238
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.21
X-RAY DIFFRACTIONr_mcbond_it0.5621.5386
X-RAY DIFFRACTIONr_mcangle_it1.0042599
X-RAY DIFFRACTIONr_scbond_it1.26231330
X-RAY DIFFRACTIONr_scangle_it1.9774.51389
LS refinement shellResolution: 2.751→2.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 24 -
Rwork0.253 328 -
all-352 -
obs--100 %
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)
12.35041.6149-1.35065.38480.85535.44750.00690.26-0.8129-0.4882-0.1643-1.23460.38370.62070.15740.03830.19020.1510.25460.14230.379225.0085-11.5796-1.7137
24.82031.9245-2.47665.827-1.59734.1348-0.0770.5033-0.1479-0.4991-0.2235-0.24880.1549-0.38180.3005-0.04390.11130.0220.26930.0628-0.072113.1432-4.6958-0.9446
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 16
2X-RAY DIFFRACTION1B1 - 16
3X-RAY DIFFRACTION2D67 - 141

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