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- PDB-3u2b: Structure of the Sox4 HMG domain bound to DNA -

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Basic information

Entry
Database: PDB / ID: 3u2b
TitleStructure of the Sox4 HMG domain bound to DNA
Components
  • DNA (5'-D(*CP*CP*AP*GP*GP*AP*CP*AP*AP*TP*AP*GP*AP*GP*AP*C)-3')
  • DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*TP*GP*TP*CP*CP*TP*GP*G)-3')
  • Transcription factor SOX-4
KeywordsTRANSCRIPTION/DNA / HMG domain / transcriptional regulation / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


positive regulation of N-terminal peptidyl-lysine acetylation / : / cardiac ventricle formation / ascending aorta morphogenesis / kidney morphogenesis / noradrenergic neuron differentiation / glial cell development / neural tube formation / cardiac right ventricle morphogenesis / : ...positive regulation of N-terminal peptidyl-lysine acetylation / : / cardiac ventricle formation / ascending aorta morphogenesis / kidney morphogenesis / noradrenergic neuron differentiation / glial cell development / neural tube formation / cardiac right ventricle morphogenesis / : / Deactivation of the beta-catenin transactivating complex / spinal cord motor neuron differentiation / mitral valve morphogenesis / atrial septum primum morphogenesis / positive regulation of gamma-delta T cell differentiation / pro-B cell differentiation / limb bud formation / neuroepithelial cell differentiation / endocrine pancreas development / sympathetic nervous system development / spinal cord development / ventricular septum morphogenesis / somatic stem cell population maintenance / T cell differentiation / anatomical structure morphogenesis / glial cell proliferation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / negative regulation of protein ubiquitination / positive regulation of translation / skeletal system development / cellular response to glucose stimulus / regulation of protein stability / positive regulation of insulin secretion / positive regulation of canonical Wnt signaling pathway / sequence-specific double-stranded DNA binding / glucose homeostasis / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / cell differentiation / response to hypoxia / protein stabilization / transcription cis-regulatory region binding / 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 cell population proliferation / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transcription factor SOX-12/11/4 / 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-4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsJauch, R. / Ng, C.K.L. / Kolatkar, P.R.
CitationJournal: Biochem.J. / Year: 2012
Title: The crystal structure of the Sox4 HMG domain-DNA complex suggests a mechanism for positional interdependence in DNA recognition
Authors: Jauch, R. / Ng, C.K.L. / Narasimhan, K. / Kolatkar, P.R.
History
DepositionOct 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*TP*GP*TP*CP*CP*TP*GP*G)-3')
B: DNA (5'-D(*CP*CP*AP*GP*GP*AP*CP*AP*AP*TP*AP*GP*AP*GP*AP*C)-3')
C: Transcription factor SOX-4


Theoretical massNumber of molelcules
Total (without water)19,5153
Polymers19,5153
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-18 kcal/mol
Surface area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.941, 69.941, 63.205
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 4871.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA
#2: DNA chain DNA (5'-D(*CP*CP*AP*GP*GP*AP*CP*AP*AP*TP*AP*GP*AP*GP*AP*C)-3')


Mass: 4925.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA
#3: Protein Transcription factor SOX-4


Mass: 9718.521 Da / Num. of mol.: 1 / Fragment: UNP residues 57-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sox4, Sox-4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06831
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 100mM Hepes pH 7.2, 20% PEG 3350 pH 7.2, 50mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2011
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 7155 / Num. obs: 7040 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 50.57 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.402→43.732 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6894 / SU ML: 0.37 / σ(F): 0.22 / Phase error: 35.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2795 376 5.49 %RAMDOM
Rwork0.2353 ---
all0.27 7129 --
obs0.2377 6855 94.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.21 Å2 / ksol: 0.259 e/Å3
Displacement parametersBiso max: 179.84 Å2 / Biso mean: 72.89 Å2 / Biso min: 23.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.0061 Å2-0 Å2-0 Å2
2--2.0061 Å2-0 Å2
3----4.0122 Å2
Refinement stepCycle: LAST / Resolution: 2.402→43.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms655 650 0 8 1313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031399
X-RAY DIFFRACTIONf_angle_d0.6982014
X-RAY DIFFRACTIONf_dihedral_angle_d24.89587
X-RAY DIFFRACTIONf_chiral_restr0.037212
X-RAY DIFFRACTIONf_plane_restr0.003146
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4022-2.74980.45021220.3591206092
2.7498-3.46420.29921270.2791219297
3.4642-43.73880.23851270.1908222794
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)
17.6374-1.2494-5.63141.59720.96297.445-0.8943-0.2544-0.23710.16730.3079-0.42252.86291.23550.56510.6340.22180.1990.45380.04320.220427.5302-7.5161-8.4456
22.85970.8426-2.14811.16321.56536.61350.5902-0.6225-1.04520.25130.05230.72331.5990.334-0.26030.9253-0.2281-0.22150.56920.18950.334121.851-19.58958.9273
32.6121-0.9410.762.96491.4231.24450.08470.7993-0.23280.2106-0.17750.05180.66910.40620.16270.5272-0.2526-0.01030.53270.11820.211923.0406-11.44282.3563
46.0928-2.0125-0.38513.70131.24652.7565-1.20340.75650.05440.21810.5447-0.24860.7093-0.34440.20630.62630.00480.46170.6622-0.17760.598834.644-4.8566-16.7356
59.6933-2.99015.00923.8631-2.5764.1938-0.0264-0.1858-0.49121.1903-0.3155-0.0117-0.5069-0.87820.63140.4437-0.5075-0.34280.96230.22680.283614.1041-14.6357-5.681
62.83252.7483-1.82773.7934-0.44935.13850.42170.48150.2950.4255-0.62310.74070.2253-1.56360.10270.0463-0.053-0.04490.86960.01450.12213.6968-1.2435-0.1227
70.51740.6392-1.41062.1135-2.47766.33020.13081.02690.06360.11780.77330.33930.1043-2.4853-0.72550.20920.08450.05780.81430.17430.238715.54226.2999-9.3945
87.8883-5.81121.56369.3547-3.23271.18351.17571.49090.7496-0.8439-0.9111-0.3870.3114-0.0050.18480.5927-0.03140.14660.76890.19350.579525.14985.5569-12.6161
90.3476-0.75071.45963.3255-1.08772.1810.14770.0320.76661.3762-1.16912.1082-1.3788-4.3178-0.813-0.09920.1589-0.24740.22220.4858-0.52915.46964.78993.1427
100.9268-1.519-1.00665.46980.04523.8632-0.303-0.16640.036-1.57231.1893-0.65650.7749-2.7487-0.93290.4583-0.7068-0.06141.90280.11090.15214.2748-11.3080.0428
118.4039-0.9141-6.90380.80120.66085.7957-1.50040.8187-0.74541.31080.75010.00392.2174-1.10470.81682.2215-0.2727-0.19770.5172-0.13520.391315.2937-21.4458-2.2962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:10)A1 - 10
2X-RAY DIFFRACTION2(chain A and resid 11:16)A11 - 16
3X-RAY DIFFRACTION3(chain B and resid 1:11)B1 - 11
4X-RAY DIFFRACTION4(chain B and resid 12:16)B12 - 16
5X-RAY DIFFRACTION5(chain C and resid 1:7)C1 - 7
6X-RAY DIFFRACTION6(chain C and resid 8:13)C8 - 13
7X-RAY DIFFRACTION7(chain C and resid 14:25)C14 - 25
8X-RAY DIFFRACTION8(chain C and resid 26:30)C26 - 30
9X-RAY DIFFRACTION9(chain C and resid 31:54)C31 - 54
10X-RAY DIFFRACTION10(chain C and resid 55:65)C55 - 65
11X-RAY DIFFRACTION11(chain C and resid 66:76)C66 - 76

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