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- PDB-4s2q: Crystal Structure of HMG domain of the chondrogenesis master regu... -

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Basic information

Entry
Database: PDB / ID: 4s2q
TitleCrystal Structure of HMG domain of the chondrogenesis master regulator, Sox9 in complex with ChIP-Seq identified DNA element
Components
  • DNA (5'-D(P*AP*GP*GP*AP*GP*AP*AP*CP*AP*AP*AP*GP*CP*CP*TP*G)-3')
  • DNA (5'-D(P*AP*GP*GP*CP*TP*TP*TP*GP*TP*TP*CP*TP*CP*CP*TP*G)-3')
  • Transcription factor SOX-9
KeywordsDNA BINDING PROTEIN/DNA / DNA Bending / Minor groove binding / Transcription Regulation / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


heart valve formation / male germ-line sex determination / epithelial cell proliferation involved in prostatic bud elongation / regulation of cell proliferation involved in tissue homeostasis / regulation of branching involved in lung morphogenesis / morphogenesis of a branching epithelium / cell proliferation involved in heart morphogenesis / renal vesicle induction / metanephric tubule development / ureter urothelium development ...heart valve formation / male germ-line sex determination / epithelial cell proliferation involved in prostatic bud elongation / regulation of cell proliferation involved in tissue homeostasis / regulation of branching involved in lung morphogenesis / morphogenesis of a branching epithelium / cell proliferation involved in heart morphogenesis / renal vesicle induction / metanephric tubule development / ureter urothelium development / positive regulation of kidney development / negative regulation of beta-catenin-TCF complex assembly / positive regulation of mesenchymal stem cell differentiation / regulation of epithelial cell proliferation involved in lung morphogenesis / neural crest cell fate specification / ureter smooth muscle cell differentiation / metanephric nephron tubule formation / negative regulation of immune system process / : / glial cell fate specification / intrahepatic bile duct development / astrocyte fate commitment / bronchus cartilage development / lung smooth muscle development / ureter development / ureter morphogenesis / chondrocyte differentiation involved in endochondral bone morphogenesis / Transcriptional regulation by RUNX2 / negative regulation of fatty acid oxidation / anterior head development / chondrocyte hypertrophy / Harderian gland development / cellular response to heparin / Sertoli cell differentiation / otic vesicle development / trachea cartilage development / retinal rod cell differentiation / growth plate cartilage chondrocyte growth / chondrocyte development / positive regulation of cell proliferation involved in heart morphogenesis / negative regulation of photoreceptor cell differentiation / intestinal epithelial cell differentiation / positive regulation of epithelial cell differentiation / regulation of cell cycle process / glandular epithelial cell differentiation / lacrimal gland development / prostate gland morphogenesis / otic vesicle formation / positive regulation of male gonad development / Deactivation of the beta-catenin transactivating complex / extracellular matrix assembly / endochondral bone morphogenesis / negative regulation of mesenchymal cell apoptotic process / positive regulation of cartilage development / bHLH transcription factor binding / neuron fate specification / positive regulation of chondrocyte differentiation / prostate gland development / notochord development / limb bud formation / positive regulation of extracellular matrix assembly / heart valve morphogenesis / mesenchymal cell apoptotic process / neural crest cell development / lung epithelial cell differentiation / Sertoli cell development / cochlea morphogenesis / negative regulation of bone mineralization / endocrine pancreas development / mesenchymal cell proliferation / intestinal epithelial structure maintenance / response to fatty acid / positive regulation of chondrocyte proliferation / positive regulation of branching involved in ureteric bud morphogenesis / tissue homeostasis / cellular response to BMP stimulus / negative regulation of biomineral tissue development / male sex determination / heart valve development / negative regulation of myoblast differentiation / mammary gland development / cartilage development / negative regulation of chondrocyte differentiation / negative regulation of ossification / aortic valve morphogenesis / positive regulation of mesenchymal cell proliferation / endocardial cushion morphogenesis / branching involved in ureteric bud morphogenesis / cartilage condensation / negative regulation of epithelial cell differentiation / positive regulation of stem cell proliferation / epithelial tube branching involved in lung morphogenesis / bone mineralization / protein kinase A catalytic subunit binding / type I pneumocyte differentiation / regulation of cell differentiation / oligodendrocyte differentiation / positive regulation of epithelial cell migration / epithelial to mesenchymal transition / cellular response to interleukin-1
Similarity search - Function
Sox developmental protein N-terminal / : / Sox developmental protein N terminal / 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 ...Sox developmental protein N-terminal / : / Sox developmental protein N terminal / 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-9
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsVivekanandan, S. / Moovarkumudalvan, B. / Lescar, J. / Kolatkar, P.R.
CitationJournal: To be Published
Title: Crystal Structure of HMG domain of the chondrogenesis master regulator, Sox9 in complex with ChIP-Seq identified DNA element
Authors: Vivekanandan, S. / Moovarkumudalvan, B. / Lescar, J. / Kolatkar, P.R.
History
DepositionJan 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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(P*AP*GP*GP*CP*TP*TP*TP*GP*TP*TP*CP*TP*CP*CP*TP*G)-3')
B: DNA (5'-D(P*AP*GP*GP*AP*GP*AP*AP*CP*AP*AP*AP*GP*CP*CP*TP*G)-3')
D: Transcription factor SOX-9


Theoretical massNumber of molelcules
Total (without water)19,1013
Polymers19,1013
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-13 kcal/mol
Surface area10610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.492, 99.492, 45.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 4871.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*GP*GP*AP*GP*AP*AP*CP*AP*AP*AP*GP*CP*CP*TP*G)-3')


Mass: 4965.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Transcription factor SOX-9


Mass: 9264.711 Da / Num. of mol.: 1 / Fragment: UNP residues 103-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sox9, Sox-9 / Plasmid: pETG20A-Sox9HMG / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q04887
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 3350, 200mM Sodium/potassium phosphate, 100mM Bis Tris propane, pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: Aug 10, 2012
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: 2.7→50 Å / Num. all: 6721 / Num. obs: 6675 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 30.3 % / Rsym value: 0.133 / Net I/σ(I): 19
Reflection shellResolution: 2.7→3.4011 Å / Redundancy: 30.3 % / Mean I/σ(I) obs: 19 / Num. unique all: 6721 / Rsym value: 0.133 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F27

3f27


Resolution: 2.7→24.873 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 32.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2688 316 4.73 %RANDOM
Rwork0.2134 ---
obs0.2162 6675 99.69 %-
all-6721 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→24.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms653 659 0 2 1314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081410
X-RAY DIFFRACTIONf_angle_d1.492038
X-RAY DIFFRACTIONf_dihedral_angle_d26.547582
X-RAY DIFFRACTIONf_chiral_restr0.069216
X-RAY DIFFRACTIONf_plane_restr0.005149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-3.40110.40131550.25813094X-RAY DIFFRACTION100
3.4011-24.8740.24151610.20283265X-RAY DIFFRACTION100
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)
12.3093-0.61.21662.42841.08064.64420.37970.2757-0.4596-0.2644-0.24570.26210.5429-0.2253-0.13420.3766-0.0053-0.13810.3453-0.02010.422-16.7256-0.6508-0.2605
24.17552.94861.11882.78582.08842.26060.2035-0.4833-0.3472-0.17380.15181.216-0.4893-1.4533-0.01040.56030.1756-0.04290.74830.05570.5124-29.52270.31931.8315
33.52640.8023-0.23171.152.24144.64760.10820.4528-0.5019-0.21130.0521.6161-0.082-1.0791-0.57950.62930.0167-0.23520.60740.11890.9497-32.03822.5412-2.4048
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN D AND RESID 66:141 )D66 - 141
2X-RAY DIFFRACTION2( CHAIN B AND RESID 0:15 )B0 - 15
3X-RAY DIFFRACTION3( CHAIN A AND RESID 3:18 )A3 - 18

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