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- PDB-4euw: Crystal structure of a HMG domain of transcription factor SOX-9 b... -

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Entry
Database: PDB / ID: 4euw
TitleCrystal structure of a HMG domain of transcription factor SOX-9 bound to DNA (SOX-9/DNA) from Homo sapiens at 2.77 A resolution
Components
  • DNA (5'-D(*CP*TP*CP*TP*TP*TP*GP*AP*GP*AP*AP*G)-3')
  • DNA (5'-D(*CP*TP*TP*CP*TP*CP*AP*AP*AP*GP*AP*G)-3')
  • Transcription factor SOX-9
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / HMG DOMAIN / ACTIVATOR / DNA-BINDING / NUCLEUS / TRANSCRIPTION / TRANSCRIPTION REGULATION / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for Stem Cell Biology / STEMCELL / TRANSCRIPTION-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 / ureter urothelium development / positive regulation of kidney 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 / 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 morphogenesis / chondrocyte differentiation involved in endochondral bone morphogenesis / negative regulation of fatty acid oxidation / anterior head development / chondrocyte hypertrophy / Harderian gland development / cellular response to heparin / Sertoli cell differentiation / trachea cartilage development / retinal rod cell differentiation / growth plate cartilage chondrocyte growth / 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 / otic vesicle formation / positive regulation of male gonad development / extracellular matrix assembly / negative regulation of mesenchymal cell apoptotic process / Transcriptional regulation of testis differentiation / 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 / Sertoli cell development / cochlea morphogenesis / negative regulation of bone mineralization / endocrine pancreas development / mesenchymal cell proliferation / intestinal epithelial structure maintenance / Transcriptional regulation by RUNX2 / 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 / heart valve development / negative regulation of myoblast differentiation / Developmental Lineage of Pancreatic Acinar Cells / mammary gland development / cartilage development / negative regulation of chondrocyte differentiation / cell fate specification / 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 / oligodendrocyte differentiation / positive regulation of epithelial cell migration / epithelial to mesenchymal transition / cellular response to interleukin-1 / somatic stem cell population maintenance / protein localization to nucleus / hair follicle development / chondrocyte differentiation / canonical Wnt signaling pathway / negative regulation of osteoblast differentiation / pre-mRNA intronic binding / cellular response to transforming growth factor beta stimulus
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.77 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology (STEMCELL)
CitationJournal: To be published
Title: Crystal structure of a HMG domain of transcription factor SOX-9 bound to DNA (SOX-9/DNA) from Homo sapiens at 2.77 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology
History
DepositionApr 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor SOX-9
B: DNA (5'-D(*CP*TP*CP*TP*TP*TP*GP*AP*GP*AP*AP*G)-3')
C: DNA (5'-D(*CP*TP*TP*CP*TP*CP*AP*AP*AP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)20,2423
Polymers20,2423
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-11 kcal/mol
Surface area7920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.772, 134.654, 49.987
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein Transcription factor SOX-9


Mass: 12917.722 Da / Num. of mol.: 1 / Fragment: HMG box containing residues 98-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SGT82680, SOX9 / Plasmid: pRSF2Ek6TevLIC / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3)PhageR20080807 / References: UniProt: P48436
#2: DNA chain DNA (5'-D(*CP*TP*CP*TP*TP*TP*GP*AP*GP*AP*AP*G)-3')


Mass: 3677.415 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: sequence matching the SOX-9 binding site from the anti-Mullerian hormone (AMH) promoter, top strand
Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*TP*TP*CP*TP*CP*AP*AP*AP*GP*AP*G)-3')


Mass: 3646.405 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: sequence matching the SOX-9 binding site from the anti-Mullerian hormone (AMH) promoter, bottom strand
Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (RESIDUES 98 - 181) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MAHHHHHHVDDDDKMSENLYFQ.

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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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30.00% polyethylene glycol 8000, 0.20M ammonium acetate, 0.010 M magnesium acetate, 0.1M sodium cacodylate pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 21, 2011
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.77→27.922 Å / Num. obs: 4880 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 86.94 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.3 / Num. measured all: 18522
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.77-2.843.990.5752.6139935198.8
2.84-2.923.970.4153.4142035899.1
2.92-34.010.2844.81356338100
3-3.13.960.2625.2135134199.4
3.1-3.23.980.1667.7129032499.7
3.2-3.313.950.12410124831699.5
3.31-3.443.950.10312.6121330799.7
3.44-3.583.640.10412.9105328994.8
3.58-3.742.830.05922.449017363
3.74-3.923.660.07318.594525896.4
3.92-4.133.660.06219.290024694.4
4.13-4.383.860.05222.894624599.2
4.38-4.683.790.04524.590123898.8
4.68-5.063.840.04923821214100
5.06-5.543.80.04325.4787207100
5.54-6.193.630.04822.667818798.2
6.19-7.153.650.03228.2606166100
7.15-8.763.730.02735.9529142100
8.76-12.393.360.02139.440011999
12.39-27.923.080.01638.41886187.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0127refinement
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
XSCALEDecember 6, 2010data scaling
PHENIX1.7.3refinement
MolProbity3beta29model building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F27

3f27


Resolution: 2.77→27.92 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 1 / SU B: 34.503 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R: 1.261 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM TLS ASSIGNMENT. 4. REFMAC JELLY-MODEL (RIDGE - 0.02) RESTRAINTS WERE INCLUDED. 5. B-FACTOR WEIGHTING WAS 1.0 2.0 3.0 2.0 3.0.
RfactorNum. reflection% reflectionSelection details
Rfree0.27835 223 4.6 %RANDOM
Rwork0.2469 ---
obs0.24826 4656 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 66.57 Å2
Baniso -1Baniso -2Baniso -3
1--2.68 Å20 Å20 Å2
2--3.13 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.77→27.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms586 486 0 7 1079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0151148
X-RAY DIFFRACTIONr_bond_other_d0.0020.02834
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.6421655
X-RAY DIFFRACTIONr_angle_other_deg1.15331927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.605571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.28522.90331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3171597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.148155
X-RAY DIFFRACTIONr_chiral_restr0.070.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02964
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02265
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.77→2.841 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 22 -
Rwork0.358 327 -
obs--99.15 %
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)
15.4117-0.374-0.29891.7822-0.59131.91610.12040.2965-0.0696-0.0476-0.0432-0.1422-0.02750.0714-0.07720.2789-0.06610.11430.2255-0.03250.3127-15.012-23.014216.6718
22.1191.2595-0.59223.5442-1.71274.7779-0.25550.06930.0542-0.3195-0.0103-0.3695-0.80390.33670.26580.4591-0.03960.09360.2726-0.07670.3325-13.0094-11.201910.9385
310.6180.5166-2.74611.3614-2.35464.4243-0.07450.15081.11050.23550.0788-0.0857-0.4556-0.1976-0.00430.57030.00880.06850.4191-0.08560.6198-16.7055-13.14959.7912
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A103 - 174
2X-RAY DIFFRACTION2B1 - 12
3X-RAY DIFFRACTION3C1 - 12

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