+Open data
-Basic information
Entry | Database: PDB / ID: 4a3n | ||||||
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Title | Crystal Structure of HMG-BOX of Human SOX17 | ||||||
Components | TRANSCRIPTION FACTOR SOX-17 | ||||||
Keywords | TRANSCRIPTION | ||||||
Function / homology | Function and homology information cardiogenic plate morphogenesis / endodermal cell fate determination / regulation of cardiac cell fate specification / stem cell fate specification / endocardium formation / common bile duct development / endodermal digestive tract morphogenesis / ureter development / gallbladder development / inner cell mass cellular morphogenesis ...cardiogenic plate morphogenesis / endodermal cell fate determination / regulation of cardiac cell fate specification / stem cell fate specification / endocardium formation / common bile duct development / endodermal digestive tract morphogenesis / ureter development / gallbladder development / inner cell mass cellular morphogenesis / heart formation / cardiac cell fate determination / rostrocaudal neural tube patterning / endodermal cell fate specification / regulation of stem cell division / cell migration involved in gastrulation / endoderm formation / Specification of primordial germ cells / endocardial cell differentiation / positive regulation of endodermal cell differentiation / positive regulation of stem cell differentiation / embryonic foregut morphogenesis / regulation of stem cell proliferation / signal transduction involved in regulation of gene expression / Formation of definitive endoderm / metanephros development / embryonic heart tube development / embryonic heart tube morphogenesis / heart looping / outflow tract morphogenesis / regulation of embryonic development / anatomical structure morphogenesis / vasculogenesis / cellular response to leukemia inhibitory factor / Deactivation of the beta-catenin transactivating complex / protein destabilization / negative regulation of canonical Wnt signaling pathway / negative regulation of cell growth / beta-catenin binding / Wnt signaling pathway / positive regulation of protein catabolic process / gene expression / heart development / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / protein stabilization / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Gao, N. / Gao, H. / Qian, H. / Si, S. / Xie, Y. | ||||||
Citation | Journal: Protein Pept.Lett. / Year: 2013 Title: Structural Basis of Human Transcription Factor Sry-Related Box 17 Binding to DNA. Authors: Gao, N. / Jiang, W. / Gao, H. / Cheng, Z. / Qian, H. / Si, S. / Xie, Y. #1: Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a3n.cif.gz | 28.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a3n.ent.gz | 17.9 KB | Display | PDB format |
PDBx/mmJSON format | 4a3n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/4a3n ftp://data.pdbj.org/pub/pdb/validation_reports/a3/4a3n | HTTPS FTP |
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-Related structure data
Related structure data | 3f27S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8445.764 Da / Num. of mol.: 1 / Fragment: HMG-BOX, RESIDUES 68-136 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H6I2 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.19 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 4389 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 23.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3F27 Resolution: 2.4→23.66 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1313405.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.9136 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→23.66 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
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Xplor file |
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