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Yorodumi- PDB-9doc: The von Willebrand factor A domain of human capillary morphogenes... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9doc | ||||||
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Title | The von Willebrand factor A domain of human capillary morphogenesis gene II, flexibly fused to the 1TEL crystallization chaperone, Thr-Val linker variant, at 1.2 Angstrom resolution | ||||||
Components | Transcription factor ETV6,Capillary morphogenesis gene 2 protein | ||||||
Keywords | PEPTIDE BINDING PROTEIN / TELSAM / 1TEL / Pointed Domain / Sterile Alpha Motif domain / ETS / TEL / CMG2 / vWA Domain / Anthrax toxin receptor 2 / ONCOPROTEIN | ||||||
Function / homology | Function and homology information Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Uptake and function of anthrax toxins / Signaling by FLT3 fusion proteins / neurogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / transmembrane signaling receptor activity ...Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Uptake and function of anthrax toxins / Signaling by FLT3 fusion proteins / neurogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / transmembrane signaling receptor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / endosome membrane / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / endoplasmic reticulum membrane / chromatin / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of transcription by RNA polymerase II / cell surface / extracellular region / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å | ||||||
Authors | Samarawickrama, P. / Probst, R. / Ludlow, K. / Doukov, T. / Moody, J.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: 1TEL Fusions Outperform 2TEL and 3TEL Fusions in Controlled Comparisons Authors: Samarawickrama, P. / Ludlow, K. / Probst, R. / Abiodun, W. / Averett, J. / Hansen, D. / Doukov, T. / Moody, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9doc.cif.gz | 183.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9doc.ent.gz | 132.1 KB | Display | PDB format |
PDBx/mmJSON format | 9doc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9doc_validation.pdf.gz | 449.9 KB | Display | wwPDB validaton report |
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Full document | 9doc_full_validation.pdf.gz | 453.4 KB | Display | |
Data in XML | 9doc_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 9doc_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/9doc ftp://data.pdbj.org/pub/pdb/validation_reports/do/9doc | HTTPS FTP |
-Related structure data
Related structure data | 9cplC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30234.422 Da / Num. of mol.: 1 / Fragment: von Willebrand factor A domain of CMG2 Mutation: TELSAM: R80S,V112E (Uniprot numbering),vWA: C175A (Uniprot numbering) Source method: isolated from a genetically manipulated source Details: Tandem fusion of 1TEL followed by the vWA domain of CMG2 Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1, ANTXR2, CMG2 / Plasmid: pET42-His-1TEL-XhoI Details (production host): N-term 10xHis, Kanamycin resistant Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B / References: UniProt: P41212, UniProt: P58335 |
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-Non-polymers , 5 types, 260 molecules
#2: Chemical | ChemComp-GOL / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-NA / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.53 % Description: Large Hexagonal prism tapered to a point at one end |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.25 Details: 100 mM Bis-Tris, pH 7.25, 1350 mM Sodium Potassium Phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2023 / Details: Rh coated collimating mirror, K-B focusing mirrors |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal monochromator, non fixed exit slit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→43.92 Å / Num. obs: 91358 / % possible obs: 97.19 % / Redundancy: 9 % / Biso Wilson estimate: 17.06 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04722 / Rpim(I) all: 0.01608 / Rrim(I) all: 0.04997 / Net I/σ(I): 15.17 |
Reflection shell | Resolution: 1.19→1.233 Å / Rmerge(I) obs: 2.286 / Mean I/σ(I) obs: 0.62 / Num. unique obs: 7752 / CC1/2: 0.523 / CC star: 0.829 / Rpim(I) all: 0.8955 / Rrim(I) all: 2.463 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→43.92 Å / SU ML: 0.1758 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3064 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.19→43.92 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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