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Yorodumi- PDB-8fzv: The von Willebrand factor A domain of human capillary morphogenes... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fzv | ||||||
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Title | The von Willebrand factor A domain of human capillary morphogenesis gene II, flexibly fused to the 1TEL crystallization chaperone, Ala-Ala linker variant, expressed with SUMO tag | ||||||
Components | Transcription factor ETV6,Anthrax toxin receptor 2 | ||||||
Keywords | PEPTIDE BINDING PROTEIN / TELSAM Fusion / Polymer forming crystallization chaperone | ||||||
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 / endosome membrane / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin / endoplasmic reticulum membrane / nucleolus / regulation of transcription by RNA polymerase II / 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: 3.29 Å | ||||||
Authors | Pedroza Romo, M.J. / Soleimani, S. / Doukov, T. / Lebedev, A. / Moody, J.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 Title: Increasing the bulk of the 1TEL-target linker and retaining the 10×His tag in a 1TEL-CMG2-vWa construct improves crystal order and diffraction limits. Authors: Gajjar, P.L. / Pedroza Romo, M.J. / Litchfield, C.M. / Callahan, M. / Redd, N. / Nawarathnage, S. / Soleimani, S. / Averett, J. / Wilson, E. / Lewis, A. / Stewart, C. / Tseng, Y.J. / Doukov, ...Authors: Gajjar, P.L. / Pedroza Romo, M.J. / Litchfield, C.M. / Callahan, M. / Redd, N. / Nawarathnage, S. / Soleimani, S. / Averett, J. / Wilson, E. / Lewis, A. / Stewart, C. / Tseng, Y.J. / Doukov, T. / Lebedev, A. / Moody, J.D. #1: Journal: Biorxiv / Year: 2023 Title: Decreasing the flexibility of the TELSAM-target protein linker and omitting the cleavable fusion tag improves crystal order and diffraction limits. Authors: Gajjar, P.L. / Romo, M.J.P. / Litchfield, C.M. / Callahan, M. / Redd, N. / Nawarathnage, S. / Soleimani, S. / Averett, J. / Wilson, E. / Lewis, A. / Stewart, C. / Tseng, Y.J. / Doukov, T. / ...Authors: Gajjar, P.L. / Romo, M.J.P. / Litchfield, C.M. / Callahan, M. / Redd, N. / Nawarathnage, S. / Soleimani, S. / Averett, J. / Wilson, E. / Lewis, A. / Stewart, C. / Tseng, Y.J. / Doukov, T. / Lebedev, A. / 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 | 8fzv.cif.gz | 254.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fzv.ent.gz | 179.4 KB | Display | PDB format |
PDBx/mmJSON format | 8fzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fzv_validation.pdf.gz | 474.9 KB | Display | wwPDB validaton report |
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Full document | 8fzv_full_validation.pdf.gz | 479.9 KB | Display | |
Data in XML | 8fzv_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 8fzv_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/8fzv ftp://data.pdbj.org/pub/pdb/validation_reports/fz/8fzv | HTTPS FTP |
-Related structure data
Related structure data | 8ft6C 8ft8C 8fz4C 8fzuC 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 28647.684 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1, ANTXR2, CMG2 / Production host: Escherichia coli (E. coli) / References: UniProt: P41212, UniProt: P58335 #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 100 mM sodium acetate, pH 4.6, 2.0 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.29→70.39 Å / Num. obs: 12820 / % possible obs: 90.65 % / Redundancy: 7.9 % / Biso Wilson estimate: 118.63 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.3371 / Net I/σ(I): 6.02 |
Reflection shell | Resolution: 3.292→3.409 Å / Rmerge(I) obs: 3.593 / Num. unique obs: 515 / CC1/2: 0.283 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.29→70.39 Å / SU ML: 0.4006 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.5111 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: 121.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.29→70.39 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
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