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- PDB-7n1o: The von Willebrand factor A domain of human capillary morphogenes... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7n1o | ||||||
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Title | The von Willebrand factor A domain of human capillary morphogenesis gene II, flexibly fused to the 1TEL crystallization chaperone | ||||||
![]() | Transcription factor ETV6,Isoform 4 of Anthrax toxin receptor 2 | ||||||
![]() | PROTEIN BINDING / von Willebrand factor type A domain / Collagen binding / alpha-beta / MIDAS | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mathis, M.H. / Bezzant, B.D. / Ramirez, D.T. / Sarath Nawarathnage, S.D. / Doukov, T. / Moody, J.D. | ||||||
![]() | ![]() Title: Crystals of TELSAM-target protein fusions that exhibit minimal crystal contacts and lack direct inter-TELSAM contacts. Authors: Nawarathnage, S. / Soleimani, S. / Mathis, M.H. / Bezzant, B.D. / Ramirez, D.T. / Gajjar, P. / Bunn, D.R. / Stewart, C. / Smith, T. / Pedroza Romo, M.J. / Brown, S. / Doukov, T. / Moody, J.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127 KB | Display | ![]() |
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PDB format | ![]() | 86.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 415.9 KB | Display | ![]() |
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Full document | ![]() | 418.2 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 14.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7n2bC ![]() 1shuS ![]() 2qb1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 28647.684 Da / Num. of mol.: 1 Mutation: 1TEL: R41A,D46G,V112E,K122A,vWa: R49A,C175A,V112A,K112A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.59 % / Description: rod-like hexagonal prism |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.7 / Details: 100 mM BisTris, 3.0 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.77→38.16 Å / Num. obs: 8679 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 71.13 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05193 / Rpim(I) all: 0.024 / Rrim(I) all: 0.05753 / Net I/σ(I): 18.35 |
Reflection shell | Resolution: 2.77→2.869 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.6253 / Mean I/σ(I) obs: 2.88 / Num. unique obs: 878 / CC1/2: 0.899 / CC star: 0.973 / Rpim(I) all: 0.2779 / Rrim(I) all: 0.6876 / % possible all: 97.99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2QB1, 1SHU Resolution: 2.77→38.16 Å / SU ML: 0.3932 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5672 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.77→38.16 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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