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Open data
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Basic information
Entry | Database: PDB / ID: 8c6i | ||||||
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Title | TMEM2 ectodomain | ||||||
![]() | Cell surface hyaluronidase | ||||||
![]() | UNKNOWN FUNCTION / Hyaluronidase / carbohydrate-binding protein / beta-helix | ||||||
Function / homology | ![]() hyaluronoglucosaminidase / regulation of sprouting angiogenesis / hyalurononglucosaminidase activity / hyaluronan catabolic process / angiogenesis / cadherin binding / intracellular membrane-bounded organelle / calcium ion binding / nucleolus / extracellular exosome ...hyaluronoglucosaminidase / regulation of sprouting angiogenesis / hyalurononglucosaminidase activity / hyaluronan catabolic process / angiogenesis / cadherin binding / intracellular membrane-bounded organelle / calcium ion binding / nucleolus / extracellular exosome / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hohenester, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the transmembrane protein 2 (TMEM2) ectodomain and its apparent lack of hyaluronidase activity. Authors: Niu, M. / McGrath, M. / Sammon, D. / Gardner, S. / Morgan, R.M. / Di Maio, A. / Liu, Y. / Bubeck, D. / Hohenester, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 241.7 KB | Display | ![]() |
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PDB format | ![]() | 192.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 46.9 KB | Display | |
Data in CIF | ![]() | 63.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 145486.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 6 types, 9 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #9: Sugar | |
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-Non-polymers , 2 types, 2 molecules ![](data/chem/img/NI.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CL.gif)
#7: Chemical | ChemComp-NI / |
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#8: Chemical | ChemComp-CL / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1 M sodium acetate, pH 4.5, 30% polyethyleneglycol 3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 3, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→92.35 Å / Num. obs: 23570 / % possible obs: 100 % / Redundancy: 26.8 % / CC1/2: 0.997 / Rpim(I) all: 0.073 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 3.5→3.56 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1159 / CC1/2: 0.424 / Rpim(I) all: 0.871 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→91.55 Å
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Refine LS restraints |
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LS refinement shell |
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