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Yorodumi- PDB-7tmc: TMEM106B singlet filament extracted from MSTD neurodegenerative h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tmc | |||||||||
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Title | TMEM106B singlet filament extracted from MSTD neurodegenerative human brain | |||||||||
Components | Transmembrane protein 106B | |||||||||
Keywords | NEUROPEPTIDE / TMEM106B / TMEM filament / MSTD | |||||||||
Function / homology | Function and homology information lysosomal protein catabolic process / regulation of lysosome organization / lysosomal lumen acidification / lysosome localization / positive regulation of dendrite development / dendrite morphogenesis / lysosomal transport / lysosome organization / neuron cellular homeostasis / late endosome membrane ...lysosomal protein catabolic process / regulation of lysosome organization / lysosomal lumen acidification / lysosome localization / positive regulation of dendrite development / dendrite morphogenesis / lysosomal transport / lysosome organization / neuron cellular homeostasis / late endosome membrane / ATPase binding / lysosome / endosome / lysosomal membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.25 Å | |||||||||
Authors | Hoq, M.R. / Bharath, S.R. / Jiang, W. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Acta Neuropathol / Year: 2023 Title: Cross-β helical filaments of Tau and TMEM106B in gray and white matter of multiple system tauopathy with presenile dementia. Authors: Md Rejaul Hoq / Sakshibeedu R Bharath / Grace I Hallinan / Anllely Fernandez / Frank S Vago / Kadir A Ozcan / Daoyi Li / Holly J Garringer / Ruben Vidal / Bernardino Ghetti / Wen Jiang / | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tmc.cif.gz | 101.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tmc.ent.gz | 75.6 KB | Display | PDB format |
PDBx/mmJSON format | 7tmc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tmc_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7tmc_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7tmc_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 7tmc_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/7tmc ftp://data.pdbj.org/pub/pdb/validation_reports/tm/7tmc | HTTPS FTP |
-Related structure data
Related structure data | 25995MC 8f9kC M: map data used to model this data 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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-Components
#1: Protein | Mass: 31156.318 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM106B / Production host: Homo sapiens (human) / References: UniProt: Q9NUM4 #2: Sugar | ChemComp-NAG / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: TMEM106B / Type: TISSUE / Entity ID: #1 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.2 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GRAPHENE OXIDE / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 1.103 sec. / Electron dose: 50.46 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||
Helical symmerty | Angular rotation/subunit: -0.43 ° / Axial rise/subunit: 4.79 Å / Axial symmetry: C1 | |||||||||||||||
3D reconstruction | Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16484 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: HELICAL |