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Yorodumi- EMDB-28943: TMEM106B doublet filaments extracted from MSTD neurodegenerative ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28943 | |||||||||
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Title | TMEM106B doublet filaments extracted from MSTD neurodegenerative human brain | |||||||||
Map data | ||||||||||
Sample |
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Keywords | TMEM106B / TMEM filament / MSTD / NEUROPEPTIDE | |||||||||
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 | helical reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Hoq MR / Bharath SR / Jiang W | |||||||||
Funding support | United States, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28943.map.gz | 78.5 MB | EMDB map data format | |
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Header (meta data) | emd-28943-v30.xml emd-28943.xml | 14.2 KB 14.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28943_fsc.xml | 18.1 KB | Display | FSC data file |
Images | emd_28943.png | 79.9 KB | ||
Filedesc metadata | emd-28943.cif.gz | 5.5 KB | ||
Others | emd_28943_half_map_1.map.gz emd_28943_half_map_2.map.gz | 67 MB 67 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28943 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28943 | HTTPS FTP |
-Validation report
Summary document | emd_28943_validation.pdf.gz | 945.8 KB | Display | EMDB validaton report |
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Full document | emd_28943_full_validation.pdf.gz | 945.4 KB | Display | |
Data in XML | emd_28943_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | emd_28943_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28943 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28943 | HTTPS FTP |
-Related structure data
Related structure data | 8f9kMC 7tmcC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28943.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_28943_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28943_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TMEM106B
Entire | Name: TMEM106B |
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Components |
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-Supramolecule #1: TMEM106B
Supramolecule | Name: TMEM106B / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Transmembrane protein 106B
Macromolecule | Name: Transmembrane protein 106B / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 31.156318 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGKSLSHLPL HSSKEDAYDG VTSENMRNGL VNSEVHNEDG RNGDVSQFPY VEFTGRDSVT CPTCQGTGRI PRGQENQLVA LIPYSDQRL RPRRTKLYVM ASVFVCLLLS GLAVFFLFPR SIDVKYIGVK SAYVSYDVQK RTIYLNITNT LNITNNNYYS V EVENITAQ ...String: MGKSLSHLPL HSSKEDAYDG VTSENMRNGL VNSEVHNEDG RNGDVSQFPY VEFTGRDSVT CPTCQGTGRI PRGQENQLVA LIPYSDQRL RPRRTKLYVM ASVFVCLLLS GLAVFFLFPR SIDVKYIGVK SAYVSYDVQK RTIYLNITNT LNITNNNYYS V EVENITAQ VQFSKTVIGK ARLNNITIIG PLDMKQIDYT VPTVIAEEMS YMYDFCTLIS IKVHNIVLMM QVTVTTTYFG HS EQISQER YQYVDCGRNT TYQLGQSEYL NVLQPQQ UniProtKB: Transmembrane protein 106B |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 24 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.2 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 1.103 sec. / Average electron dose: 50.46 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |