+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33054 | |||||||||
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Title | Cryo-EM structure of the TMEM106B fibril from normal elder | |||||||||
Map data | ||||||||||
Sample |
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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) / human (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Xia WC / Zhao QY / Fan Y / Sun YP / Tao YQ / Liu C | |||||||||
Funding support | 1 items
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Citation | Journal: Cell Res / Year: 2022 Title: Generic amyloid fibrillation of TMEM106B in patient with Parkinson's disease dementia and normal elders. Authors: Yun Fan / Qinyue Zhao / Wencheng Xia / Youqi Tao / Wenbo Yu / Mingjia Chen / Yiqi Liu / Jue Zhao / Yan Shen / Yunpeng Sun / Chenfang Si / Shenqing Zhang / Yaoyang Zhang / Wensheng Li / Cong ...Authors: Yun Fan / Qinyue Zhao / Wencheng Xia / Youqi Tao / Wenbo Yu / Mingjia Chen / Yiqi Liu / Jue Zhao / Yan Shen / Yunpeng Sun / Chenfang Si / Shenqing Zhang / Yaoyang Zhang / Wensheng Li / Cong Liu / Jian Wang / Dan Li / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33054.map.gz | 31.8 MB | EMDB map data format | |
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Header (meta data) | emd-33054-v30.xml emd-33054.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33054_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_33054.png | 41.5 KB | ||
Others | emd_33054_half_map_1.map.gz emd_33054_half_map_2.map.gz | 139.7 MB 139.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33054 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33054 | HTTPS FTP |
-Related structure data
Related structure data | 7x83MC 7x84C 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_33054.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33054_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33054_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : the fibril formed by TMEM106B from normal elder
Entire | Name: the fibril formed by TMEM106B from normal elder |
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Components |
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-Supramolecule #1: the fibril formed by TMEM106B from normal elder
Supramolecule | Name: the fibril formed by TMEM106B from normal elder / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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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: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: human (human) |
Molecular weight | Theoretical: 31.156318 KDa |
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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.4000000000000001 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |