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Yorodumi- PDB-7x84: Cryo-EM structure of the TMEM106B fibril from Parkinson's disease... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7x84 | ||||||
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Title | Cryo-EM structure of the TMEM106B fibril from Parkinson's disease dementia | ||||||
Components | Transmembrane protein 106BTransmembrane protein | ||||||
Keywords | PROTEIN FIBRIL / amyloid | ||||||
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 Å | ||||||
Authors | Zhao, Q.Y. / Xia, W.C. / Fan, Y. / Sun, Y.P. / Tao, Y.Q. / Liu, C. | ||||||
Funding support | 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x84.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x84.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 7x84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/7x84 ftp://data.pdbj.org/pub/pdb/validation_reports/x8/7x84 | HTTPS FTP |
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-Related structure data
Related structure data | 33055MC 7x83C 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: 15502.680 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NUM4 |
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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: the fibril formed by TMEM106B from Parkinson's disease dementia Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2200 nm / Nominal defocus min: 1400 nm |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -0.45 ° / Axial rise/subunit: 4.83 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17752 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Refine LS restraints |
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