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Yorodumi- EMDB-8765: MicroED structure of the segment, DLIIKGISVHI, from the RRM2 of T... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8765 | |||||||||
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Title | MicroED structure of the segment, DLIIKGISVHI, from the RRM2 of TDP-43, residues 247-257 | |||||||||
Map data | Peptide DLIIKGISVHI from the RRM2 of TDP-43, residues 247-257 | |||||||||
Sample |
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Keywords | Amyloid / steric zipper / PROTEIN FIBRIL | |||||||||
Function / homology | Function and homology information nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / intracellular non-membrane-bounded organelle / negative regulation by host of viral transcription / pre-mRNA intronic binding / response to endoplasmic reticulum stress / RNA splicing ...nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / intracellular non-membrane-bounded organelle / negative regulation by host of viral transcription / pre-mRNA intronic binding / response to endoplasmic reticulum stress / RNA splicing / negative regulation of protein phosphorylation / mRNA 3'-UTR binding / molecular condensate scaffold activity / regulation of circadian rhythm / regulation of protein stability / positive regulation of insulin secretion / positive regulation of protein import into nucleus / cytoplasmic stress granule / mRNA processing / rhythmic process / double-stranded DNA binding / regulation of gene expression / regulation of apoptotic process / amyloid fibril formation / regulation of cell cycle / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / lipid binding / chromatin / mitochondrion / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | electron crystallography / cryo EM | |||||||||
Authors | Guenther EL / Sawaya MR | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2018 Title: Atomic-level evidence for packing and positional amyloid polymorphism by segment from TDP-43 RRM2. Authors: Elizabeth L Guenther / Peng Ge / Hamilton Trinh / Michael R Sawaya / Duilio Cascio / David R Boyer / Tamir Gonen / Z Hong Zhou / David S Eisenberg / Abstract: Proteins in the fibrous amyloid state are a major hallmark of neurodegenerative disease. Understanding the multiple conformations, or polymorphs, of amyloid proteins at the molecular level is a ...Proteins in the fibrous amyloid state are a major hallmark of neurodegenerative disease. Understanding the multiple conformations, or polymorphs, of amyloid proteins at the molecular level is a challenge of amyloid research. Here, we detail the wide range of polymorphs formed by a segment of human TAR DNA-binding protein 43 (TDP-43) as a model for the polymorphic capabilities of pathological amyloid aggregation. Using X-ray diffraction, microelectron diffraction (MicroED) and single-particle cryo-EM, we show that the DLIIKGISVHI segment from the second RNA-recognition motif (RRM2) forms an array of amyloid polymorphs. These associations include seven distinct interfaces displaying five different symmetry classes of steric zippers. Additionally, we find that this segment can adopt three different backbone conformations that contribute to its polymorphic capabilities. The polymorphic nature of this segment illustrates at the molecular level how amyloid proteins can form diverse fibril structures. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8765.map.gz | 413.6 KB | EMDB map data format | |
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Header (meta data) | emd-8765-v30.xml emd-8765.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
Images | emd_8765.png | 347.3 KB | ||
Filedesc metadata | emd-8765.cif.gz | 4.5 KB | ||
Filedesc structureFactors | emd_8765_sf.cif.gz | 32.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8765 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8765 | HTTPS FTP |
-Validation report
Summary document | emd_8765_validation.pdf.gz | 456 KB | Display | EMDB validaton report |
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Full document | emd_8765_full_validation.pdf.gz | 455.6 KB | Display | |
Data in XML | emd_8765_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | emd_8765_validation.cif.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8765 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8765 | HTTPS FTP |
-Related structure data
Related structure data | 5w52MC 8781C 5w50C 5w7vC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8765.map.gz / Format: CCP4 / Size: 1.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Peptide DLIIKGISVHI from the RRM2 of TDP-43, residues 247-257 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.443 Å / Y: 0.338 Å / Z: 0.417 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : DLIIKGISVHI fibril
Entire | Name: DLIIKGISVHI fibril |
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Components |
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-Supramolecule #1: DLIIKGISVHI fibril
Supramolecule | Name: DLIIKGISVHI fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: This peptide was synthesized and crystallized. |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 5.03 kDa/nm |
-Macromolecule #1: TAR DNA-binding protein 43
Macromolecule | Name: TAR DNA-binding protein 43 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 1.209479 KDa |
Sequence | String: DLIIKGISVH I UniProtKB: TAR DNA-binding protein 43 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron crystallography |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 8.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 3.4 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 1840 mm |
-Image processing
Final reconstruction | Resolution method: DIFFRACTION PATTERN/LAYERLINES |
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Molecular replacement | Software - Name: Phaser |
Merging software list | Software - Name: XSCALE |
Crystallography statistics | Number intensities measured: 9353 / Number structure factors: 1037 / Fourier space coverage: 73.4 / R sym: 20.3 / R merge: 20.3 / Overall phase error: 0.001 / Overall phase residual: 0.001 / Phase error rejection criteria: 1 / High resolution: 1.4 Å / Shell - Shell ID: 1 / Shell - High resolution: 1.4 Å / Shell - Low resolution: 1.48 Å / Shell - Number structure factors: 139 / Shell - Phase residual: 0.001 / Shell - Fourier space coverage: 62.1 / Shell - Multiplicity: 6.71 |