+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28014 | |||||||||
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Title | HnRNPA2 D290V LCD PM3 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Amyloid / PROTEIN FIBRIL | |||||||||
Function / homology | Function and homology information positive regulation of telomerase RNA reverse transcriptase activity / miRNA transport / positive regulation of telomere maintenance via telomere lengthening / RNA transport / G-quadruplex DNA unwinding / primary miRNA processing / single-stranded telomeric DNA binding / N6-methyladenosine-containing RNA reader activity / G-rich strand telomeric DNA binding / miRNA binding ...positive regulation of telomerase RNA reverse transcriptase activity / miRNA transport / positive regulation of telomere maintenance via telomere lengthening / RNA transport / G-quadruplex DNA unwinding / primary miRNA processing / single-stranded telomeric DNA binding / N6-methyladenosine-containing RNA reader activity / G-rich strand telomeric DNA binding / miRNA binding / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / Cajal body / mRNA export from nucleus / pre-mRNA intronic binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / catalytic step 2 spliceosome / molecular condensate scaffold activity / mRNA Splicing - Major Pathway / mRNA 3'-UTR binding / spliceosomal complex / mRNA processing / mRNA splicing, via spliceosome / nuclear matrix / chromosome, telomeric region / ribonucleoprotein complex / negative regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Eisenberg DS / Lu J / Ge P / Boyer DR | |||||||||
Funding support | United States, 2 items
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Citation | Journal: J Biol Chem / Year: 2024 Title: Cryo-EM structures of the D290V mutant of the hnRNPA2 low-complexity domain suggests how D290V affects phase separation and aggregation. Authors: Jiahui Lu / Peng Ge / Michael R Sawaya / Michael P Hughes / David R Boyer / Qin Cao / Romany Abskharon / Duilio Cascio / Einav Tayeb-Fligelman / David S Eisenberg / Abstract: Heterogeneous nuclear ribonucleoprotein A2 (hnRNPA2) is a human ribonucleoprotein that transports RNA to designated locations for translation via its ability to phase separate. Its mutated form, ...Heterogeneous nuclear ribonucleoprotein A2 (hnRNPA2) is a human ribonucleoprotein that transports RNA to designated locations for translation via its ability to phase separate. Its mutated form, D290V, is implicated in multisystem proteinopathy known to afflict two families, mainly with myopathy and Paget's disease of bone. Here, we investigate this mutant form of hnRNPA2 by determining cryo-EM structures of the recombinant D290V low complexity domain. We find that the mutant form of hnRNPA2 differs from the WT fibrils in four ways. In contrast to the WT fibrils, the PY-nuclear localization signals in the fibril cores of all three mutant polymorphs are less accessible to chaperones. Also, the mutant fibrils are more stable than WT fibrils as judged by phase separation, thermal stability, and energetic calculations. Similar to other pathogenic amyloids, the mutant fibrils are polymorphic. Thus, these structures offer evidence to explain how a D-to-V missense mutation diverts the assembly of reversible, functional amyloid-like fibrils into the assembly of pathogenic amyloid, and may shed light on analogous conversions occurring in other ribonucleoproteins that lead to neurological diseases such as amyotrophic lateral sclerosis and frontotemporal dementia. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28014.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-28014-v30.xml emd-28014.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
Images | emd_28014.png | 33.2 KB | ||
Filedesc metadata | emd-28014.cif.gz | 5.1 KB | ||
Others | emd_28014_half_map_1.map.gz emd_28014_half_map_2.map.gz | 19.8 MB 19.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28014 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28014 | HTTPS FTP |
-Related structure data
Related structure data | 8ec7MC 8du2C 8duwC 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_28014.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.078 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_28014_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28014_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Fibrils of hnRNPA2 D290V LCD PM3
Entire | Name: Fibrils of hnRNPA2 D290V LCD PM3 |
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Components |
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-Supramolecule #1: Fibrils of hnRNPA2 D290V LCD PM3
Supramolecule | Name: Fibrils of hnRNPA2 D290V LCD PM3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Heterogeneous nuclear ribonucleoproteins A2/B1
Macromolecule | Name: Heterogeneous nuclear ribonucleoproteins A2/B1 / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 15.391775 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MQEVQSSRSG RGGNFGFGDS RGGGGNFGPG PGSNFRGGSD GYGSGRGFGD GYNGYGGGPG GGNFGGSPGY GGGRGGYGGG GPGYGNQGG GYGGGYDNYG GGNYGSGNYN VFGNYNQQPS NYGPMKSGNF GGSRNMGGPY GGGNYGPGGS GGSGGYGGRS R Y UniProtKB: Heterogeneous nuclear ribonucleoproteins A2/B1 |
-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: 5.0 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 36.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: Gaussian blob |
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Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Applied symmetry - Helical parameters - Δz: 4.88 Å Applied symmetry - Helical parameters - Δ&Phi: -0.72 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16114 |