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- EMDB-14739: Amyloid fibril (in vitro) from full-length hnRNPA1 protein -

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Basic information

Entry
Database: EMDB / ID: EMD-14739
TitleAmyloid fibril (in vitro) from full-length hnRNPA1 protein
Map dataFinal map
Sample
  • Complex: Amyloid fibril (in vitro) from full-length hnRNPA1 protein
    • Protein or peptide: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
KeywordsAmyloidosis / Misfolding disease / Inflammation / Prion / Protein fibril / NUCLEAR PROTEIN
Function / homology
Function and homology information


cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing ...cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / intracellular non-membrane-bounded organelle / SARS-CoV-1 modulates host translation machinery / regulation of RNA splicing / negative regulation of telomere maintenance via telomerase / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / localization / cellular response to glucose starvation / positive regulation of telomere maintenance via telomerase / catalytic step 2 spliceosome / molecular condensate scaffold activity / mRNA Splicing - Major Pathway / mRNA 3'-UTR binding / spliceosomal complex / mRNA splicing, via spliceosome / single-stranded DNA binding / amyloid fibril formation / single-stranded RNA binding / ribonucleoprotein complex / protein domain specific binding / DNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
hnRNP A3, RNA recognition motif 2 / hnRNP A1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Heterogeneous nuclear ribonucleoprotein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsSharma K / Banerjee S / Schmidt M / Faendrich M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Mol Biol / Year: 2023
Title: Cryo-EM Structure of the Full-length hnRNPA1 Amyloid Fibril.
Authors: Kartikay Sharma / Sambhasan Banerjee / Dilan Savran / Cedric Rajes / Sebastian Wiese / Amandeep Girdhar / Nadine Schwierz / Christopher Lee / James Shorter / Matthias Schmidt / Lin Guo / Marcus Fändrich /
Abstract: Heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) is a multifunctional RNA-binding protein that is associated with neurodegenerative diseases, such as amyotrophic lateral sclerosis and multisystem ...Heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) is a multifunctional RNA-binding protein that is associated with neurodegenerative diseases, such as amyotrophic lateral sclerosis and multisystem proteinopathy. In this study, we have used cryo-electron microscopy to investigate the three-dimensional structure of amyloid fibrils from full-length hnRNPA1 protein. We find that the fibril core is formed by a 45-residue segment of the prion-like low-complexity domain of the protein, whereas the remaining parts of the protein (275 residues) form a fuzzy coat around the fibril core. The fibril consists of two fibril protein stacks that are arranged into a pseudo-2 screw symmetry. The ordered core harbors several of the positions that are known to be affected by disease-associated mutations, but does not encompass the most aggregation-prone segments of the protein. These data indicate that the structures of amyloid fibrils from full-length proteins may be more complex than anticipated by current theories on protein misfolding.
History
DepositionApr 8, 2022-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14739.png

Downloads & links

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Map

FileDownload / File: emd_14739.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.3
Minimum - Maximum-6.934637 - 13.954295999999999
Average (Standard dev.)0.03204524 (±0.40907103)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Relion half map-1

Fileemd_14739_half_map_1.map
AnnotationRelion half map-1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Relion half map-2

Fileemd_14739_half_map_2.map
AnnotationRelion half map-2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Amyloid fibril (in vitro) from full-length hnRNPA1 protein

EntireName: Amyloid fibril (in vitro) from full-length hnRNPA1 protein
Components
  • Complex: Amyloid fibril (in vitro) from full-length hnRNPA1 protein
    • Protein or peptide: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1

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Supramolecule #1: Amyloid fibril (in vitro) from full-length hnRNPA1 protein

SupramoleculeName: Amyloid fibril (in vitro) from full-length hnRNPA1 protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: In vitro full-length hnRNPA1 amyloid fibril
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1

MacromoleculeName: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.246227 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKSESPKEP EQLRKLFIGG LSFETTDESL RSHFEQWGTL TDCVVMRDPN TKRSRGFGFV TYATVEEVDA AMNARPHKVD GRVVEPKRA VSREDSQRPG AHLTVKKIFV GGIKEDTEEH HLRDYFEQYG KIEVIEIMTD RGSGKKRGFA FVTFDDHDSV D KIVIQKYH ...String:
MSKSESPKEP EQLRKLFIGG LSFETTDESL RSHFEQWGTL TDCVVMRDPN TKRSRGFGFV TYATVEEVDA AMNARPHKVD GRVVEPKRA VSREDSQRPG AHLTVKKIFV GGIKEDTEEH HLRDYFEQYG KIEVIEIMTD RGSGKKRGFA FVTFDDHDSV D KIVIQKYH TVNGHNCEVR KALSKQEMAS ASSSQRGRSG SGNFGGGRGG GFGGNDNFGR GGNFSGRGGF GGSRGGGGYG GS GDGYNGF GNDGSNFGGG GSYNDFGNYN NQSSNFGPMK GGNFGGRSSG PYGGGGQYFA KPRNQGGYGG SSSSSSYGSG RRF

UniProtKB: Heterogeneous nuclear ribonucleoprotein A1

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 2624 / Average exposure time: 10.0 sec. / Average electron dose: 42.64 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 184301 / Software - Name: RELION (ver. 3.1.1)
Startup modelType of model: EMDB MAP
EMDB ID:

30235

Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 2.37 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.05 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 54408
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7bx7

RefinementSpace: REAL / Protocol: BACKBONE TRACE / Target criteria: correlation coefficient
Output model

PDB-7zj2:
Amyloid fibril (in vitro) from full-length hnRNPA1 protein

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