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

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Basic information

Entry
Database: PDB / ID: 7zj2
TitleAmyloid fibril (in vitro) from full-length hnRNPA1 protein
ComponentsIsoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
KeywordsNUCLEAR PROTEIN / Amyloidosis / Misfolding disease / Inflammation / Prion / Protein fibril
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 / negative regulation of telomere maintenance via telomerase / regulation of RNA splicing / SARS-CoV-1 modulates host translation machinery / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / cellular response to glucose starvation / positive regulation of telomere maintenance via telomerase / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / single-stranded DNA binding / single-stranded RNA binding / protein domain specific binding / ribonucleoprotein complex / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / 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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsSharma, K. / Banerjee, S. / Schmidt, M. / Faendrich, M.
Funding support1items
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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jul 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
B: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
C: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
D: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
E: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
F: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
G: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
H: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
I: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
J: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
K: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
L: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1


Theoretical massNumber of molelcules
Total (without water)410,95512
Polymers410,95512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1 / hnRNP A1 / Helix-destabilizing protein / Single-strand RNA-binding protein / hnRNP core protein A1


Mass: 34246.227 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPA1, HNRPA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09651

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Amyloid fibril (in vitro) from full-length hnRNPA1 protein
Type: COMPLEX / Details: In vitro full-length hnRNPA1 amyloid fibril / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 10 sec. / Electron dose: 42.64 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2624
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1RELION3.1.1particle selection
2SerialEMimage acquisition
4CTFFIND4.1CTF correction
7Coot0.9.1model fitting
9PHENIX1.18-3874model refinement
12RELION3.1.1classification
13RELION3.1.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.05 ° / Axial rise/subunit: 2.37 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 184301
3D reconstructionResolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54408 / Symmetry type: HELICAL
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL / Target criteria: correlation coefficient
Atomic model buildingPDB-ID: 7BX7

7bx7


Accession code: 7BX7 / Source name: PDB / Type: experimental model

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