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- EMDB-51419: Amyloid Fibril of Heterogeneous nuclear ribonucleoprotein A1A ind... -

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Basic information

Entry
Database: EMDB / ID: EMD-51419
TitleAmyloid Fibril of Heterogeneous nuclear ribonucleoprotein A1A induced by RNA binding
Map data
Sample
  • Complex: hnRNPA1A with poly U RNA
    • Protein or peptide: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
KeywordsAmyloid Fibril of Heterogeneous nuclear ribonucleoprotein A1A induced by RNA binding / RNA BINDING 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 / alternative mRNA splicing, via spliceosome / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus / miRNA binding ...cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / alternative mRNA splicing, via spliceosome / 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 / ribonucleoprotein complex / protein domain specific binding / synapse / 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 speciesEscherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsFrey L / Riek RP / Arosio P / Morelli C
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
ETH Zurich Switzerland
CitationJournal: To Be Published
Title: hnRNPA1A and RNA binding
Authors: Frey L / Riek RP
History
DepositionAug 23, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51419.png

Downloads & links

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Map

FileDownload / File: emd_51419.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 256 pix.
= 332.8 Å		1.3 Å/pix.
x 256 pix.
= 332.8 Å		1.3 Å/pix.
x 256 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.08652618 - 0.17080222
Average (Standard dev.)0.0001226972 (±0.002767556)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51419_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51419_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : hnRNPA1A with poly U RNA

EntireName: hnRNPA1A with poly U RNA
Components
  • Complex: hnRNPA1A with poly U RNA
    • Protein or peptide: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1

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Supramolecule #1: hnRNPA1A with poly U RNA

SupramoleculeName: hnRNPA1A with poly U RNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)

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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: 20 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.246227 KDa
Recombinant expressionOrganism: Bacteria (eubacteria)
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 statefilament

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: OTHER / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.83 Å
Applied symmetry - Helical parameters - Δ&Phi: -2.94 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 100000
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: NONE
Segment selectionNumber selected: 120000 / Software - Name: crYOLO
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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