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- PDB-9gkf: Amyloid Fibril of Heterogeneous nuclear ribonucleoprotein A1A ind... -

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Basic information

Entry
Database: PDB / ID: 9gkf
TitleAmyloid Fibril of Heterogeneous nuclear ribonucleoprotein A1A induced by RNA binding
ComponentsIsoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
KeywordsRNA BINDING PROTEIN / Amyloid Fibril of Heterogeneous nuclear ribonucleoprotein A1A induced by RNA binding
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 / pre-mRNA binding / G-rich strand telomeric DNA 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 / pre-mRNA binding / G-rich strand telomeric DNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / negative regulation of telomere maintenance via telomerase / 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 speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsFrey, L. / Riek, R.P. / Arosio, P. / Morelli, C.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
ETH Zurich Switzerland
CitationJournal: To Be Published
Title: hnRNPA1A and RNA binding
Authors: Frey, L. / Riek, R.P.
History
DepositionAug 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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
M: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
N: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
O: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
P: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
Q: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
R: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
S: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1
T: Isoform A1-A of Heterogeneous nuclear ribonucleoprotein A1


Theoretical massNumber of molelcules
Total (without water)684,92520
Polymers684,92520
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPA1, HNRPA1 / Production host: Bacteria (eubacteria) / References: UniProt: P09651
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: hnRNPA1A with poly U RNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
Source (recombinant)Organism: Bacteria (eubacteria) / Strain: BL21 DE3
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV / Phase plate: OTHER

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2EPU2image acquisition
4CTFFIND4CTF correction
7RELION5model fitting
11RELIONclassification
12RELION3D reconstruction
13ISOLDEmodel refinement
CTF correctionType: NONE
Helical symmerty
IDImage processing-IDAngular rotation/subunit (°)Axial rise/subunit (Å)Axial symmetry
11-2.944.83C1
21-2.944.83C1
Particle selectionNum. of particles selected: 120000
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100000 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 78.32 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00328300
ELECTRON MICROSCOPYf_angle_d0.650911060
ELECTRON MICROSCOPYf_chiral_restr0.0478740
ELECTRON MICROSCOPYf_plane_restr0.00311680
ELECTRON MICROSCOPYf_dihedral_angle_d10.44522740

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