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- EMDB-35505: Cryo-EM structure of hnRAC1 fibril. -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-35505
TitleCryo-EM structure of hnRAC1 fibril.
Map data
Sample
  • Organelle or cellular component: Formed fibrils of hnRNP A1 reversible amyloid core GFGGNDNFG (residues 209-217)
    • Protein or peptide: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHE-GLY
Keywordsreversible fibril / RNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsLi DN / Ma YY / Li D / Dai B / Liu C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Formed fibrils of hnRNP A1 reversible amyloid core GFGGNDNFG (residues 209-217)
Authors: Li DN / Ma YY / Li D / Dai B / Liu C
History
DepositionFeb 28, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35505.png

Downloads & links

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Map

FileDownload / File: emd_35505.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0096
Minimum - Maximum-0.0142369 - 0.03356356
Average (Standard dev.)0.00032542174 (±0.0018303905)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35505_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35505_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 : Formed fibrils of hnRNP A1 reversible amyloid core GFGGNDNFG (res...

EntireName: Formed fibrils of hnRNP A1 reversible amyloid core GFGGNDNFG (residues 209-217)
Components
  • Organelle or cellular component: Formed fibrils of hnRNP A1 reversible amyloid core GFGGNDNFG (residues 209-217)
    • Protein or peptide: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHE-GLY

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Supramolecule #1: Formed fibrils of hnRNP A1 reversible amyloid core GFGGNDNFG (res...

SupramoleculeName: Formed fibrils of hnRNP A1 reversible amyloid core GFGGNDNFG (residues 209-217)
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHE-GLY

MacromoleculeName: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHE-GLY / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 883.863 Da
SequenceString:
GFGGNDNFG

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.81 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.09 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16505
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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