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- EMDB-57189: IAPP S20G growth-phase fibril polymorph 3PF-LJ -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-57189
TitleIAPP S20G growth-phase fibril polymorph 3PF-LJ
Map dataSharpened map
Sample
  • Complex: Amyloid assembly 6 weeks during growth phase
    • Protein or peptide: Islet amyloid polypeptide
KeywordsAmyloid / filament / STRUCTURAL PROTEIN
Function / homology
Function and homology information


amylin receptor 3 signaling pathway / amylin receptor 2 signaling pathway / amylin receptor 1 signaling pathway / amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / positive regulation of cAMP/PKA signal transduction / eating behavior / Regulation of gene expression in beta cells / negative regulation of protein-containing complex assembly ...amylin receptor 3 signaling pathway / amylin receptor 2 signaling pathway / amylin receptor 1 signaling pathway / amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / positive regulation of cAMP/PKA signal transduction / eating behavior / Regulation of gene expression in beta cells / negative regulation of protein-containing complex assembly / positive regulation of calcium-mediated signaling / hormone activity / cell-cell signaling / amyloid-beta binding / G alpha (s) signalling events / positive regulation of MAPK cascade / positive regulation of apoptotic process / receptor ligand activity / Amyloid fiber formation / signaling receptor binding / apoptotic process / neuronal cell body / lipid binding / signal transduction / : / extracellular region / identical protein binding
Similarity search - Function
Islet amyloid polypeptide / Calcitonin-like / Calcitonin peptide-like / Calcitonin, conserved site / Calcitonin / CGRP / IAPP family signature. / calcitonin / Calcitonin/adrenomedullin / Calcitonin / CGRP / IAPP family
Similarity search - Domain/homology
Islet amyloid polypeptide
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLovestam S / Scheres SHW
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM image processing of amyloid filaments in RELION-5.1
Authors: Lovestam S / Shi J / Li DB / Scheres SHW
History
DepositionMar 12, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57189.png

Downloads & links

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Map

FileDownload / File: emd_57189.map.gz / Format: CCP4 / Size: 93 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 290 pix.
= 319. Å		1.1 Å/pix.
x 290 pix.
= 319. Å		1.1 Å/pix.
x 290 pix.
= 319. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00656
Minimum - Maximum-0.02193302 - 0.04858874
Average (Standard dev.)0.00010207926 (±0.002019967)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions290290290
Spacing290290290
CellA=B=C: 319.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_57189_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_57189_half_map_2.map
AnnotationHalf 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 assembly 6 weeks during growth phase

EntireName: Amyloid assembly 6 weeks during growth phase
Components
  • Complex: Amyloid assembly 6 weeks during growth phase
    • Protein or peptide: Islet amyloid polypeptide

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Supramolecule #1: Amyloid assembly 6 weeks during growth phase

SupramoleculeName: Amyloid assembly 6 weeks during growth phase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Islet amyloid polypeptide

MacromoleculeName: Islet amyloid polypeptide / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.083354 KDa
SequenceString:
TQRLANFLVH SGNNFGAILS STNVGSNTY(NH2)

UniProtKB: Islet amyloid polypeptide

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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: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 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: 4.75 Å
Applied symmetry - Helical parameters - Δ&Phi: -2.13 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.1) / Number images used: 7373
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: De novo
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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