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- EMDB-10671: Amyloid fibril structure of islet amyloid polypeptide - polymorph 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-10671
TitleAmyloid fibril structure of islet amyloid polypeptide - polymorph 3
Map data
Sample
  • Complex: Amyloid fibril of the islet amyloid polypeptide (IAPP)
    • Protein or peptide: islet amyloid polypeptide
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 8.1 Å
AuthorsRoeder C / Kupreichyk T / Gremer L / Schaefer LU / Pothula KR / Ravelli RBG / Willbold D / Schroder GF
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)726368European Union
Citation
Journal: Nat Struct Mol Biol / Year: 2020
Title: Cryo-EM structure of islet amyloid polypeptide fibrils reveals similarities with amyloid-β fibrils.
Authors: Christine Röder / Tatsiana Kupreichyk / Lothar Gremer / Luisa U Schäfer / Karunakar R Pothula / Raimond B G Ravelli / Dieter Willbold / Wolfgang Hoyer / Gunnar F Schröder /
Abstract: Amyloid deposits consisting of fibrillar islet amyloid polypeptide (IAPP) in pancreatic islets are associated with beta-cell loss and have been implicated in type 2 diabetes (T2D). Here, we applied ...Amyloid deposits consisting of fibrillar islet amyloid polypeptide (IAPP) in pancreatic islets are associated with beta-cell loss and have been implicated in type 2 diabetes (T2D). Here, we applied cryo-EM to reconstruct densities of three dominant IAPP fibril polymorphs, formed in vitro from synthetic human IAPP. An atomic model of the main polymorph, built from a density map of 4.2-Å resolution, reveals two S-shaped, intertwined protofilaments. The segment 21-NNFGAIL-27, essential for IAPP amyloidogenicity, forms the protofilament interface together with Tyr37 and the amidated C terminus. The S-fold resembles polymorphs of Alzheimer's disease (AD)-associated amyloid-β (Aβ) fibrils, which might account for the epidemiological link between T2D and AD and reports on IAPP-Aβ cross-seeding in vivo. The results structurally link the early-onset T2D IAPP genetic polymorphism (encoding Ser20Gly) with the AD Arctic mutation (Glu22Gly) of Aβ and support the design of inhibitors and imaging probes for IAPP fibrils.
#1: Journal: Biorxiv / Year: 2020
Title: Amyloid fibril structure of islet amyloid polypeptide by cryo-electron microscopy reveals similarities with amyloid beta
Authors: Roeder C / Kupreichyk T / Gremer L / Schaefer LU / Pothula KR / Ravelli RBG / Willbold D / Hoyer W / Schroder GF
History
DepositionFeb 11, 2020-
Header (metadata) releaseMar 4, 2020-
Map releaseMar 4, 2020-
UpdateJul 22, 2020-
Current statusJul 22, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10671.png

Downloads & links

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Map

FileDownload / File: emd_10671.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 220 pix.
= 205.7 Å		0.94 Å/pix.
x 220 pix.
= 205.7 Å		0.94 Å/pix.
x 220 pix.
= 205.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.935 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.008407407 - 0.017573582
Average (Standard dev.)0.0011355984 (±0.0030118295)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 205.7 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9350.9350.935
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z205.700205.700205.700
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0080.0180.001

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Supplemental data

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Half map: half map 1

Fileemd_10671_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_10671_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 fibril of the islet amyloid polypeptide (IAPP)

EntireName: Amyloid fibril of the islet amyloid polypeptide (IAPP)
Components
  • Complex: Amyloid fibril of the islet amyloid polypeptide (IAPP)
    • Protein or peptide: islet amyloid polypeptide

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Supramolecule #1: Amyloid fibril of the islet amyloid polypeptide (IAPP)

SupramoleculeName: Amyloid fibril of the islet amyloid polypeptide (IAPP)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: The fibril consists of IAPP monomers.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.6 kDa/nm

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Macromolecule #1: islet amyloid polypeptide

MacromoleculeName: islet amyloid polypeptide / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
KCNTATCATQ RLANFLVHSS NNFGAILSST NVGSNTY

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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
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Specialist opticsPhase plate: OTHER
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1330 / Average exposure time: 46.0 sec. / Average electron dose: 41.4 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.323 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.47 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 8.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.5) / Number images used: 4591
Startup modelType of model: OTHER / Details: noise filled cylinder
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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