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- EMDB-11380: amyloid structure of amylin (IAPP - islet amyloid polypeptide) -

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Basic information

Entry
Database: EMDB / ID: EMD-11380
Titleamyloid structure of amylin (IAPP - islet amyloid polypeptide)
Map datapost-processed-masked map
Sample
  • Complex: amyloid fibril of amylin (islet amyloid polipeptide)
    • Protein or peptide: Islet amyloid polypeptide
Keywordsamyloid fibril type-2-diabetes hormone / PROTEIN FIBRIL
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 / negative regulation of bone resorption / eating behavior / negative regulation of osteoclast differentiation / Regulation of gene expression in beta cells ...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 / negative regulation of bone resorption / eating behavior / negative regulation of osteoclast differentiation / Regulation of gene expression in beta cells / positive regulation of cAMP/PKA signal transduction / bone resorption / negative regulation of protein-containing complex assembly / sensory perception of pain / positive regulation of calcium-mediated signaling / osteoclast differentiation / 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 / neuronal cell body / apoptotic process / lipid binding / signal transduction / extracellular space / 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 speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGallardo RU / Iadanza MG
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust204963 United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Fibril structures of diabetes-related amylin variants reveal a basis for surface-templated assembly.
Authors: Rodrigo Gallardo / Matthew G Iadanza / Yong Xu / George R Heath / Richard Foster / Sheena E Radford / Neil A Ranson /
Abstract: Aggregation of the peptide hormone amylin into amyloid deposits is a pathological hallmark of type-2 diabetes (T2D). While no causal link between T2D and amyloid has been established, the S20G ...Aggregation of the peptide hormone amylin into amyloid deposits is a pathological hallmark of type-2 diabetes (T2D). While no causal link between T2D and amyloid has been established, the S20G mutation in amylin is associated with early-onset T2D. Here we report cryo-EM structures of amyloid fibrils of wild-type human amylin and its S20G variant. The wild-type fibril structure, solved to 3.6-Å resolution, contains two protofilaments, each built from S-shaped subunits. S20G fibrils, by contrast, contain two major polymorphs. Their structures, solved at 3.9-Å and 4.0-Å resolution, respectively, share a common two-protofilament core that is distinct from the wild-type structure. Remarkably, one polymorph contains a third subunit with another, distinct, cross-β conformation. The presence of two different backbone conformations within the same fibril may explain the increased aggregation propensity of S20G, and illustrates a potential structural basis for surface-templated fibril assembly.
History
DepositionJul 13, 2020-
Header (metadata) releaseSep 30, 2020-
Map releaseSep 30, 2020-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
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  • Surface view colored by cylindrical radius
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  • Surface view with fitted model
  • Atomic models: PDB-6zrf
  • Surface level: 0.05
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Structure viewerEM map:
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Supplemental images

emd_11380.png

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Map

FileDownload / File: emd_11380.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpost-processed-masked map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 200 pix.
= 213. Å		1.07 Å/pix.
x 200 pix.
= 213. Å		1.07 Å/pix.
x 200 pix.
= 213. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.07081846 - 0.12453157
Average (Standard dev.)0.00023238864 (±0.0030413785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 213.00002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z213.000213.000213.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0710.1250.000

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Supplemental data

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Mask #1

Fileemd_11380_msk_1.map
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AxesZYX

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Additional map: 3D-auto-refined map

Fileemd_11380_additional_1.map
Annotation3D-auto-refined map
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Additional map: post-processed not-masked map

Fileemd_11380_additional_2.map
Annotationpost-processed not-masked map
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Half map: 3D-auto-refined half1 map

Fileemd_11380_half_map_1.map
Annotation3D-auto-refined half1 map
Projections & Slices
AxesZYX

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Half map: 3D-auto-refined half2 map

Fileemd_11380_half_map_2.map
Annotation3D-auto-refined half2 map
Projections & Slices
AxesZYX

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Sample components

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Entire : amyloid fibril of amylin (islet amyloid polipeptide)

EntireName: amyloid fibril of amylin (islet amyloid polipeptide)
Components
  • Complex: amyloid fibril of amylin (islet amyloid polipeptide)
    • Protein or peptide: Islet amyloid polypeptide

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Supramolecule #1: amyloid fibril of amylin (islet amyloid polipeptide)

SupramoleculeName: amyloid fibril of amylin (islet amyloid polipeptide) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: produced synthetically, oxidised, C-terminally amidated, fibrillated in vitro
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.625 kDa/nm

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Macromolecule #1: Islet amyloid polypeptide

MacromoleculeName: Islet amyloid polypeptide / type: protein_or_peptide / ID: 1 / Details: TYC = C-terminal amidated Tyr / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.908319 KDa
SequenceString:
KCNTATCATQ RLANFLVHSS NNFGAILSST NVGSNT(TYC)

UniProtKB: Islet amyloid polypeptide

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration0.18 mg/mL
BufferpH: 6.8 / Component - Concentration: 20.0 mM / Component - Formula: NH4CH3CO2 / Component - Name: Ammonium acetate
GridModel: Homemade / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 14.0 sec. / Average electron dose: 50.07 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
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: 2.43 Å
Applied symmetry - Helical parameters - Δ&Phi: 178.23 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32846
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE

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