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- EMDB-18672: Cryo-EM structure of human islet amyloid polypeptide (hIAPP) muta... -

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Basic information

Entry
Database: EMDB / ID: EMD-18672
TitleCryo-EM structure of human islet amyloid polypeptide (hIAPP) mutant S29P, polymorph 2
Map data
Sample
  • Cell: Human islet amyloid polypeptide (hIAPP)
    • Protein or peptide: Islet amyloid polypeptide
Keywordsamyloid / 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 / osteoclast differentiation / 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 / 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 speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.07 Å
AuthorsOoi SA / Valli D / Maj M
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Swedish Research CouncilVR 2020-05403 Sweden
Other privateSwedish Society for Medical Research (S20-0156)
CitationJournal: To Be Published
Title: Cryo-EM structure of human islet amyloid polypeptide (hIAPP) mutant S29P, polymorph 2
Authors: Ooi SA / Valli D / Maj M
History
DepositionOct 18, 2023-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18672.png

Downloads & links

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Map

FileDownload / File: emd_18672.map.gz / Format: CCP4 / Size: 24.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 51 pix.
= 41.871 Å		0.82 Å/pix.
x 352 pix.
= 288.992 Å		0.82 Å/pix.
x 352 pix.
= 288.992 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.821 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.02327034 - 0.04259971
Average (Standard dev.)0.00016645151 (±0.001606579)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00200
Dimensions35235251
Spacing35235251
CellA: 288.992 Å / B: 288.992 Å / C: 41.871002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_18672_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_18672_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 : Human islet amyloid polypeptide (hIAPP)

EntireName: Human islet amyloid polypeptide (hIAPP)
Components
  • Cell: Human islet amyloid polypeptide (hIAPP)
    • Protein or peptide: Islet amyloid polypeptide

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Supramolecule #1: Human islet amyloid polypeptide (hIAPP)

SupramoleculeName: Human islet amyloid polypeptide (hIAPP) / type: cell / 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: 3.917349 KDa
SequenceString:
KCNTATCATQ RLANFLVHSS NNFGAILSPT NVGSNTY(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

Concentration0.4 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.76 Å
Applied symmetry - Helical parameters - Δ&Phi: -3.61 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.0) / Number images used: 4442
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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