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- EMDB-33903: Structure of hIAPP-TF-type3 -

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Basic information

Entry
Database: EMDB / ID: EMD-33903
TitleStructure of hIAPP-TF-type3
Map datahIAPP-WF-type3
Sample
  • Organelle or cellular component: no
    • Protein or peptide: Islet amyloid polypeptideAmylin
Function / homology
Function and homology information


: / 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 / positive regulation of protein kinase A signaling / Regulation of gene expression in beta cells / negative regulation of protein-containing complex assembly ...: / 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 / positive regulation of protein kinase A signaling / Regulation of gene expression in beta cells / negative regulation of protein-containing complex assembly / positive regulation of cAMP-mediated signaling / positive regulation of calcium-mediated signaling / bone resorption / sensory perception of pain / osteoclast differentiation / hormone activity / cell-cell signaling / amyloid-beta binding / G alpha (s) signalling events / positive regulation of MAPK cascade / receptor ligand activity / positive regulation of apoptotic process / Amyloid fiber formation / signaling receptor binding / lipid binding / apoptotic process / 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 / Resolution: 3.3 Å
AuthorsLi D / Zhang X
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2017YFA0504700 China
National Natural Science Foundation of China (NSFC)2018YFE0203300 China
National Natural Science Foundation of China (NSFC)2021YFA1300100 China
CitationJournal: Iscience / Year: 2022
Title: A new polymorphism of human amylin fibrils with similar protofilaments and a conserved core
Authors: Li D / Zhang X / Wang Y / Zhang H / Song K / Bao K / Zhu P
History
DepositionJul 25, 2022-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateDec 28, 2022-
Current statusDec 28, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33903.png

Downloads & links

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Map

FileDownload / File: emd_33903.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationhIAPP-WF-type3
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.029765634 - 0.105826475
Average (Standard dev.)0.0002068732 (±0.0022994797)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 274.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33903_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33903_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 : no

EntireName: no
Components
  • Organelle or cellular component: no
    • Protein or peptide: Islet amyloid polypeptideAmylin

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Supramolecule #1: no

SupramoleculeName: no / type: organelle_or_cellular_component / 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: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.908319 KDa
SequenceString:
KCNTATCATQ RLANFLVHSS NNFGAILSST NVGSNT(TYC)

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Experimental details

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Structure determination

Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.8 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Helical parameters - Δz: 2.35 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.41 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 29587
FSC plot (resolution estimation)

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