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Yorodumi- EMDB-8272: Human Islet Amyloid Polypeptide Segment 19-SGNNFGAILSS-29 with Ea... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8272 | |||||||||
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Title | Human Islet Amyloid Polypeptide Segment 19-SGNNFGAILSS-29 with Early Onset S20G Mutation Determined by MicroED | |||||||||
Map data | Sigma-A-weighted 2Fo-Fc map | |||||||||
Sample |
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Keywords | Amyloid / islet amyloid polypeptide / Type II Diabetes / Toxic Spine / MicroED / PROTEIN FIBRIL | |||||||||
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 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | electron crystallography / cryo EM / Resolution: 1.9 Å | |||||||||
Authors | Krotee PAL / Rodriguez JA | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Elife / Year: 2017 Title: Atomic structures of fibrillar segments of hIAPP suggest tightly mated β-sheets are important for cytotoxicity. Authors: Pascal Krotee / Jose A Rodriguez / Michael R Sawaya / Duilio Cascio / Francis E Reyes / Dan Shi / Johan Hattne / Brent L Nannenga / Marie E Oskarsson / Stephan Philipp / Sarah Griner / Lin ...Authors: Pascal Krotee / Jose A Rodriguez / Michael R Sawaya / Duilio Cascio / Francis E Reyes / Dan Shi / Johan Hattne / Brent L Nannenga / Marie E Oskarsson / Stephan Philipp / Sarah Griner / Lin Jiang / Charles G Glabe / Gunilla T Westermark / Tamir Gonen / David S Eisenberg / Abstract: hIAPP fibrils are associated with Type-II Diabetes, but the link of hIAPP structure to islet cell death remains elusive. Here we observe that hIAPP fibrils are cytotoxic to cultured pancreatic β- ...hIAPP fibrils are associated with Type-II Diabetes, but the link of hIAPP structure to islet cell death remains elusive. Here we observe that hIAPP fibrils are cytotoxic to cultured pancreatic β-cells, leading us to determine the structure and cytotoxicity of protein segments composing the amyloid spine of hIAPP. Using the cryoEM method MicroED, we discover that one segment, 19-29 S20G, forms pairs of β-sheets mated by a dry interface that share structural features with and are similarly cytotoxic to full-length hIAPP fibrils. In contrast, a second segment, 15-25 WT, forms non-toxic labile β-sheets. These segments possess different structures and cytotoxic effects, however, both can seed full-length hIAPP, and cause hIAPP to take on the cytotoxic and structural features of that segment. These results suggest that protein segment structures represent polymorphs of their parent protein and that segment 19-29 S20G may serve as a model for the toxic spine of hIAPP. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8272.map.gz | 130.1 KB | EMDB map data format | |
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Header (meta data) | emd-8272-v30.xml emd-8272.xml | 16.8 KB 16.8 KB | Display Display | EMDB header |
Images | emd_8272.png | 95.3 KB | ||
Filedesc metadata | emd-8272.cif.gz | 5.5 KB | ||
Filedesc structureFactors | emd_8272_sf.cif.gz | 10.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8272 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8272 | HTTPS FTP |
-Validation report
Summary document | emd_8272_validation.pdf.gz | 376.7 KB | Display | EMDB validaton report |
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Full document | emd_8272_full_validation.pdf.gz | 376.2 KB | Display | |
Data in XML | emd_8272_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | emd_8272_validation.cif.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8272 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8272 | HTTPS FTP |
-Related structure data
Related structure data | 5knzMC 8273C 5ko0C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8272.map.gz / Format: CCP4 / Size: 291 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sigma-A-weighted 2Fo-Fc map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.3983 Å / Y: 0.5813 Å / Z: 0.6321 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Amyloid fiber
Entire | Name: Amyloid fiber |
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Components |
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-Supramolecule #1: Amyloid fiber
Supramolecule | Name: Amyloid fiber / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Molecular weight | Theoretical: 4.441 kDa/nm |
-Macromolecule #1: hIAPP(residues 19-29)S20G
Macromolecule | Name: hIAPP(residues 19-29)S20G / type: protein_or_peptide / ID: 1 / Details: islet amyloid / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 1.066125 KDa |
Sequence | String: SGNNFGAILS S UniProtKB: Islet amyloid polypeptide |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 1 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron crystallography |
Aggregation state | 3D array |
-Sample preparation
Concentration | 1.066 mg/mL | ||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 30 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR | ||||||
Vitrification | Cryogen name: ETHANE | ||||||
Crystal formation | Instrument: 1.5 mL Eppendorf tube / Atmosphere: Air, sealed chamber. / Temperature: 298.0 K / Time: 2.0 DAY Details: 1 mM lyophilized peptide in PBS with 1% DMSO at room temperature under quiescent conditions. Crystals grew in a few hours and reached full size within 15 hours. |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Temperature | Min: 100.0 K / Max: 100.0 K |
Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number diffraction images: 879 / Average exposure time: 2.0 sec. / Average electron dose: 0.01 e/Å2 Details: The detector was operated in rolling shutter mode with 2x2 pixel binning. |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 1840 mm |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES | ||||||||||||||||||||||||||||||||||||||||||
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Startup model | Type of model: INSILICO MODEL / Details: idealized 7-residue polyalanine beta-strand | ||||||||||||||||||||||||||||||||||||||||||
Molecular replacement | Software - Name: Phaser (ver. 2.5.6) | ||||||||||||||||||||||||||||||||||||||||||
Crystallography statistics | Number intensities measured: 1380 / Number structure factors: 548 / Fourier space coverage: 83 / R sym: 0.106 / R merge: 0.106 / Overall phase error: 0.01 / Overall phase residual: 0.01 / Phase error rejection criteria: 0 / High resolution: 1.9 Å Details: Phasing statistics are not applicable. No imaging was used. The phases were obtained using molecular replacement. Shell:
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-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: OTHER / Overall B value: 14.512 / Target criteria: maximum likelihood |
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Output model | PDB-5knz: |