+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26800 | |||||||||||||||
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Title | Cryo-EM of self-assembling pyrene IDP | |||||||||||||||
Map data | Cryo-EM of self-assembling pyrene-containing peptide fibril | |||||||||||||||
Sample |
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Keywords | peptides / nanofibers / self-assembly peptide filament / PROTEIN FIBRIL | |||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
Authors | Wang F / Guo J / Xu B / Egelman EH | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Chem / Year: 2023 Title: Hierarchical Assembly of Intrinsically Disordered Short Peptides. Authors: Jiaqi Guo / Shane T Rich-New / Chen Liu / Yimeng Huang / Weiyi Tan / Hongjian He / Meihui Yi / Xixiang Zhang / Edward H Egelman / Fengbin Wang / Bing Xu / Abstract: The understanding on how short peptide assemblies transit from disorder to order remains limited due to the lack of atomistic structures. Here we report cryo-EM structure of the nanofibers short ...The understanding on how short peptide assemblies transit from disorder to order remains limited due to the lack of atomistic structures. Here we report cryo-EM structure of the nanofibers short intrinsically disordered peptides (IDPs). Upon lowering pH or adding calcium ions, the IDP transitions from individual nanoparticles to nanofibers containing an aromatic core and a disordered periphery comprised of 2 to 5 amino acids. Protonating the phosphate or adding more metal ions further assembles the nanofibers into filament bundles. The assemblies of the IDP analogs with controlled chemistry, such as phosphorylation site, hydrophobic interactions, and sequences indicate that metal ions interact with the flexible periphery of the nanoparticles of the IDPs to form fibrils and enhance the interfibrillar interactions to form filament bundles. Illustrating that an IDP self-assembles from disorder to order, this work offers atomistic molecular insights to understand assemblies of short peptides driven by noncovalent interactions. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26800.map.gz | 3.4 MB | EMDB map data format | |
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Header (meta data) | emd-26800-v30.xml emd-26800.xml | 13.8 KB 13.8 KB | Display Display | EMDB header |
Images | emd_26800.png | 47.7 KB | ||
Filedesc metadata | emd-26800.cif.gz | 4.4 KB | ||
Others | emd_26800_half_map_1.map.gz emd_26800_half_map_2.map.gz | 116.2 MB 116.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26800 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26800 | HTTPS FTP |
-Validation report
Summary document | emd_26800_validation.pdf.gz | 746.7 KB | Display | EMDB validaton report |
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Full document | emd_26800_full_validation.pdf.gz | 746.3 KB | Display | |
Data in XML | emd_26800_validation.xml.gz | 14 KB | Display | |
Data in CIF | emd_26800_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26800 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26800 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_26800.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM of self-assembling pyrene-containing peptide fibril | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half A
File | emd_26800_half_map_1.map | ||||||||||||
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Annotation | half A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half B
File | emd_26800_half_map_2.map | ||||||||||||
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Annotation | half B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Pyrene IDR
Entire | Name: Pyrene IDR |
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Components |
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-Supramolecule #1: Pyrene IDR
Supramolecule | Name: Pyrene IDR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: synthetic construct (others) / Synthetically produced: Yes |
-Macromolecule #1: Pyrene-containing peptide fibril
Macromolecule | Name: Pyrene-containing peptide fibril / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 1.060007 KDa |
Sequence | String: (OG9)YSPTSP(SEP) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 4.74 Å Applied symmetry - Helical parameters - Δ&Phi: -5.38 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 461253 |
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Startup model | Type of model: NONE |
Final angle assignment | Type: NOT APPLICABLE |