+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40061 | |||||||||||||||
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Title | Cryo-EM of self-assembling pyrene peptide with Ca2+ | |||||||||||||||
Map data | Cryo-EM of self-assembling pyrene peptide with Ca2 | |||||||||||||||
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: 3.0 Å | |||||||||||||||
Authors | Rich-New ST / Guo J / Xu B / Wang F | |||||||||||||||
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_40061.map.gz | 27.8 MB | EMDB map data format | |
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Header (meta data) | emd-40061-v30.xml emd-40061.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
Images | emd_40061.png | 69.5 KB | ||
Filedesc metadata | emd-40061.cif.gz | 4.5 KB | ||
Others | emd_40061_half_map_1.map.gz emd_40061_half_map_2.map.gz | 115.7 MB 115.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40061 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40061 | HTTPS FTP |
-Validation report
Summary document | emd_40061_validation.pdf.gz | 676.4 KB | Display | EMDB validaton report |
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Full document | emd_40061_full_validation.pdf.gz | 676 KB | Display | |
Data in XML | emd_40061_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | emd_40061_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40061 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40061 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40061.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 peptide with Ca2 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.11 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_40061_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_40061_half_map_2.map | ||||||||||||
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Annotation | Half B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Pyrene peptide with Ca2+
Entire | Name: Pyrene peptide with Ca2+ |
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Components |
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-Supramolecule #1: Pyrene peptide with Ca2+
Supramolecule | Name: Pyrene peptide with Ca2+ / 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 peptide
Macromolecule | Name: Pyrene peptide / type: protein_or_peptide / ID: 1 / Number of copies: 4 / 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: 7.4 |
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Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
-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: 2.0 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: 4.95 Å Applied symmetry - Helical parameters - Δ&Phi: -3.8 ° Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic) Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1380792 |
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Startup model | Type of model: NONE |
Final angle assignment | Type: NOT APPLICABLE |