+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42434 | |||||||||
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Title | Cryo-EM of (L, L)-2NapFF micelle | |||||||||
Map data | ||||||||||
Sample |
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Keywords | dipeptides / micelle / stereoisomers / PROTEIN FIBRIL | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Sonani RR / Adams DJ / Egelman EH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell Rep Phys Sci / Year: 2024 Title: Atomic structures of naphthalene dipeptide micelles unravel mechanisms of assembly and gelation. Authors: Ravi R Sonani / Simona Bianco / Bart Dietrich / James Doutch / Emily R Draper / Dave J Adams / Edward H Egelman / Abstract: Peptide-based biopolymers have gained increasing attention due to their versatile applications. A naphthalene dipeptide (2NapFF) can form chirality-dependent tubular micelles, leading to ...Peptide-based biopolymers have gained increasing attention due to their versatile applications. A naphthalene dipeptide (2NapFF) can form chirality-dependent tubular micelles, leading to supramolecular gels. The precise molecular arrangement within these micelles and the mechanism governing gelation have remained enigmatic. We determined, at near-atomic resolution, cryoelectron microscopy structures of the 2NapFF micelles LL-tube and LD-tube, generated by the stereoisomers (l,l)-2NapFF and (l,d)-2NapFF, respectively. The structures reveal that the fundamental packing of dipeptides is driven by the systematic π-π stacking of aromatic rings and that same-charge repulsion between the carbonyl groups is responsible for the stiffness of both tubes. The structural analysis elucidates how a single residue's altered chirality gives rise to markedly distinct tubular structures and sheds light on the mechanisms underlying the pH-dependent gelation of LL- and LD-tubes. The understanding of dipeptide packing and gelation mechanisms provides insights for the rational design of 2NapFF derivatives, enabling the modulation of micellar dimensions. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42434.map.gz | 32.9 MB | EMDB map data format | |
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Header (meta data) | emd-42434-v30.xml emd-42434.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42434_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_42434.png | 45.4 KB | ||
Filedesc metadata | emd-42434.cif.gz | 4 KB | ||
Others | emd_42434_half_map_1.map.gz emd_42434_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42434 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42434 | HTTPS FTP |
-Validation report
Summary document | emd_42434_validation.pdf.gz | 1020.8 KB | Display | EMDB validaton report |
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Full document | emd_42434_full_validation.pdf.gz | 1020.4 KB | Display | |
Data in XML | emd_42434_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_42434_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42434 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42434 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_42434.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.67 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_42434_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_42434_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : (L, L)-2NapFF micelle
Entire | Name: (L, L)-2NapFF micelle |
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Components |
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-Supramolecule #1: (L, L)-2NapFF micelle
Supramolecule | Name: (L, L)-2NapFF micelle / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: synthetic construct (others) / Synthetically produced: Yes |
-Macromolecule #1: (L, L)-2NapFF dipeptide
Macromolecule | Name: (L, L)-2NapFF dipeptide / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Sequence | String: (NwF)F |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 11 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS 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: 2.2 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |