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Yorodumi- EMDB-44406: Cryo-EM structure of the DES-1 collagen-like peptide octadecameri... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44406 | |||||||||
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Title | Cryo-EM structure of the DES-1 collagen-like peptide octadecameric assembly with C6 symmetry | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Collagen / de novo peptide design / STRUCTURAL PROTEIN | |||||||||
Biological species | unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.3 Å | |||||||||
Authors | Kreutzberger MA / Yu LT / Egelman EH / Hartgerink JD | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Exploration of the hierarchical assembly space of collagen-like peptides beyond the triple helix. Authors: Le Tracy Yu / Mark A B Kreutzberger / Thi H Bui / Maria C Hancu / Adam C Farsheed / Edward H Egelman / Jeffrey D Hartgerink / Abstract: The de novo design of self-assembling peptides has garnered significant attention in scientific research. While alpha-helical assemblies have been extensively studied, exploration of polyproline type ...The de novo design of self-assembling peptides has garnered significant attention in scientific research. While alpha-helical assemblies have been extensively studied, exploration of polyproline type II helices, such as those found in collagen, remains relatively limited. In this study, we focus on understanding the sequence-structure relationship in hierarchical assemblies of collagen-like peptides, using defense collagen Surfactant Protein A as a model. By dissecting the sequence derived from Surfactant Protein A and synthesizing short collagen-like peptides, we successfully construct a discrete bundle of hollow triple helices. Amino acid substitution studies pinpoint hydrophobic and charged residues that are critical for oligomer formation. These insights guide the de novo design of collagen-like peptides, resulting in the formation of diverse quaternary structures, including discrete and heterogenous bundled oligomers, two-dimensional nanosheets, and pH-responsive nanoribbons. Our study represents a significant advancement in the understanding and harnessing of collagen higher-order assemblies beyond the triple helix. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_44406.map.gz | 171.5 KB | EMDB map data format | |
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Header (meta data) | emd-44406-v30.xml emd-44406.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_44406_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_44406.png | 69 KB | ||
Masks | emd_44406_msk_1.map | 38.4 MB | Mask map | |
Filedesc metadata | emd-44406.cif.gz | 4 KB | ||
Others | emd_44406_half_map_1.map.gz emd_44406_half_map_2.map.gz | 35.6 MB 35.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44406 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44406 | HTTPS FTP |
-Validation report
Summary document | emd_44406_validation.pdf.gz | 754.2 KB | Display | EMDB validaton report |
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Full document | emd_44406_full_validation.pdf.gz | 753.7 KB | Display | |
Data in XML | emd_44406_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | emd_44406_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44406 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44406 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_44406.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_44406_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_44406_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_44406_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : DES-1 collagen-like peptide assembly
Entire | Name: DES-1 collagen-like peptide assembly |
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Components |
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-Supramolecule #1: DES-1 collagen-like peptide assembly
Supramolecule | Name: DES-1 collagen-like peptide assembly / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: unidentified (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.1 |
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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: 60.0 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: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |