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- EMDB-44405: Low-resolution cryo-EM structure of the DES-1 collagen-like pepti... -

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Basic information

Entry
Database: EMDB / ID: EMD-44405
TitleLow-resolution cryo-EM structure of the DES-1 collagen-like peptide doublet assembly
Map data
Sample
  • Complex: DES-1 collagen-like peptide assembly
KeywordsCollagen / de novo peptide design / STRUCTURAL PROTEIN
Biological speciesunidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.2 Å
AuthorsKreutzberger MA / Yu LT / Egelman EH / Hartgerink JD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE2203937 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: 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
DepositionApr 4, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44405.png

Downloads & links

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Map

FileDownload / File: emd_44405.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 160 pix.
= 214.4 Å		1.34 Å/pix.
x 160 pix.
= 214.4 Å		1.34 Å/pix.
x 160 pix.
= 214.4 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0987
Minimum - Maximum-0.14014079 - 0.55963564
Average (Standard dev.)0.00049325835 (±0.017379524)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 214.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44405_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44405_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DES-1 collagen-like peptide assembly

EntireName: DES-1 collagen-like peptide assembly
Components
  • Complex: DES-1 collagen-like peptide assembly

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Supramolecule #1: DES-1 collagen-like peptide assembly

SupramoleculeName: DES-1 collagen-like peptide assembly / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: unidentified (others)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.1
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35293
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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