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- EMDB-48818: Low resolution cryo-EM reconstruction of the DY2 collagen mimetic... -

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Basic information

Entry
Database: EMDB / ID: EMD-48818
TitleLow resolution cryo-EM reconstruction of the DY2 collagen mimetic fibrils
Map dataLow resolution cryo-EM reconstruction of the DY2 collagen mimetic fibrils
Sample
  • Complex: Collagen peptide assembly
KeywordsCollagen peptide / STRUCTURAL PROTEIN
Biological speciesunidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsKreutzberger MAB / Cole CC / Egelman EH / Hartgerink JD
Funding support United States, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 2203937 United States
Welch FoundationC-2141 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Biomacromolecules / Year: 2026
Title: Supramolecular Assembly of Collagen-Mimetic Peptide D-Periodic Fibrils and Nanoassemblies.
Authors: Carson C Cole / Mark A B Kreutzberger / Kevin Klein / Kiana A Cahue / Brett H Pogostin / Adam C Farsheed / Joseph W R Swain / Thi H Bui / Arghadip Dey / Jonathan T Makhoul / Marija Dubackic ...Authors: Carson C Cole / Mark A B Kreutzberger / Kevin Klein / Kiana A Cahue / Brett H Pogostin / Adam C Farsheed / Joseph W R Swain / Thi H Bui / Arghadip Dey / Jonathan T Makhoul / Marija Dubackic / Antara Pal / Ulf Olsson / Anđela Šarić / Edward H Egelman / Jeffrey D Hartgerink /
Abstract: The collagen triple helix assembles hierarchically into bundled oligomers, solvated networks, and fibers. Synthetic peptide assemblies, driven by supramolecular interactions, can form single triple ...The collagen triple helix assembles hierarchically into bundled oligomers, solvated networks, and fibers. Synthetic peptide assemblies, driven by supramolecular interactions, can form single triple helices through intrahelical amino acid pairs; however, the principles guiding interhelical associations into higher-order structures remain unclear. Here, we incorporate cation-π and electrostatic charge pairs to probe interhelical interactions and elucidate the mechanisms driving triple helix assembly into fibrils, nanotubes, and nanosheets. Introducing cation-π pairs into a fibrillating collagen mimetic resulted in D-periodic fibrils with pH-sensitive gelation. By alternating the presentation of electrostatic and cation-π pairs, the assembly of another D-periodic fibril featuring inner and outer triple-helical layers was resolved by cryo electron microscopy to a resolution of 8 Å. At physiological pH, antiparallel association of these triple helices leads to the formation of nanotubes. The packing behavior of triple helices correlates with the interhelical interactions, where parallel associations favor fibril formation and antiparallel interactions drive nanotube and nanosheet assembly. These self-assembling triple-helical peptides demonstrate how packing of higher-order structures can be tailored with supramolecular interactions and establish the relationship of different hierarchical collagen-mimetic assemblies as pH-dependent.
History
DepositionJan 26, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48818.png

Downloads & links

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Map

FileDownload / File: emd_48818.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLow resolution cryo-EM reconstruction of the DY2 collagen mimetic fibrils
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.0738
Minimum - Maximum-0.11894701 - 0.20435278
Average (Standard dev.)0.00058327755 (±0.012768837)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48818_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_48818_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_48818_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Collagen peptide assembly

EntireName: Collagen peptide assembly
Components
  • Complex: Collagen peptide assembly

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Supramolecule #1: Collagen peptide assembly

SupramoleculeName: Collagen peptide assembly / type: complex / ID: 1 / Parent: 0 / Details: Collagen peptide assembly
Source (natural)Organism: unidentified (others)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 4.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: OTHER / Details: Low pass filter to 8 angstroms / Number images used: 40233
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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