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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: To Be Published
Title: Supramolecular Assembly of Collagen Mimetic Peptide D-periodic Fibrils and Nanoassemblies
Authors: Cole CC / Kreutzberger MAB / Klein K / Cahue K / Pogostin BH / Farsheed AC / Swain JWR / Bui TH / Dey A / Makhoul J / Dubackic M / Pal A / Olsson U / Saric A / Egelman EH / Hartgerink JD
History
DepositionJan 26, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
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
FSC plot (resolution estimation)

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