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- EMDB-28960: Cryo-electron microscopy structure of the octadecameric collagen-... -

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Basic information

Entry
Database: EMDB / ID: EMD-28960
TitleCryo-electron microscopy structure of the octadecameric collagen-like (ABC-Ala)6 peptide triple helical assembly
Map data
Sample
  • Complex: Collagen-like (ABC-Ala)6 octadecameric assembly
Biological speciesunidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsKreutzberger MA / Yu LT / Hancu MC / Egelman EH / Hartgerink JD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2203937 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: J Am Chem Soc / Year: 2023
Title: Hollow Octadecameric Self-Assembly of Collagen-like Peptides.
Authors: Le Tracy Yu / Maria C Hancu / Mark A B Kreutzberger / Amy Henrickson / Borries Demeler / Edward H Egelman / Jeffrey D Hartgerink /
Abstract: The folding of collagen is a hierarchical process that starts with three peptides associating into the characteristic triple helical fold. Depending on the specific collagen in question, these triple ...The folding of collagen is a hierarchical process that starts with three peptides associating into the characteristic triple helical fold. Depending on the specific collagen in question, these triple helices then assemble into bundles reminiscent of α-helical coiled-coils. Unlike α-helices, however, the bundling of collagen triple helices is very poorly understood with almost no direct experimental data available. In order to shed light on this critical step of collagen hierarchical assembly, we have examined the collagenous region of complement component 1q. Thirteen synthetic peptides were prepared to dissect the critical regions allowing for its octadecameric self-assembly. We find that short peptides (under 40 amino acids) are able to self-assemble into specific (ABC) octadecamers. This requires the ABC heterotrimeric composition as the self-assembly subunit, but does not require disulfide bonds. Self-assembly into this octadecamer is aided by short noncollagenous sequences at the N-terminus, although they are not entirely required. The mechanism of self-assembly appears to begin with the very slow formation of the ABC heterotrimeric helix, followed by rapid bundling of triple helices into progressively larger oligomers, terminating in the formation of the (ABC) octadecamer. Cryo-electron microscopy reveals the (ABC) assembly as a remarkable, hollow, crown-like structure with an open channel approximately 18 Å at the narrow end and 30 Å at the wide end. This work helps to illuminate the structure and assembly mechanism of a critical protein in the innate immune system and lays the groundwork for the design of higher order collagen mimetic peptide assemblies.
History
DepositionNov 28, 2022-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateMar 22, 2023-
Current statusMar 22, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28960.png

Downloads & links

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Map

FileDownload / File: emd_28960.map.gz / Format: CCP4 / Size: 9.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 136 pix.
= 111.52 Å		0.82 Å/pix.
x 136 pix.
= 111.52 Å		0.82 Å/pix.
x 136 pix.
= 111.52 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.469
Minimum - Maximum-0.6222735 - 1.7467179
Average (Standard dev.)0.0001108093 (±0.047906123)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions136136136
Spacing136136136
CellA=B=C: 111.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_28960_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_28960_half_map_2.map
Projections & Slices
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Sample components

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Entire : Collagen-like (ABC-Ala)6 octadecameric assembly

EntireName: Collagen-like (ABC-Ala)6 octadecameric assembly
Components
  • Complex: Collagen-like (ABC-Ala)6 octadecameric assembly

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Supramolecule #1: Collagen-like (ABC-Ala)6 octadecameric assembly

SupramoleculeName: Collagen-like (ABC-Ala)6 octadecameric assembly / type: complex / ID: 1 / Chimera: Yes / Parent: 0
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 71.4 KDa

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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: 7.2
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: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: OTHER
Details: The 0.143 Map:Map FSC is estimated at 3 Angstrom, but inspection yields a resolution of 5 Angstrom, which is approximately the lowest resolution at which the triple helix is resolvable.
Number images used: 108000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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