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- EMDB-45372: Cryo-EM structure of the human C1q collagenous stem -

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Basic information

Entry
Database: EMDB / ID: EMD-45372
TitleCryo-EM structure of the human C1q collagenous stem
Map data
Sample
  • Complex: The C1q A, B-crt, C peptide assembly
KeywordsC1q / complement / collagen / triple helix / cryo-EM / IMMUNE SYSTEM
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsKreutzberger MA / Yu LT / Egelman EH / Hartgerink JD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
National Science Foundation (NSF, United States)CHE 2203937 United States
CitationJournal: ACS Cent Sci / Year: 2025
Title: A Collagen Triple Helix without the Superhelical Twist.
Authors: Mark A B Kreutzberger / Le Tracy Yu / Thi H Bui / Maria C Hancu / Michael D Purdy / Tomasz Osinski / Peter M Kasson / Edward H Egelman / Jeffrey D Hartgerink /
Abstract: Collagens are ubiquitous in biology: functioning as the backbone of the extracellular matrix, forming the primary structural components of key immune system complexes, and fulfilling numerous other ...Collagens are ubiquitous in biology: functioning as the backbone of the extracellular matrix, forming the primary structural components of key immune system complexes, and fulfilling numerous other structural roles in a variety of systems. Despite this, there is limited understanding of how triple helices, the basic collagen structural units, pack into collagenous assemblies. Here we use a peptide self-assembly system to design collagenous assemblies based on the C1q collagen-like region. Using cryo-EM we solved a structure of one assembly to 3.5 Å resolution and built an atomic model. From this, we identify a triple helix conformation with no superhelical twist, starkly in contrast to the canonical right-handed triple helix. This nontwisting region allows for unique hydroxyproline stacking between adjacent triple helices and also results in the formation of an exposed cavity with rings of hydrophobic amino acids packed symmetrically. We find no precedent for such an arrangement of collagen triple helices and designed assemblies with substituted amino acids in various locations to probe key stabilizing amino acid interactions in the complex. The stability of these altered complexes behaves as predicted by our atomic model. Our findings, combined with the extremely limited experimental structural data on triple helix packing in the literature, suggest that collagen and collagen-like assemblies may adopt a far more varied conformational landscape than previously appreciated. We hypothesize that this is particularly likely in packed assemblies of triple helices, adjacent to the termini of these helices and at discontinuities in the required Xaa-Yaa-Gly repeating primary sequence, a discontinuity found in the majority of this class of proteins and in many collagen-associated diseases.
History
DepositionJun 15, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45372.png

Downloads & links

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Map

FileDownload / File: emd_45372.map.gz / Format: CCP4 / Size: 38.4 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.)
1.34 Å/pix.
x 216 pix.
= 289.44 Å		1.34 Å/pix.
x 216 pix.
= 289.44 Å		1.34 Å/pix.
x 216 pix.
= 289.44 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.34
Minimum - Maximum-0.61697096 - 1.6795428
Average (Standard dev.)0.00076030666 (±0.021405805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 289.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45372_msk_1.map
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Half map: #1

Fileemd_45372_half_map_1.map
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Half map: #2

Fileemd_45372_half_map_2.map
Projections & Slices
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Sample components

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Entire : The C1q A, B-crt, C peptide assembly

EntireName: The C1q A, B-crt, C peptide assembly
Components
  • Complex: The C1q A, B-crt, C peptide assembly

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Supramolecule #1: The C1q A, B-crt, C peptide assembly

SupramoleculeName: The C1q A, B-crt, C peptide assembly / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: synthetic construct (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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: 3.0 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: 4.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 79400
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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