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- EMDB-45363: Cryo-EM structure of the C1q A, B-crt, C peptide assembly narrow ... -

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Basic information

Entry
Database: EMDB / ID: EMD-45363
TitleCryo-EM structure of the C1q A, B-crt, C peptide assembly narrow region
Map dataThis is the primary map that should be view for interpretation of our atomic modeling results. Achieved after filtering, masking out the uninterpretable density and then sharpening with EM ready.
Sample
  • Complex: Narrow region structure of the octadecameric C1q A, B-crt, C peptide assembly
    • Protein or peptide: Peptide from Complement C1q subcomponent subunit B
    • Protein or peptide: Peptide from Complement C1q subcomponent subunit A
    • Protein or peptide: Peptide from Complement C1q subcomponent subunit C
KeywordsC1q / complement / collagen / triple helix / IMMUNE SYSTEM
Function / homology
Function and homology information


complement component C1 complex / complement component C1q complex / extrinsic component of postsynaptic membrane / negative regulation of macrophage differentiation / synapse pruning / extrinsic component of presynaptic membrane / negative regulation of granulocyte differentiation / vertebrate eye-specific patterning / complement-mediated synapse pruning / collagen trimer ...complement component C1 complex / complement component C1q complex / extrinsic component of postsynaptic membrane / negative regulation of macrophage differentiation / synapse pruning / extrinsic component of presynaptic membrane / negative regulation of granulocyte differentiation / vertebrate eye-specific patterning / complement-mediated synapse pruning / collagen trimer / complement activation / Classical antibody-mediated complement activation / Initial triggering of complement / neuron remodeling / complement activation, classical pathway / Regulation of Complement cascade / astrocyte activation / microglial cell activation / synapse organization / cell-cell signaling / amyloid-beta binding / : / blood microparticle / postsynapse / immune response / innate immune response / synapse / glutamatergic synapse / extracellular space / extracellular region
Similarity search - Function
: / C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies)
Similarity search - Domain/homology
Complement C1q subcomponent subunit A / Complement C1q subcomponent subunit B / Complement C1q subcomponent subunit C
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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 14, 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_45363.png

Downloads & links

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Map

FileDownload / File: emd_45363.map.gz / Format: CCP4 / Size: 92.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the primary map that should be view for interpretation of our atomic modeling results. Achieved after filtering, masking out the uninterpretable density and then sharpening with EM ready.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 289 pix.
= 289. Å		1 Å/pix.
x 289 pix.
= 289. Å		1 Å/pix.
x 289 pix.
= 289. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.4
Minimum - Maximum-0.20163742 - 13.552288000000001
Average (Standard dev.)0.003928212 (±0.17507961)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions289289289
Spacing289289289
CellA=B=C: 289.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45363_msk_1.map
Projections & Slices
AxesZYX

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Additional map: This is the map prior to sharpening by...

Fileemd_45363_additional_1.map
AnnotationThis is the map prior to sharpening by EMReady. Achieved by low pass filtering the initial map and then cutting out the density with a mask generated from preliminary model.
Projections & Slices
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Additional map: This is the initial sharpened map from cryoSPARC

Fileemd_45363_additional_2.map
AnnotationThis is the initial sharpened map from cryoSPARC
Projections & Slices
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Half map: This is the half map A from cryoSPARC

Fileemd_45363_half_map_1.map
AnnotationThis is the half map A from cryoSPARC
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Histogram

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Half map: This is half map B from cryoSPARC

Fileemd_45363_half_map_2.map
AnnotationThis is half map B from cryoSPARC
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Sample components

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Entire : Narrow region structure of the octadecameric C1q A, B-crt, C pept...

EntireName: Narrow region structure of the octadecameric C1q A, B-crt, C peptide assembly
Components
  • Complex: Narrow region structure of the octadecameric C1q A, B-crt, C peptide assembly
    • Protein or peptide: Peptide from Complement C1q subcomponent subunit B
    • Protein or peptide: Peptide from Complement C1q subcomponent subunit A
    • Protein or peptide: Peptide from Complement C1q subcomponent subunit C

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Supramolecule #1: Narrow region structure of the octadecameric C1q A, B-crt, C pept...

SupramoleculeName: Narrow region structure of the octadecameric C1q A, B-crt, C peptide assembly
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human) / Synthetically produced: Yes
Molecular weightTheoretical: 70 kDa/nm

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Macromolecule #1: Peptide from Complement C1q subcomponent subunit B

MacromoleculeName: Peptide from Complement C1q subcomponent subunit B / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.2504 KDa
SequenceString:
P(HYP)AI(HYP)GI(HYP)GI (HYP)GT

UniProtKB: Complement C1q subcomponent subunit B

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Macromolecule #2: Peptide from Complement C1q subcomponent subunit A

MacromoleculeName: Peptide from Complement C1q subcomponent subunit A / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.258363 KDa
SequenceString:
APDGKKGEAG R(HYP)G

UniProtKB: Complement C1q subcomponent subunit A

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Macromolecule #3: Peptide from Complement C1q subcomponent subunit C

MacromoleculeName: Peptide from Complement C1q subcomponent subunit C / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.313502 KDa
SequenceString:
GI(HYP)GM(HYP)GL(HYP)G A(HYP)GK

UniProtKB: Complement C1q subcomponent subunit C

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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 / Details: 20 mM PBS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K

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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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 374558
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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