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- PDB-9c9u: Cryo-EM structure of the C1q A, B-crt, C peptide full assembly -

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Basic information

Entry
Database: PDB / ID: 9c9u
TitleCryo-EM structure of the C1q A, B-crt, C peptide full assembly
Components
  • Complement C1q subcomponent subunit A
  • Complement C1q subcomponent subunit B
  • Complement C1q subcomponent subunit C
KeywordsIMMUNE SYSTEM / C1q / complement / collagen / triple helix / cryo-EM
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsKreutzberger, M.A. / Yu, L.T. / Egelman, E.H. / Hartgerink, J.D.
Funding support United States, 2items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
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Revision 1.1Mar 19, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2May 28, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C1q subcomponent subunit B
B: Complement C1q subcomponent subunit A
C: Complement C1q subcomponent subunit C
D: Complement C1q subcomponent subunit B
I: Complement C1q subcomponent subunit A
N: Complement C1q subcomponent subunit C
E: Complement C1q subcomponent subunit B
J: Complement C1q subcomponent subunit A
O: Complement C1q subcomponent subunit C
F: Complement C1q subcomponent subunit B
K: Complement C1q subcomponent subunit A
P: Complement C1q subcomponent subunit C
G: Complement C1q subcomponent subunit B
L: Complement C1q subcomponent subunit A
Q: Complement C1q subcomponent subunit C
H: Complement C1q subcomponent subunit B
M: Complement C1q subcomponent subunit A
R: Complement C1q subcomponent subunit C


Theoretical massNumber of molelcules
Total (without water)69,19018
Polymers69,19018
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide
Complement C1q subcomponent subunit B


Mass: 4241.628 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02746
#2: Protein/peptide
Complement C1q subcomponent subunit A


Mass: 3854.304 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02745
#3: Protein/peptide
Complement C1q subcomponent subunit C


Mass: 3435.753 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02747
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The C1q A, B-crt, C peptide assembly / Type: COMPLEX / Entity ID: all / Source: SYNTHETIC
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44364 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0043114
ELECTRON MICROSCOPYf_angle_d0.9874176
ELECTRON MICROSCOPYf_dihedral_angle_d9.528540
ELECTRON MICROSCOPYf_chiral_restr0.056438
ELECTRON MICROSCOPYf_plane_restr0.007522

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