9C9U | pdb_00009c9u

Cryo-EM structure of the C1q A, B-crt, C peptide full assembly


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Collagen Triple Helix without the Superhelical Twist.

Kreutzberger, M.A.B.Yu, L.T.Bui, T.H.Hancu, M.C.Purdy, M.D.Osinski, T.Kasson, P.M.Egelman, E.H.Hartgerink, J.D.

(2025) ACS Cent Sci 11: 331-345

  • DOI: https://doi.org/10.1021/acscentsci.5c00018
  • Primary Citation of Related Structures:  
    9C9L, 9C9U

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22903, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C1q subcomponent subunit B44Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02746 (Homo sapiens)
Explore P02746 
Go to UniProtKB:  P02746
PHAROS:  P02746
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02746
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C1q subcomponent subunit A37Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02745 (Homo sapiens)
Explore P02745 
Go to UniProtKB:  P02745
PHAROS:  P02745
GTEx:  ENSG00000173372 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02745
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C1q subcomponent subunit C35Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02747 (Homo sapiens)
Explore P02747 
Go to UniProtKB:  P02747
PHAROS:  P02747
GTEx:  ENSG00000159189 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02747
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HYP
Query on HYP
A
D
G [auth E]
J [auth F]
M [auth G]
A,
D,
G [auth E],
J [auth F],
M [auth G],
P [auth H]
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM122510
National Science Foundation (NSF, United States)United StatesCHE 2203937

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release
  • Version 1.1: 2025-03-19
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-28
    Changes: Data collection