9GTU | pdb_00009gtu

Collagen VI alpha 1, 2, 3 heterotrimer recombinant C terminal region. Local refinement.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Collagen VI microfibril structure reveals mechanism for molecular assembly and clustering of inherited pathogenic mutations.

Godwin, A.R.F.Becker, M.H.Dajani, R.Snee, M.Roseman, A.M.Baldock, C.

(2025) Nat Commun 16: 7549-7549

  • DOI: https://doi.org/10.1038/s41467-025-62923-3
  • Primary Citation of Related Structures:  
    9GTU, 9HAN

  • PubMed Abstract: 

    Collagen VI links the cell surface to the extracellular matrix to provide mechanical strength to most mammalian tissues, and is linked to human diseases including muscular dystrophy, fibrosis, cardiovascular disease and osteoarthritis. Collagen VI assembles from heterotrimers of three different α-chains into microfibrils, but there are many gaps in our knowledge of the molecular assembly process. Here, we determine the structures of both heterotrimeric mini-collagen VI constructs and collagen VI microfibrils, from mammalian tissue, using cryogenic-electron microscopy. These structures reveal a cysteine-rich coiled coil region involved in trimerisation as well as microfibril assembly. Furthermore, our structures show that pathogenic mutations are located at interaction sites involved in different steps of collagen VI assembly, from the trimeric-coiled coil region that mediates heterotrimerisation, to clusters of mutations in the triple-helical region involved in microfibril formation. Our microfibril structure provides a template for understanding supramolecular assembly, and offers a platform for rationale design of therapeutics for collagen VI pathologies.


  • Organizational Affiliation
    • Division of Cell-Matrix Biology and Regenerative Medicine, Manchester Cell-Matrix Centre, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Collagen alpha-3(VI) chainA [auth C]492Homo sapiensMutation(s): 1 
Gene Names: COL6A3
UniProt & NIH Common Fund Data Resources
Find proteins for P12111 (Homo sapiens)
Explore P12111 
Go to UniProtKB:  P12111
PHAROS:  P12111
GTEx:  ENSG00000163359 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12111
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P12111-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Collagen alpha-2(VI) chain476Homo sapiensMutation(s): 0 
Gene Names: COL6A2
UniProt & NIH Common Fund Data Resources
Find proteins for P12110 (Homo sapiens)
Explore P12110 
Go to UniProtKB:  P12110
PHAROS:  P12110
GTEx:  ENSG00000142173 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12110
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P12110-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Collagen alpha-1(VI) chainC [auth A]479Homo sapiensMutation(s): 0 
Gene Names: COL6A1
UniProt & NIH Common Fund Data Resources
Find proteins for P12109 (Homo sapiens)
Explore P12109 
Go to UniProtKB:  P12109
PHAROS:  P12109
GTEx:  ENSG00000142156 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12109
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
D, E
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release
  • Version 1.1: 2025-08-27
    Changes: Data collection, Database references