6GK3

Two protofilament beta-2-microglobulin amyloid fibril

  • Classification: PROTEIN FIBRIL
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2018-05-18 Released: 2018-11-14 
  • Deposition Author(s): Iadanza, M.G., Ranson, N.A.
  • Funding Organization(s): European Research Council, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Wellcome Trust

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.98 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The structure of a beta2-microglobulin fibril suggests a molecular basis for its amyloid polymorphism.

Iadanza, M.G.Silvers, R.Boardman, J.Smith, H.I.Karamanos, T.K.Debelouchina, G.T.Su, Y.Griffin, R.G.Ranson, N.A.Radford, S.E.

(2018) Nat Commun 9: 4517-4517

  • DOI: https://doi.org/10.1038/s41467-018-06761-6
  • Primary Citation of Related Structures:  
    6GK3

  • PubMed Abstract: 

    All amyloid fibrils contain a cross-β fold. How this structure differs in fibrils formed from proteins associated with different diseases remains unclear. Here, we combine cryo-EM and MAS-NMR to determine the structure of an amyloid fibril formed in vitro from β 2 -microglobulin (β 2 m), the culprit protein of dialysis-related amyloidosis. The fibril is composed of two identical protofilaments assembled from subunits that do not share β 2 m's native tertiary fold, but are formed from similar β-strands. The fibrils share motifs with other amyloid fibrils, but also contain unique features including π-stacking interactions perpendicular to the fibril axis and an intramolecular disulfide that stabilises the subunit fold. We also describe a structural model for a second fibril morphology and show that it is built from the same subunit fold. The results provide insights into the mechanisms of fibril formation and the commonalities and differences within the amyloid fold in different protein sequences.


  • Organizational Affiliation

    Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
A, B, C, D, E
A, B, C, D, E, F, G, H
64Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.98 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.11.1
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited Kingdom322408
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesEB-002026
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesAG-058504
Wellcome TrustUnited Kingdom092896MA
Wellcome TrustUnited Kingdom204963

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2022-03-30
    Changes: Author supporting evidence, Database references