Crystal structure of an alpha-1-antitrypsin trimer

Experimental Data Snapshot

  • Resolution: 3.90 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.238 

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Molecular basis of alpha 1-antitrypsin deficiency revealed by the structure of a domain-swapped trimer.

Yamasaki, M.Sendall, T.J.Pearce, M.C.Whisstock, J.C.Huntington, J.A.

(2011) EMBO Rep 12: 1011-1017

  • DOI: https://doi.org/10.1038/embor.2011.171
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    α(1)-Antitrypsin (α1AT) deficiency is a disease with multiple manifestations, including cirrhosis and emphysema, caused by the accumulation of stable polymers of mutant protein in the endoplasmic reticulum of hepatocytes. However, the molecular basis of misfolding and polymerization remain unknown. We produced and crystallized a trimeric form of α1AT that is recognized by an antibody specific for the pathological polymer. Unexpectedly, this structure reveals a polymeric linkage mediated by domain swapping the carboxy-terminal 34 residues. Disulphide-trapping and antibody-binding studies further demonstrate that runaway C-terminal domain swapping, rather than the s4A/s5A domain swap previously proposed, underlies polymerization of the common Z-mutant of α1AT in vivo.

  • Organizational Affiliation

    Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-1-antitrypsin371Homo sapiensMutation(s): 4 
UniProt & NIH Common Fund Data Resources
Find proteins for P01009 (Homo sapiens)
Explore P01009 
Go to UniProtKB:  P01009
GTEx:  ENSG00000197249 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01009
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.90 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.238 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.691α = 90
b = 163.691β = 90
c = 163.691γ = 90
Software Package:
Software NamePurpose
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2017-06-21
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Refinement description