9GGP | pdb_00009ggp

Alpha-1-antitrypsin in complex with the Fab fragment of an anti-polymer antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 
    0.206 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

High-resolution characterization of ex vivo AAT polymers by solution-state NMR spectroscopy.

Lowen, S.M.Waudby, C.A.Jagger, A.M.Aldobiyan, I.Laffranchi, M.Fra, A.Christodoulou, J.Irving, J.A.Lomas, D.A.

(2025) Sci Adv 11: eadu7064-eadu7064

  • DOI: https://doi.org/10.1126/sciadv.adu7064
  • Primary Citation of Related Structures:  
    9GGP

  • PubMed Abstract: 

    Serpins, protease inhibitors whose regulated conformational instability renders them susceptible to mutations that cause misfolding, represent a system for the study of non-amyloid protein aggregation. The E342K "Z" variant of α-1-antitrypsin (AAT) undergoes oligomeric self-assembly into polymer chains that are associated with liver and lung pathologies in AAT deficiency. Structural characterization of polymers from human tissue has been limited by their heterogeneity and flexibility; here, we have studied their internal structure, which provides insights into the molecular linkage and the pathway by which they are formed. NMR spectra of heat-induced 13 C-ILV-methyl-labeled polymers, and 1 H-methyl spectra of liver-derived polymers, show equivalence to that of AAT in a post-protease-encounter conformation. This is corroborated by x-ray crystallography, which reveals a cryptic epitope recognized by the conformationally selective 2C1 antibody, common to both forms. These data definitively preclude most models of polymerization and are compatible with sequential intermolecular donation of the carboxyl terminus of one molecule into the next during polymer formation.


  • Organizational Affiliation
    • UCL Respiratory, Rayne Institute, and the Institute of Structural and Molecular Biology, University College London, London WC1E 6JF, UK.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-1-antitrypsin
A, B
404Homo sapiensMutation(s): 0 
Gene Names: SERPINA1AATPIPRO0684PRO2209
UniProt & NIH Common Fund Data Resources
Find proteins for P01009 (Homo sapiens)
Explore P01009 
Go to UniProtKB:  P01009
PHAROS:  P01009
GTEx:  ENSG00000197249 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01009
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab fragment heavy chain of 2C1 monoclonal antibodyC [auth H]222Mus musculusMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab fragment light chain of 2C1 monoclonal antibodyD [auth L]212Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free:  0.206 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.946α = 90
b = 75.554β = 90
c = 87.146γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/V034243/1
Other privateUnited States1036784

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release