6QU9 | pdb_00006qu9

Fab fragment of an antibody that inhibits polymerisation of alpha-1-antitrypsin

• PDB DOI: https://doi.org/10.2210/pdb6QU9/pdb

• Classification: PROTEIN BINDING
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2019-02-26 Released: 2020-03-18 
• Deposition Author(s): Jagger, A.M., Heyer-Chauhan, N., Lomas, D.A., Irving, J.A.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom), Other government, Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.233 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: other

Literature

The structural basis for Z alpha 1 -antitrypsin polymerization in the liver.

Faull, S.V., Elliston, E.L.K., Gooptu, B., Jagger, A.M., Aldobiyan, I., Redzej, A., Badaoui, M., Heyer-Chauhan, N., Rashid, S.T., Reynolds, G.M., Adams, D.H., Miranda, E., Orlova, E.V., Irving, J.A., Lomas, D.A.

(2020) Sci Adv 6

• PubMed: 33087346 
• DOI: https://doi.org/10.1126/sciadv.abc1370
• Primary Citation Related Structures: 
  6QU9


• PubMed Abstract: 
  

  The serpinopathies are among a diverse set of conformational diseases that involve the aberrant self-association of proteins into ordered aggregates. α ₁ -Antitrypsin deficiency is the archetypal serpinopathy and results from the formation and deposition of mutant forms of α ₁ -antitrypsin as "polymer" chains in liver tissue. No detailed structural analysis has been performed of this material. Moreover, there is little information on the relevance of well-studied artificially induced polymers to these disease-associated molecules. We have isolated polymers from the liver tissue of Z α ₁ -antitrypsin homozygotes (E342K) who have undergone transplantation, labeled them using a Fab fragment, and performed single-particle analysis of negative-stain electron micrographs. The data show structural equivalence between heat-induced and ex vivo polymers and that the intersubunit linkage is best explained by a carboxyl-terminal domain swap between molecules of α ₁ -antitrypsin.

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Organizational Affiliation: 
• UCL Respiratory, University College London, 5 University Street, London WC1E 6JF, UK.
Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BN, UK.
Leicester Institute of Structural and Chemical Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 7HB, UK.
National Institute for Health Research (NIHR) Leicester BRC-Respiratory, Leicester, UK.
Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, University of London, London WC1E 7HX, UK.
Centre for Stem Cells and Regenerative Medicine and Institute for Liver Studies, King's College London, London WC2R 2LS, UK.
Centre for Liver Research and NIHR Birmingham Liver Biomedical Research Unit, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK.
Department of Biology and Biotechnologies "Charles Darwin" and Pasteur Institute-Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy.
UCL Respiratory, University College London, 5 University Street, London WC1E 6JF, UK. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, native gel electrophoresis, homology

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, native gel electrophoresis, homology

Macromolecule Content 

• Total Structure Weight: 94.12 kDa 
• Atom Count: 6,885 
• Modeled Residue Count: 848 
• Deposited Residue Count: 854 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB 4B12 heavy chain	A [auth H], C [auth A]	215	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB 4B12 light chain	B [auth L], D [auth B]	212	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth H], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	F [auth L]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.233 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.268	α = 90
b = 105.102	β = 90
c = 105.128	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Jagger, A.M., Heyer-Chauhan, N., Lomas, D.A., Irving, J.A.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N024842/1
Other government	United Kingdom	UCLH/NIHR Biomedical Research Centre
Other private	United States	Alpha-1 Foundation project grant to J. Irving

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2020-11-04
  Changes: Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary