6I3Z

Fab fragment of an antibody selective for wild-type alpha-1-antitrypsin in complex with its antigen

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Intrahepatic heteropolymerization of M and Z alpha-1-antitrypsin.

Laffranchi, M., Elliston, E.L., Miranda, E., Perez, J., Ronzoni, R., Jagger, A.M., Heyer-Chauhan, N., Brantly, M.L., Fra, A., Lomas, D.A., Irving, J.A.

(2020) JCI Insight 5

  • DOI: https://doi.org/10.1172/jci.insight.135459
  • Primary Citation of Related Structures:  
    6I1O, 6I3Z

  • PubMed Abstract: 

    • The α-1-antitrypsin (or alpha-1-antitrypsin, A1AT) Z variant is the primary cause of severe A1AT deficiency and forms polymeric chains that aggregate in the endoplasmic reticulum of hepatocytes. Around 2%-5% of Europeans are heterozygous for the Z and WT M allele, and there is evidence of increased risk of liver disease when compared with MM A1AT individuals ...

    The α-1-antitrypsin (or alpha-1-antitrypsin, A1AT) Z variant is the primary cause of severe A1AT deficiency and forms polymeric chains that aggregate in the endoplasmic reticulum of hepatocytes. Around 2%-5% of Europeans are heterozygous for the Z and WT M allele, and there is evidence of increased risk of liver disease when compared with MM A1AT individuals. We have shown that Z and M A1AT can copolymerize in cell models, but there has been no direct observation of heteropolymer formation in vivo. To this end, we developed a monoclonal antibody (mAb2H2) that specifically binds to M in preference to Z A1AT, localized its epitope using crystallography to a region perturbed by the Z (Glu342Lys) substitution, and used Fab fragments to label polymers isolated from an MZ heterozygote liver explant. Glu342 is critical to the affinity of mAb2H2, since it also recognized the mild S-deficiency variant (Glu264Val) present in circulating polymers from SZ heterozygotes. Negative-stain electron microscopy of the Fab2H2-labeled liver polymers revealed that M comprises around 6% of the polymer subunits in the MZ liver sample. These data demonstrate that Z A1AT can form heteropolymers with polymerization-inert variants in vivo with implications for liver disease in heterozygous individuals.

    Organizational Affiliation: 

    UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, London, United Kingdom.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-1-antitrypsin356Homo sapiensMutation(s): 0 
Gene Names: SERPINA1, AAT, PI, PRO0684, PRO2209
UniProt & NIH Common Fund Data Resources
Find proteins for P01009 (Homo sapiens)
Explore P01009 
Go to UniProtKB:  P01009
PHAROS:  P01009
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UniProt GroupP01009
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-1-antitrypsin41Homo sapiensMutation(s): 0 
Gene Names: SERPINA1, AAT, PI, PRO0684, PRO2209
UniProt & NIH Common Fund Data Resources
Find proteins for P01009 (Homo sapiens)
Explore P01009 
Go to UniProtKB:  P01009
PHAROS:  P01009
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UniProt GroupP01009
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab 2H2 heavy chainC [auth H]216Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Fab 2H2 light chainD [auth L]214Mus musculusMutation(s): 0 
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
E [auth A],
G [auth L]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.538α = 84.31
b = 51.93β = 81.47
c = 105.869γ = 78.95
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/N024842/1
Other privateItalyFondazione Cariplo 2013-0967
Other privateUnited StatesAlpha-1 Foundation project grant to James Irving
Other governmentUnited KingdomUCLH/NIHR Biomedical Research Centre

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references