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: 10.1172/jci.insight.135459
  • Structures With Same Primary Citation

  • 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 an ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-1-antitrypsinA356Homo sapiensMutation(s): 0 
Gene Names: SERPINA1AATPIPRO0684PRO2209
Find proteins for P01009 (Homo sapiens)
Explore P01009 
Go to UniProtKB:  P01009
NIH Common Fund Data Resources
PHAROS  P01009
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Alpha-1-antitrypsinB41Homo sapiensMutation(s): 0 
Gene Names: SERPINA1AATPIPRO0684PRO2209
Find proteins for P01009 (Homo sapiens)
Explore P01009 
Go to UniProtKB:  P01009
NIH Common Fund Data Resources
PHAROS  P01009
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab 2H2 heavy chainH216Mus musculusMutation(s): 0 
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Fab 2H2 light chainL214Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, 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 

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