1D5S | pdb_00001d5s

CRYSTAL STRUCTURE OF CLEAVED ANTITRYPSIN POLYMER

• PDB DOI: https://doi.org/10.2210/pdb1D5S/pdb

• Classification: HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-10-11 Released: 2000-04-02 
• Deposition Author(s): Dunstone, M.A., Dai, W., Whisstock, J.C., Rossjohn, J., Pike, R.N., Feil, S.C., Le Bonneic, B.F., Parker, M.W., Bottomley, S.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.262 (Depositor) 
• R-Value Work: 
  0.208 (Depositor) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Cleaved antitrypsin polymers at atomic resolution.

Dunstone, M.A., Dai, W., Whisstock, J.C., Rossjohn, J., Pike, R.N., Feil, S.C., Le Bonniec, B.F., Parker, M.W., Bottomley, S.P.

(2000) Protein Sci 9: 417-420

• PubMed: 10716194 
• DOI: https://doi.org/10.1110/ps.9.2.417
• Primary Citation Related Structures: 
  1D5S


• PubMed Abstract: 
  

  Alpha1-antitrypsin deficiency, which can lead to both emphysema and liver disease, is a result of the accumulation of alpha1-antitrypsin polymers within the hepatocyte. A wealth of biochemical and biophysical data suggests that alpha1-antitrypsin polymers form via insertion of residues from the reactive center loop of one molecule into the beta-sheet of another. However, this long-standing hypothesis has not been confirmed by direct structural evidence. Here, we describe the first crystallographic evidence of a beta-strand linked polymer form of alpha1-antitrypsin: the crystal structure of a cleaved alpha1-antitrypsin polymer.

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Organizational Affiliation: 
• The Ian Potter Foundation Protein Crystallography Laboratory, St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 42.34 kDa 
• Atom Count: 2,984 
• Modeled Residue Count: 375 
• Deposited Residue Count: 375 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P1-ARG ANTITRYPSIN	A	334	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01009 (Homo sapiens) Explore P01009  Go to UniProtKB:  P01009
PHAROS:  P01009 GTEx:  ENSG00000197249

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P1-ARG ANTITRYPSIN	B	41	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P01009 (Homo sapiens) Explore P01009  Go to UniProtKB:  P01009
PHAROS:  P01009 GTEx:  ENSG00000197249

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.262 (Depositor) 
• R-Value Work:  0.208 (Depositor) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.17	α = 90
b = 110.17	β = 90
c = 76.67	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-04-02 
Deposition Author(s): Dunstone, M.A., Dai, W., Whisstock, J.C., Rossjohn, J., Pike, R.N., Feil, S.C., Le Bonneic, B.F., Parker, M.W., Bottomley, S.P.

Revision History  

• Version 1.0: 2000-04-02
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references
• Version 1.4: 2024-02-07
  Changes: Data collection