6HGE

Crystal structure of Alpha1-antichymotrypsin variant NewBG-I in the uncleaved S-conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.192 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

NewBG: A surrogate corticosteroid-binding globulin with an unprecedentedly high ligand release efficacy.

Gardill, B.R.Schmidt, K.Muller, Y.A.

(2019) J Struct Biol 207: 169-182

  • DOI: https://doi.org/10.1016/j.jsb.2019.05.006
  • Primary Citation of Related Structures:  
    6HGD, 6HGE, 6HGF, 6HGG, 6HGH, 6HGI, 6HGJ, 6HGK, 6HGL, 6HGM, 6HGN

  • PubMed Abstract: 

    The introduction of ligand-binding sites into proteins and the engineering of molecular allosteric coupling pathways are topical issues in protein design. Here, we show that these issues can be addressed concurrently, using the serpin human α1-antichymotrypsin (ACT) as a model. We have introduced up to 15 amino acid substitutions into ACT, converting it into a surrogate corticosteroid-binding globulin (CBG), thereby creating a new binding globulin (NewBG). Human CBG and ACT share 46% sequence identity, and CBG served as the blue-print for our design, which was guided by side-chain-packing calculations, ITC measurements and crystal structure determinations. Upon transfer of ligand-interacting residues from CBG to ACT and mutation of specific second shell residues, a NewBG variant was obtained, which binds cortisol with 1.5 µM affinity. This novel serpin (NewBG-III) binds cortisol with a 33-fold lower affinity than CBG, but shares a similar ligand-binding profile and binding mode when probed with different steroid ligands and site-directed mutagenesis. An additional substitution, i.e. A349R, created NewBG-III-allo, which introduced an allosteric coupling between ligand binding and the serpin-like S-to-R transition in ACT. In NewBG-III-allo, the proteinase-triggered S-to-R transition leads to a greater than 200-fold reduction in ligand affinity, and crystal structures suggest that this is mediated by the L55V and A349R substitutions. This reduction significantly exceeds the 10-fold reduction in binding affinity observed in human CBG.


  • Organizational Affiliation

    Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Henkestr. 91, D-91052 Erlangen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-1-antichymotrypsin409Homo sapiensMutation(s): 12 
Gene Names: SERPINA3AACTGIG24GIG25
UniProt & NIH Common Fund Data Resources
Find proteins for P01011 (Homo sapiens)
Explore P01011 
Go to UniProtKB:  P01011
PHAROS:  P01011
GTEx:  ENSG00000196136 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01011
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-1-antichymotrypsin409Homo sapiensMutation(s): 12 
Gene Names: SERPINA3AACTGIG24GIG25
UniProt & NIH Common Fund Data Resources
Find proteins for P01011 (Homo sapiens)
Explore P01011 
Go to UniProtKB:  P01011
PHAROS:  P01011
GTEx:  ENSG00000196136 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01011
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-1-antichymotrypsin409Homo sapiensMutation(s): 12 
Gene Names: SERPINA3AACTGIG24GIG25
UniProt & NIH Common Fund Data Resources
Find proteins for P01011 (Homo sapiens)
Explore P01011 
Go to UniProtKB:  P01011
PHAROS:  P01011
GTEx:  ENSG00000196136 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01011
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-1-antichymotrypsin409Homo sapiensMutation(s): 12 
Gene Names: SERPINA3AACTGIG24GIG25
UniProt & NIH Common Fund Data Resources
Find proteins for P01011 (Homo sapiens)
Explore P01011 
Go to UniProtKB:  P01011
PHAROS:  P01011
GTEx:  ENSG00000196136 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01011
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58α = 90
b = 124.71β = 90.91
c = 127.5γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description