6HGI

Crystal structure of Alpha1-antichymotrypsin variant NewBG-III: a new binding globulin in complex with corticosterone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.jsb.2019.05.006
  • Primary Citation of Related Structures:  
    6HGN, 6HGM, 6HGF, 6HGE, 6HGH, 6HGG, 6HGJ, 6HGI, 6HGL, 6HGK

  • 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-antich ...

    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. Electronic address: yves.muller@fau.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-1-antichymotrypsinA369Homo sapiensMutation(s): 10 
Gene Names: SERPINA3AACTGIG24GIG25
Find proteins for P01011 (Homo sapiens)
Explore P01011 
Go to UniProtKB:  P01011
NIH Common Fund Data Resources
PHAROS  P01011
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-1-antichymotrypsinB40Homo sapiensMutation(s): 5 
Gene Names: SERPINA3AACTGIG24GIG25
Find proteins for P01011 (Homo sapiens)
Explore P01011 
Go to UniProtKB:  P01011
NIH Common Fund Data Resources
PHAROS  P01011
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C0R
Query on C0R

Download CCD File 
A
CORTICOSTERONE
C21 H30 O4
OMFXVFTZEKFJBZ-HJTSIMOOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C0RKd:  600   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.615α = 90
b = 75.49β = 90
c = 79.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyGRK-1962

Revision History 

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references