4BB2

Crystal structure of cleaved corticosteroid-binding globulin in complex with progesterone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.183 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Corticosteroid-Binding Globulin: Structure-Function Implications from Species Differences

Gardill, B.R.Vogl, M.R.Lin, H.Hammond, G.L.Muller, Y.A.

(2012) PLoS One 7: 52759

  • DOI: https://doi.org/10.1371/journal.pone.0052759
  • Primary Citation of Related Structures:  
    4BB2

  • PubMed Abstract: 

    Corticosteroid-binding globulin (CBG) transports glucocorticoids and progesterone in the blood and thereby modulates the tissue availability of these hormones. As a member of the serine protease inhibitor (SERPIN) family, CBG displays a reactive center loop (RCL) that is targeted by proteinases. Cleavage of the RCL is thought to trigger a SERPIN-typical stressed-to-relaxed (S-to-R) transition that leads to marked structural rearrangements and a reduced steroid-binding affinity. To characterize structure-function relationships in CBG we studied various conformational states of E. coli-produced rat and human CBG. In the 2.5 Å crystal structure of human CBG in complex with progesterone, the RCL is cleaved at a novel site that differs from the known human neutrophil elastase recognition site. Although the cleaved RCL segment is five residues longer than anticipated, it becomes an integral part of β-sheet A as a result of the S-to-R transition. The atomic interactions observed between progesterone and CBG explain the lower affinity of progesterone in comparison to corticosteroids. Surprisingly, CD measurements in combination with thermal unfolding experiments show that rat CBG fails to undergo an S-to-R transition upon proteolytic cleavage of the RCL hinting that the S-to-R transition observed in human CBG is not a prerequisite for CBG function in rat. This observation cautions against drawing general conclusions about molecular mechanisms by comparing and merging structural data from different species.


  • Organizational Affiliation

    Department of Biology, Lehrstuhl für Biotechnik, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CORTICOSTEROID-BINDING GLOBULIN340Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P08185 (Homo sapiens)
Explore P08185 
Go to UniProtKB:  P08185
PHAROS:  P08185
GTEx:  ENSG00000170099 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08185
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CORTICOSTEROID-BINDING GLOBULIN34Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P08185 (Homo sapiens)
Explore P08185 
Go to UniProtKB:  P08185
PHAROS:  P08185
GTEx:  ENSG00000170099 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08185
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
STR BindingDB:  4BB2 Ki: 42 (nM) from 1 assay(s)
PDBBind:  4BB2 Kd: 85 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.183 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.19α = 90
b = 122.7β = 90
c = 81.93γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-01-23
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description