1DBA

THREE-DIMENSIONAL STRUCTURE OF AN ANTI-STEROID FAB' AND PROGESTERONE-FAB' COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

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This is version 1.2 of the entry. See complete history. 


Literature

Three-dimensional structure of an anti-steroid Fab' and progesterone-Fab' complex.

Arevalo, J.H., Stura, E.A., Taussig, M.J., Wilson, I.A.

(1993) J Mol Biol 231: 103-118

  • DOI: 10.1006/jmbi.1993.1260
  • Primary Citation of Related Structures:  
    1DBA, 1DBB

  • PubMed Abstract: 

    • The monoclonal anti-progesterone antibody DB3 binds progesterone with nanomolar affinity (Ka approximately 10(9) M-1), suggesting high specificity. However, DB3 also cross-reacts with similar affinity with a subgroup of structurally distinct, progesterone-like steroids ...

    The monoclonal anti-progesterone antibody DB3 binds progesterone with nanomolar affinity (Ka approximately 10(9) M-1), suggesting high specificity. However, DB3 also cross-reacts with similar affinity with a subgroup of structurally distinct, progesterone-like steroids. Crystals of the unliganded Fab' and various steroid-Fab' complexes are isomorphous and belong to the hexagonal space group, P6(4)22, with unit cell dimensions of a = b = 135 A, c = 124 A. Structures of free and progesterone-bound Fab' have been determined by X-ray crystallography at 2.7 A resolution using molecular replacement techniques. Progesterone is bound in a hydrophobic pocket formed mainly by the interaction of three complementarity determining regions L1, H2 and H3. The orientation of the ligand in the binding site was aided by both crystallographic and biochemical analyses of substituted steroids. The indole side-chain of TrpH100 of the DB3 has two different conformations, inter-converting "open" and "closed" forms of the antibody combining site. The TrpH100 indole thus appears to be acting as an antibody-derived surrogate ligand for its own hydrophobic binding pocket. These structures provide the first atomic view of how a steroid interacts with a protein and offer a structural explanation for the restriction of the anti-progesterone response to the VGAM3.8 family of VH genes.

    Related Citations: 
    • Analysis of an Anti-Progesterone Antibody: Variable Crystal Morphology of the Fab' and Steroid-Fab' Complexes
      Stura, E.A., Arevalo, J.H., Feinstein, A., Heap, R.B., Taussig, M.J., Wilson, I.A.
      (1987) Immunology 62: 511
    Organizational Affiliation: 

    Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IGG1-KAPPA DB3 FAB (LIGHT CHAIN)A [auth L]216Mus musculusMutation(s): 0 
Entity Groups  
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Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IGG1-KAPPA DB3 FAB (HEAVY CHAIN)B [auth H]219Mus musculusMutation(s): 0 
Gene Names: Ighg1, Igh-4
UniProt
Find proteins for P01868 (Mus musculus)
Explore P01868 
Go to UniProtKB:  P01868
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01868
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EOH
Query on EOH
Download Ideal Coordinates CCD File 
C [auth H],
D [auth H]		ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.76α = 90
b = 134.76β = 90
c = 124.21γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance