4CKD

Model of complex between the E.coli enzyme beta-galactosidase and four single chain Fv antibody domains scFv13R4.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Molecular Mechanism of Antibody-Mediated Activation of Beta-Galactosidase.

Vinothkumar, K.R.Mcmullan, G.Henderson, R.

(2014) Structure 22: 621

  • DOI: https://doi.org/10.1016/j.str.2014.01.011
  • Primary Citation of Related Structures:  
    4CKD

  • PubMed Abstract: 

    Binding of a single-chain Fv antibody to Escherichia coli β-galactosidase (β-gal) is known to stabilize the enzyme and activate several inactive point mutants, historically called antibody-mediated enzyme formation mutants. To understand the nature of this activation, we have determined by electron cryo-microscopy the structure of the complex between β-gal and the antibody scFv13R4. Our structure localizes the scFv13R4 binding site to the crevice between domains 1 and 3 in each β-gal subunit. The mutations that scFv13R4 counteracts are located between the antibody binding site and the active site of β-gal, at one end of the TIM-barrel that forms domain 3 where the substrate lactose is hydrolyzed. The mode of binding suggests how scFv stabilizes both the active site of β-gal and the tetrameric state.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-GALACTOSIDASE
A, B, C, D
1,024Escherichia coli K-12Mutation(s): 0 
EC: 3.2.1.23
UniProt
Find proteins for P00722 (Escherichia coli (strain K12))
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Go to UniProtKB:  P00722
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UniProt GroupP00722
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SCFV13R4 ANTIBODY FV HEAVY CHAINE [auth H],
F [auth I],
G [auth J],
H [auth K]
114Mus musculusMutation(s): 0 
UniProt
Find proteins for P01823 (Mus musculus)
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UniProt GroupP01823
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SCFV13R4 ANTIBODY FV LIGHT CHAINI [auth L],
J [auth M],
K [auth N],
L [auth O]
107Mus musculusMutation(s): 0 
UniProt
Find proteins for P01642 (Mus musculus)
Explore P01642 
Go to UniProtKB:  P01642
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UniProt GroupP01642
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONFREALIGN
RECONSTRUCTIONMRC IMAGE PROCESSING PACKAGE

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-03-26
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2014-04-23
    Changes: Database references
  • Version 1.3: 2017-08-30
    Changes: Data collection
  • Version 1.4: 2019-10-23
    Changes: Data collection, Other