1MFA

STRUCTURE OF A SINGLE-CHAIN FV FRAGMENT COMPLEXED WITH A CARBOHYDRATE ANTIGEN AT 1.7 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Work: 0.166 
  • R-Value Observed: 0.166 

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Literature

Structure of a single-chain antibody variable domain (Fv) fragment complexed with a carbohydrate antigen at 1.7-A resolution.

Zdanov, A.Li, Y.Bundle, D.R.Deng, S.J.MacKenzie, C.R.Narang, S.A.Young, N.M.Cygler, M.

(1994) Proc Natl Acad Sci U S A 91: 6423-6427

  • DOI: 10.1073/pnas.91.14.6423
  • Primary Citation of Related Structures:  
    1MFA

  • PubMed Abstract: 
  • We describe here the 1.7-A resolution structure of a single-chain antibody variable domain (scFv) molecule, based on the carbohydrate-binding antibody Se155-4, complexed with the trisaccharide ligand alpha-D-Gal(1-->2)[alpha-D-Abe(1-->3)]alpha-D-Manp ...

    We describe here the 1.7-A resolution structure of a single-chain antibody variable domain (scFv) molecule, based on the carbohydrate-binding antibody Se155-4, complexed with the trisaccharide ligand alpha-D-Gal(1-->2)[alpha-D-Abe(1-->3)]alpha-D-Manp1-->OMe, where Abe is abequose. The scFv expressed in Escherichia coli has the variable region light chain to heavy chain polarity with the domains connected by a 19-residue linker. Although the linker is partially disordered in the crystal, the packing of the molecules suggests a monomeric state of the scFv. The carbohydrate adopts a different conformation about the Man-Gal linkage than was observed previously in the Fab-trisaccharide complex. Instead of a direct hydrogen bond between O2Abe and O2Gal, these two atoms are bridged by a water molecule in the present complex.


    Related Citations: 
    • The Solution Structure of a Trisaccharide-Antibody Complex: Comparison of NMR Measurements with a Crystal Structure
      Bundle, D.R., Baumann, H., Brisson, J.-R., Gagne, S., Zdanov, A., Cygler, M.
      () To be published --: --
    • Bacterial Expression and Secretion of Various Single-Chain Fv Genes Encoding Proteins Specific for a Salmonella Serotype B O-Antigen
      Anand, N.N., Mandal, S., Mackenzie, C.R., Sadowska, J., Sijurskjold, B., Young, N.M., Budle, D.R., Narang, S.A.
      (1991) J Biol Chem 266: 21874
    • Recognition of a Cell-Surface Oligo-Saccharide of Pathogenic Salmonella by an Antibody Fab Fragment
      Cygler, M., Rose, D.R., Bundle, D.R.
      (1991) Science 253: 442

    Organizational Affiliation

    Biotechnology Research Institute, National Research Council of Canada, Montreal, PQ.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IGG1-LAMBDA SE155-4 FAB (LIGHT CHAIN)L127Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IGG1-LAMBDA SE155-4 FAB (HEAVY CHAIN)H120Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-galactopyranose-(1-2)-[alpha-D-Abequopyranose-(1-3)]methyl alpha-D-mannopyranoside
A
3 N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Work: 0.166 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.1α = 90
b = 61β = 90
c = 74.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1993-10-25 
  • Released Date: 1994-01-31 
  • Deposition Author(s): Zdanov, A., Cygler, M.

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary