1FOR

STRUCTURE DETERMINATION OF AN FAB FRAGMENT THAT NEUTRALIZES HUMAN RHINOVIRUS AND ANALYSIS OF THE FAB-VIRUS COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

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This is version 1.5 of the entry. See complete history. 


Literature

Structure determination of an Fab fragment that neutralizes human rhinovirus 14 and analysis of the Fab-virus complex.

Liu, H., Smith, T.J., Lee, W.M., Mosser, A.G., Rueckert, R.R., Olson, N.H., Cheng, R.H., Baker, T.S.

(1994) J Mol Biol 240: 127-137

  • DOI: 10.1006/jmbi.1994.1427
  • Primary Citation of Related Structures:  
    1FOR

  • PubMed Abstract: 

    • The crystal structure of Fab17-IA, an antigen-binding fragment from a murine immunoglobulin that neutralizes human rhinovirus 14 (HRV14), has been solved to 2.7 A resolution. Fab17-IA crystallized into three different space groups depending upon the method used to purify the intact antibody ...

    The crystal structure of Fab17-IA, an antigen-binding fragment from a murine immunoglobulin that neutralizes human rhinovirus 14 (HRV14), has been solved to 2.7 A resolution. Fab17-IA crystallized into three different space groups depending upon the method used to purify the intact antibody. The structure was determined by use of molecular and isomorphous replacement methods. The current model has a crystallographic R-factor of approximately 19% for 10,192 independent reflections between 8 and 2.7 A. Correlation coefficient calculations showed that the Fab17-IA structure can be fit into the Fab17-IA/HRV14 image reconstruction density to within 5 A positional accuracy and to within a few degrees of rotation. The resulting interface of the docked antibody was examined and showed extensive charge and shape complementarity with the virus surface that was supported by site-directed mutagenesis experiments. The success of this approach validates the utility of combining X-ray crystallography with cryo-electron microscopy of complex macromolecular assemblies.

    Related Citations: 
    • Structure of Human Rhinovirus Complexed with Fab Fragments from a Neutralizing Antibody
      Smith, T.J., Olson, N.H., Cheng, R.H., Liu, H., Chase, E.S., Lee, W.M., Leippe, D.M., Mosser, A.G., Rueckert, R.R., Baker, T.S.
      (1993) J Virol 67: 1148
    • Structure of a Human Rhinovirus-Bivalently Bound Antibody Complex: Implications for Viral Neutralization and Antibody Flexibility
      Smith, T.J., Olson, N.H., Cheng, R.H., Chase, E.S., Baker, T.S.
      (1993) Proc Natl Acad Sci U S A 90: 7015
    Organizational Affiliation: 

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IGG2A-KAPPA 17-IA FAB (LIGHT CHAIN)A [auth L]210Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IGG2A-KAPPA 17-IA FAB (HEAVY CHAIN)B [auth H]219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.8α = 90
b = 97.3β = 90
c = 129.5γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1994-05-24 
  • Released Date: 1994-09-30 
    • Deposition Author(s): Smith, T.J., Liu, H.

Revision History  (Full details and data files)

  • Version 1.0: 1994-09-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.4: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.5: 2019-08-14
    Changes: Data collection, Refinement description