1QGC

STRUCTURE OF THE COMPLEX OF A FAB FRAGMENT OF A NEUTRALIZING ANTIBODY WITH FOOT AND MOUTH DISEASE VIRUS

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history. 


Literature

Structure of the complex of an Fab fragment of a neutralizing antibody with foot-and-mouth disease virus: positioning of a highly mobile antigenic loop.

Hewat, E.A., Verdaguer, N., Fita, I., Blakemore, W., Brookes, S., King, A., Newman, J., Domingo, E., Mateu, M.G., Stuart, D.I.

(1997) EMBO J 16: 1492-1500

  • DOI: 10.1093/emboj/16.7.1492
  • Primary Citation of Related Structures:  
    1QGC

  • PubMed Abstract: 

    • Data from cryo-electron microscopy and X-ray crystallography have been combined to study the interactions of foot-and-mouth disease virus serotype C (FMDV-C) with a strongly neutralizing monoclonal antibody (mAb) SD6. The mAb SD6 binds to the long flexible GH-loop of viral protein 1 (VP1) which also binds to an integrin receptor ...

    Data from cryo-electron microscopy and X-ray crystallography have been combined to study the interactions of foot-and-mouth disease virus serotype C (FMDV-C) with a strongly neutralizing monoclonal antibody (mAb) SD6. The mAb SD6 binds to the long flexible GH-loop of viral protein 1 (VP1) which also binds to an integrin receptor. The structure of the virus-Fab complex was determined to 30 A resolution using cryo-electron microscopy and image analysis. The known structure of FMDV-C, and of the SD6 Fab co-crystallized with a synthetic peptide corresponding to the GH-loop of VP1, were fitted to the cryo-electron microscope density map. The SD6 Fab is seen to project almost radially from the viral surface in an orientation which is only compatible with monovalent binding of the mAb. Even taking into account the mAb hinge and elbow flexibility, it is not possible to model bivalent binding without severely distorting the Fabs. The bound GH-loop is essentially in what has previously been termed the 'up' position in the best fit Fab orientation. The SD6 Fab interacts almost exclusively with the GH-loop of VP1, making very few other contacts with the viral capsid. The position and orientation of the SD6 Fab bound to FMDV-C is in accord with previous immunogenic data.

    Organizational Affiliation: 

    Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (VIRUS CAPSID PROTEIN VP1)A [auth 1]207Foot and mouth disease virus CMutation(s): 0 
EC: 3.4.22.46 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P03311 (Foot-and-mouth disease virus (isolate -/Spain/S8c1SantaPau/1970 serotype C))
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Go to UniProtKB:  P03311
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03311
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (VIRUS CAPSID PROTEIN VP2)B [auth 2]218Foot and mouth disease virus CMutation(s): 0 
EC: 3.4.22.46 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P03311 (Foot-and-mouth disease virus (isolate -/Spain/S8c1SantaPau/1970 serotype C))
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Go to UniProtKB:  P03311
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UniProt GroupP03311
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (VIRUS CAPSID PROTEIN VP3)C [auth 3]219Foot and mouth disease virus CMutation(s): 0 
EC: 3.4.22.46 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P03311 (Foot-and-mouth disease virus (isolate -/Spain/S8c1SantaPau/1970 serotype C))
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Go to UniProtKB:  P03311
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UniProt GroupP03311
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (IMMUNOGLOBULIN LIGHT CHAIN)D [auth 4]218Mus musculusMutation(s): 0 
Gene Names: Igkc
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (IMMUNOGLOBULIN HEAVY CHAIN)E [auth A]220Mus musculusMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (GH-LOOP FROM VIRUS CAPSID PROTEIN VP1)F [auth 5]24Foot and mouth disease virus CMutation(s): 0 
EC: 3.4.22.46 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P03311 (Foot-and-mouth disease virus (isolate -/Spain/S8c1SantaPau/1970 serotype C))
Explore P03311 
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UniProt GroupP03311
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Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS		D [auth 4]L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 1999-04-23 
  • Released Date: 2000-01-26 
    • Deposition Author(s): Fita, I.

Revision History  (Full details and data files)

  • Version 1.0: 2000-01-26
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-10-19
    Changes: Atomic model
  • Version 1.4: 2015-01-14
    Changes: Structure summary
  • Version 1.5: 2018-07-18
    Changes: Data collection, Database references
  • Version 1.6: 2019-04-10
    Changes: Data collection, Database references, Derived calculations