5GS2

Crystal structure of diabody complex with repebody and MBP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


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Literature

Crystal structure of mono- and bi-specific diabodies and reduction of their structural flexibility by introduction of disulfide bridges at the Fv interface.

Kim, J.H.Song, D.H.Youn, S.J.Kim, J.W.Cho, G.Kim, S.C.Lee, H.Jin, M.S.Lee, J.O.

(2016) Sci Rep 6: 34515-34515

  • DOI: 10.1038/srep34515
  • Primary Citation of Related Structures:  
    5GRY, 5GRX, 5GRZ, 5GS2, 5GS1, 5GS3, 5GRU, 5GRW, 5GRV, 5GS0

  • PubMed Abstract: 
  • Building a sophisticated protein nano-assembly requires a method for linking protein components in a predictable and stable structure. Diabodies are engineered antibody fragments that are composed of two Fv domains connected by short peptide linkers. They are attractive candidates for mediators in assembling protein nano-structures because they can simultaneously bind to two different proteins and are rigid enough to be crystallized ...

    Building a sophisticated protein nano-assembly requires a method for linking protein components in a predictable and stable structure. Diabodies are engineered antibody fragments that are composed of two Fv domains connected by short peptide linkers. They are attractive candidates for mediators in assembling protein nano-structures because they can simultaneously bind to two different proteins and are rigid enough to be crystallized. However, comparison of previous crystal structures demonstrates that there is substantial structural diversity in the Fv interface region of diabodies and, therefore, reliable prediction of its structure is not trivial. Here, we present the crystal structures of ten mono- and bi-specific diabodies. We found that changing an arginine residue in the Fv interface to threonine greatly reduced the structural diversity of diabodies. We also found that one of the bispecific diabodies underwent an unexpected process of chain swapping yielding a non-functional monospecific diabody. In order to further reduce structural flexibility and prevent chain shuffling, we introduced disulfide bridges in the Fv interface regions. The disulfide-bridged diabodies have rigid and predictable structures and may have applications in crystallizing proteins, analyzing cryo-electron microscopic images and building protein nano-assemblies.


    Organizational Affiliation

    Department of Chemistry, KAIST, Daejeon, Korea.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maltose-binding periplasmic proteinA367Escherichia coli K-12Mutation(s): 1 
Gene Names: malEb4034JW3994
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
anti-repebodyB [auth D]233Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
anti-MBPC [auth H]239Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
repebodyD [auth B]273Escherichia coliMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.222 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 278.835α = 90
b = 278.835β = 90
c = 132.322γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science, ICT and Future PlanningKorea, Republic OfNRF-2014R1A2A1A10050436
Ministry of Health & WelfareKorea, Republic OfHI15C1886

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-12
    Type: Initial release