5GS0

Crystal structure of the complex of TLR3 and bi-specific diabody

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

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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. The ...

    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
Toll-like receptor 3 A, B671Homo sapiensMutation(s): 0 
Gene Names: TLR3
Find proteins for O15455 (Homo sapiens)
Explore O15455 
Go to UniProtKB:  O15455
NIH Common Fund Data Resources
PHAROS:  O15455
GTEx:  ENSG00000164342
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
light chain (anti-TLR3) C, E107Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
heavy chain (anti-TLR3) D, F127Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
heavy chain (anti-Lid) H, X121Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
light chain (anti-Lid) L, Y107Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
BMA
Query on BMA
Download Ideal Coordinates CCD File 
A, B
beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N		 Ligand Interaction
MAN
Query on MAN
Download Ideal Coordinates CCD File 
A, B
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.519α = 90
b = 141.329β = 106.88
c = 150.831γ = 90
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 

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary