8YJ6

Characerization of a novel format scFvXVHH single-chain Biparatopic antibody against a metal binding protein, MtsA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


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Literature

Characterization of a novel format scFv×VHH single-chain biparatopic antibody against metal binding protein MtsA.

Asano, R.Takeuchi, M.Nakakido, M.Ito, S.Aikawa, C.Yokoyama, T.Senoo, A.Ueno, G.Nagatoishi, S.Tanaka, Y.Nakagawa, I.Tsumoto, K.

(2024) Protein Sci 33: e5017-e5017

  • DOI: https://doi.org/10.1002/pro.5017
  • Primary Citation of Related Structures:  
    8YJ5, 8YJ6, 8YJ7, 8YJ8

  • PubMed Abstract: 

    Biparatopic antibodies (bpAbs) are engineered antibodies that bind to multiple different epitopes within the same antigens. bpAbs comprise diverse formats, including fragment-based formats, and choosing the appropriate molecular format for a desired function against a target molecule is a challenging task. Moreover, optimizing the design of constructs requires selecting appropriate antibody modalities and adjusting linker length for individual bpAbs. Therefore, it is crucial to understand the characteristics of bpAbs at the molecular level. In this study, we first obtained single-chain variable fragments and camelid heavy-chain variable domains targeting distinct epitopes of the metal binding protein MtsA and then developed a novel format single-chain bpAb connecting these fragment antibodies with various linkers. The physicochemical properties, binding activities, complex formation states with antigen, and functions of the bpAb were analyzed using multiple approaches. Notably, we found that the assembly state of the complexes was controlled by a linker and that longer linkers tended to form more compact complexes. These observations provide detailed molecular information that should be considered in the design of bpAbs.


  • Organizational Affiliation

    Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Iron ABC transporter substrate-binding lipoprotein MtsAA [auth C]279Streptococcus pyogenesMutation(s): 0 
Gene Names: mtsASPy_0453M5005_Spy0368
UniProt
Find proteins for P0A4G4 (Streptococcus pyogenes serotype M1)
Explore P0A4G4 
Go to UniProtKB:  P0A4G4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A4G4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
B [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.935α = 90
b = 49.828β = 90
c = 147.398γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan19H05766

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release