Alphafold2 models of 47G4 (Hu19) scFv dimers and of VLVL dimers

Alphafold2 models of 47G4 (Hu19) scFv dimers show a variety of swapped VH-VL structures.

Alphafold2 dimers models of scFvs formed from VH and VL domains tend to swap to form diabodies with long linkers as for short linkers.  The 47G4 scFv used in this study uses a VL-to-VH scFv construct with a long linker (see sequence in Figure 1)

See Supplement files for:

• The 5 best Alphafold2 models of a predicted 47G4 (Hu19) scFv dimer, using the sequence in Figure 1. 
  • In PDB format.  The 5 models are ranked by AF2 in files:
    • ranked_0...4.pdb
  • The 5 models can be compared by superimposition of the VL domain of chain A: in iCn3D using an iCn3D PNG image file.  To see the models and analyze them in 3D, invoke iCn3D with the link: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html ; open “iCn3D PNG image file” using the file:
    • 5models_Hu19_scFv_AF2_icn3d_loadable.png

Alphafold2 models for 47G4 (Hu19) VL-VL dimers

• In PDB format.  The 25 models are ranked by AF2 in files:
  • Hu19-VLVL-AF2-ranked_0…24.pdb  
  • Only one out of 25 models offers an inverted interface but offers lower confidence. All other present the canonical interface.

List of PDB structures containing VL-VL quaternary interfaces (PDB accessed on 10/11/2021)

• See file:  PDB-Igs-VLVL-asu+bu-with-over-10contacts.xls
  • The file represents PDB structures that contain contacting VL domains with more than 10 arbitrary contacts in either the first biological Unit (BU) or asymmetric unit (ASU). Both BU and ASU are used as both may contain valid dimers, as in the the inverted VLVL dimer structure (7JO8)
  • Some iCn3D links are provided in the excel file to look and analyze a number of structures.  Some links compare 7JO8 to 1REI, or other VLVL parallel vs antiparallel dimer such as 1LVE vs 5LVE.

Where no link is specified, PDBids can be directly loaded in iCn3D using the link https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html