title: Variable internal flexibility characterizes the helical capsid formed by agrobacterium VirE2 protein on single-stranded DNA.
abstract: Agrobacterium is known for gene transfer to plants. In addition to a linear ssDNA oligonucleotide, Agrobacterium tumefaciens secretes an abundant ssDNA-binding effector, VirE2. In many ways VirE2 adapts the conjugation mechanism to transform the eukaryotic host. The crystal structure of VirE2 shows two compact domains joined by a flexible linker. Bound to ssDNA, VirE2 forms an ordered solenoidal shell, or capsid known as the T-complex. Here, we present a three-dimensional reconstruction of the VirE2-ssDNA complex using cryo-electron microscopy and iterative helical real-space reconstruction. High-resolution refinement was not possible due to inherent heterogeneity in the protein structure. By a combination of computational modeling, chemical modifications, mass spectroscopy, and electron paramagnetic resonance, we found that the N-terminal domain is tightly constrained by both tangential and longitudinal links, while the C terminus is weakly constrained. The quaternary structure is thus rigidly assembled while remaining locally flexible. This flexibility may be important in accommodating substrates without sequence specificity.
authors.affiliation: Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Tanmay A M
authors.initials: TA
authors.lastname: Bharat
authors.forename: David
authors.initials: D
authors.lastname: Zbaida
authors.forename: Miriam
authors.initials: M
authors.lastname: Eisenstein
authors.forename: Ziv
authors.initials: Z
authors.lastname: Frankenstein
authors.forename: Tevie
authors.initials: T
authors.lastname: Mehlman
authors.forename: Lev
authors.initials: L
authors.lastname: Weiner
authors.forename: Carlos Oscar S
authors.initials: CO
authors.lastname: Sorzano
authors.forename: Yoav
authors.initials: Y
authors.lastname: Barak
authors.forename: Shira
authors.initials: S
authors.lastname: Albeck
authors.forename: John A G
authors.initials: JA
authors.lastname: Briggs
authors.forename: Sharon G
authors.initials: SG
authors.lastname: Wolf
authors.forename: Michael
authors.initials: M
authors.lastname: Elbaum
mesh_terms: D016960:Agrobacterium tumefaciens / Q000648:ultrastructure*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000648:ultrastructure; D020285:Cryoelectron Microscopy; D004269:DNA, Bacterial / Q000737:chemistry; D004277:DNA, Single-Stranded / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000648:ultrastructure; D004578:Electron Spin Resonance Spectroscopy; D007473:Ion Channels / Q000737:chemistry* / Q000648:ultrastructure; D007700:Kinetics; D008958:Models, Molecular; D054730:Protein Interaction Domains and Motifs; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004277:DNA, Single-Stranded; D004268:DNA-Binding Proteins; D007473:Ion Channels; C051583:virE2 protein, Agrobacterium