ジャーナル: Structure / 年: 2013 タイトル: Variable internal flexibility characterizes the helical capsid formed by agrobacterium VirE2 protein on single-stranded DNA. 著者: Tanmay A M Bharat / David Zbaida / Miriam Eisenstein / Ziv Frankenstein / Tevie Mehlman / Lev Weiner / Carlos Oscar S Sorzano / Yoav Barak / Shira Albeck / John A G Briggs / Sharon G Wolf / Michael Elbaum / 要旨: 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 ...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.
The N and C terminal domain were fit separately by exhaustive molecular modeling using the fitPDB2EM program. Only the N-terminal domain could be constrained strongly.
精密化
空間: RECIPROCAL / プロトコル: FLEXIBLE FIT / 当てはまり具合の基準: Highest cross-correlation
得られたモデル
PDB-4blf: Variable internal flexibility characterizes the helical capsid formed by Agrobacterium VirE2 protein on single-stranded DNA.