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. 2018 Aug;285(15):2888-2899.
doi: 10.1111/febs.14585. Epub 2018 Jun 25.

A crystal structure of coil 1B of vimentin in the filamentous form provides a model of a high-order assembly of a vimentin filament

Allan H Pang  1 , Josiah M Obiero  1 , Arkadiusz W Kulczyk  2 , Vitaliy M Sviripa  3 , Oleg V Tsodikov  1
Affiliations

A crystal structure of coil 1B of vimentin in the filamentous form provides a model of a high-order assembly of a vimentin filament

Allan H Pang et al. FEBS J. 2018 Aug.

Abstract

Vimentin is an intermediate filament (IF) protein that is expressed in leukocytes, fibroblasts and endothelial cells of blood vessels. Vimentin filaments contribute to structural stability of the cell membrane, organelle positioning and protein transport. Vimentin self-assembles into a dimer that subsequently forms high-order structures, including tetramers and octamers. The details of IF assembly at crystallographic resolutions are limited to the tetrameric form. We describe a crystal structure of a fragment of a vimentin rod domain (coil 1B) with a dimer of tetramers in the asymmetric unit. Coil 1B in the crystal is in an infinitely high-order filamentous assembly state, in which the tetramers are packed against each other laterally in an antiparallel fashion across the crystal lattice. In one of the directions of lateral packing, the tetramers pack against each other strictly head-to-tail, and in the orthogonal direction the tetramers pack in a staggered manner. This organization of the tetramers of coil 1B in the crystal lattice, together with previously reported biochemical and structural data, yield a model of high-order vimentin filament assembly.

Database: Structural data are available in the PDB under the accession number 5WHF.

Keywords: coiled-coil; crystal structure; helical domain; intermediate filament; oligomerization.

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Figures

Figure 1.
Figure 1.
The domain organization of vimentin. The region boundaries are indicated by residue numbers.
Figure 2.
Figure 2.
A multiple sequence alignment of the ordered region of coil 1B sequences of human IF proteins. The heptad pattern is denoted by letters a-g above the alignment. Residues involved in the dimerization, tetramerization and higher-order interfaces are marked by yellow, orange and light-blue ovals, respectively. The boxes indicate the regions of the highest sequence similarity.
Figure 3.
Figure 3.
A size-exclusion (HiPrep Sephacryl 26/60 S-200 HR column) chromatogram of purified vimentin coil 1B. The column was run in the gel filtration buffer, as specified in the Materials and Methods, at 2 mL/min. The 29.8 kDa mark on the x-axis serving as a calibration standard corresponds to the dimer of the DNA binding domain of FLI1 protein (with the dimer molecular weight of 29.8 kDa) [48].
Figure 4.
Figure 4.
High-order packing of vimentin coil 1B in filamentous crystals. The rectangle with the dashed line border denotes an octameric assembly of two staggered tetramers in an asymmetric unit.
Figure 5.
Figure 5.
Assemblies of coils 1B and 2 in different crystal structures. A. The octameric assembly of coil 1B in the crystal structure reported in this study. B. A previously reported coiled-coil dimer of coil 1B (PDB ID: 3SWK). C. A previously reported tetramer of coil 1B (PDB ID: 3UF1). D. A tetramer of antiparallel coiled-coils of coil 2 ΔN (previously known as coil 2B; PDB ID: 1GK4). The PDB IDs of the respective structures are indicated under the images.
Figure 6.
Figure 6.
Dimerization and tetramerization interfaces of coil 1B and tetramerization interface of coil 2B. A. A zoomed-in view of the dimerization and tetramerization interfaces of coil 1B. The residues involved in the dimerization and tetramerization are shown as sticks in the same color scheme as in Fig. 2. Water molecules are shown as balls. Only a half of the approximately symmetrical interface is shown. B The tetramerization interface of coil 2B (PDB ID: 1GK4). Numerous water-mediated interactions are not shown to simplify the view.
Figure 7.
Figure 7.
Staggered packing of coil 1B and interactions involved in high-order assembly. A. A lateral view of the staggered antiparallel packing. B. and C. Zoomed-in views of the pairwise interactions of the coil 1B dimers shown in panel A. The residues involved in these interactions are shown as sticks and colored light blue as in Fig. 2.
Figure 8.
Figure 8.
A schematic of the proposed packing of the dimers of the rod domain in a vimentin filament. The panels show three orthogonal views. The opposite orientations of vimentin dimers are designated by symbols “+” and “-”. The horizontal dashed line indicates the N-terminal boundary of the region formerly called coil 2B. The diamonds, triangles and circles designate Lys residues that were previously observed to crosslink to each other, as indicated.
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