(c) Red lines depict the 27 intermolecular lysine cross-links easily accommodated in this individual SMC2/SMC4 dimer (three links were rejected as not compatible). These cross-links suggest a close proximity of the two coiled-coils in the rod-like conformation of the heterodimer. The Ca a distance average for these ?intermolecular cross-links was 21 + 4.3 A. Boxes enclose two clusters of intermolecular cross-links that are best modelled as a quadruple-stranded coil. (d) Fit of the assembled model to the spatial junction constraint between modelled fragments (see Results). Average distances per residue are shown for 19 junctions where between two and 10 residues were omitted in the modelling in between fragments, and constraints were imposed. For reference, typical distances for residues in a-helical and ?b-strand conformations are 1.5 and 3.4 A, SB 203580MedChemExpress SB 203580 respectively. (e) Histogram of all measurable Ca distances in the model between cross-linked lysines, including the linkages shown in panels b and c and the 57 intradomain linkages. Molecular graphics produced with UCSF CHIMERA v. 1.9.?resides not modelled and including a 1? A intentional additional off-set to emphasize and counteract the limitations of coiled-coil modelling and rigid fragment assembly (figure 8d), (iii) Ca distances between lysines found in intermo?lecular cross-links in our experiment less than 30 A (again we added some tolerance to the empirical/experimentally?determined value of 27.4 A [51], to account for modelling uncertainty). The distribution of Ca a distances for 105 measurable cross-links is shown in figure 8e. The resulting `draft’ model visualizes the approximate locations of 1096 residues (92 ) of SMC2 and 1111 residues (85 ) of SMC4, in the SMC2/SMC4 core complex captured in our cross-linking experiments (figure 8). Its atomic coordinates as well as rendering scripts for the two commonly used ?molecular visualization programs PYMOL (Schrodinger LLC, http://www.pymol.org) and UCSF CHIMERA [78] (http:// www.cgl.ucsf.edu/chimera) are provided in the electronic supplementary material, data file S1, to facilitate use of the model by other laboratories. This model stems from an experimental omputational hybrid approach, with cross-link information contributing vitally (except in the homology-modelled head and hinge domains). By contrast, a purely computational attempt would probably have failed owing to irresolvable uncertainty in the alignment of the two anti-parallel helices to one another in each coiled-coil fragment. Altogether, our three-dimensional assembly explicitly accommodates 57 intradomain cross-links (33 in SMC2, 24 in SMC4), 21 interdomain intramolecular cross-links (9 in SMC2, 12 in SMC4) and 27 intermolecular cross-links. An additional nine cross-links appeared to be implicitly compatible although only one partnering lysine was included in the model for eight of these links, and neither lysine was modelled for the ninth link (where only four residues separate them in sequence). Out of 120 high-confidence cross-links in total, we deemed only three intermolecular links to be incompatible, i.e. we could not accommodate them simultaneously with the others even by allowing a domain omain rotation between the coiled-coil and globular domains that deviated from the currently available template structures. These cross-links could possibly have arisen from contacts between adjacent condensin pentamers.4. DiscussionWe have RRx-001MedChemExpress RRx-001 combined classic molecular modelling with.(c) Red lines depict the 27 intermolecular lysine cross-links easily accommodated in this individual SMC2/SMC4 dimer (three links were rejected as not compatible). These cross-links suggest a close proximity of the two coiled-coils in the rod-like conformation of the heterodimer. The Ca a distance average for these ?intermolecular cross-links was 21 + 4.3 A. Boxes enclose two clusters of intermolecular cross-links that are best modelled as a quadruple-stranded coil. (d) Fit of the assembled model to the spatial junction constraint between modelled fragments (see Results). Average distances per residue are shown for 19 junctions where between two and 10 residues were omitted in the modelling in between fragments, and constraints were imposed. For reference, typical distances for residues in a-helical and ?b-strand conformations are 1.5 and 3.4 A, respectively. (e) Histogram of all measurable Ca distances in the model between cross-linked lysines, including the linkages shown in panels b and c and the 57 intradomain linkages. Molecular graphics produced with UCSF CHIMERA v. 1.9.?resides not modelled and including a 1? A intentional additional off-set to emphasize and counteract the limitations of coiled-coil modelling and rigid fragment assembly (figure 8d), (iii) Ca distances between lysines found in intermo?lecular cross-links in our experiment less than 30 A (again we added some tolerance to the empirical/experimentally?determined value of 27.4 A [51], to account for modelling uncertainty). The distribution of Ca a distances for 105 measurable cross-links is shown in figure 8e. The resulting `draft’ model visualizes the approximate locations of 1096 residues (92 ) of SMC2 and 1111 residues (85 ) of SMC4, in the SMC2/SMC4 core complex captured in our cross-linking experiments (figure 8). Its atomic coordinates as well as rendering scripts for the two commonly used ?molecular visualization programs PYMOL (Schrodinger LLC, http://www.pymol.org) and UCSF CHIMERA [78] (http:// www.cgl.ucsf.edu/chimera) are provided in the electronic supplementary material, data file S1, to facilitate use of the model by other laboratories. This model stems from an experimental omputational hybrid approach, with cross-link information contributing vitally (except in the homology-modelled head and hinge domains). By contrast, a purely computational attempt would probably have failed owing to irresolvable uncertainty in the alignment of the two anti-parallel helices to one another in each coiled-coil fragment. Altogether, our three-dimensional assembly explicitly accommodates 57 intradomain cross-links (33 in SMC2, 24 in SMC4), 21 interdomain intramolecular cross-links (9 in SMC2, 12 in SMC4) and 27 intermolecular cross-links. An additional nine cross-links appeared to be implicitly compatible although only one partnering lysine was included in the model for eight of these links, and neither lysine was modelled for the ninth link (where only four residues separate them in sequence). Out of 120 high-confidence cross-links in total, we deemed only three intermolecular links to be incompatible, i.e. we could not accommodate them simultaneously with the others even by allowing a domain omain rotation between the coiled-coil and globular domains that deviated from the currently available template structures. These cross-links could possibly have arisen from contacts between adjacent condensin pentamers.4. DiscussionWe have combined classic molecular modelling with.
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