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. 2018 Aug 1;7:e35898. doi: 10.7554/eLife.35898

Figure 4. The solution structure of Commd9 determined by SAXS.

(A) (Left) Experimental scattering profile Commd9 in black overlaid with the theoretical scattering curve calculated from the Commd9 rigid body model (red) and the ab initio model determined by GASBOR (green) using CRYSOL. (Middle) The Guinier plot for the experimental data at the low-angle region (qmax × Rg < 1.3). (Right) P(r) functions derived from the SAXS data. (B) (Left) Averaged (grey) and filtered (coral) molecular envelopes from GASBOR. The ab initio model of Commd9 was docked with the rigid body model of Commd9 using SUPCOMB. (Right) Model of Commd9 protein from the experimental SAXS shown in ribbon diagram with HN domains in grey and the COMM domain dimer in blue and yellow.

Figure 4.

Figure 4—figure supplement 1. SEC-SAXS profiles of Commd1, Commd7 and Commd9.

Figure 4—figure supplement 1.

(A) SEC-SAXS chromatogram (top) and Kratky plot (bottom) of Commd1, (B) Commd7 and, (C) Commd9.
Figure 4—figure supplement 2. The solution structures of Commd1 and Commd7 determined by SAXS.

Figure 4—figure supplement 2.

(A, C) (Left) Experimental scattering profiles of Commd1 and Commd7 in black overlaid with the theoretical scattering curves calculated from the Commd1 and Commd7 rigid body model (red) and the ab initio model determined by GASBOR (green) using CRYSOL. (Middle) The Guinier plot for the experimental data at the low-angle region (qmax × Rg < 1.3). (Right) P(r) functions derived from the SAXS data. (B, D) (Left) Averaged (grey) and filtered (coral) molecular envelopes from GASBOR. The ab initio models of Commd1 and Commd7 were docked with rigid body models of Commd1 and Commd7 respectively using SUPCOMB. (Right) Models of Commd1 and Commd7 generated from the experimental SAXS data shown in ribbon diagram with HN domains in grey and the COMM domain dimer in blue and yellow.
Figure 4—figure supplement 3. Structural comparison of the COMM domain of Commd9 with other similar modules.

Figure 4—figure supplement 3.

Figure 4—figure supplement 4. Structural similarity of COMMD proteins to Pur-α repeats and chlamydial proteins.

Figure 4—figure supplement 4.

(A) Ribbon representation of Commd9 COMM domain homodimer compared to the structures of Pur-α repeats (PDB ID 5FGO, 5FGP) (Graebsch et al., 2009; Weber et al., 2016). Pur-α repeat III forms a homodimer similar to Commd9, but possesses an additional β-strand at the N-terminus. Repeats I and II from Pur-α form an intramolecular ‘heterodimer’ that is responsible for binding to DNA (shown in sticks). (B) The structure of the C-terminal domain of the C. pneumoniae Cpn0803 protein (PDB ID 3Q9D) (Stone et al., 2012) is shown in ribbon diagram. The C-terminal domain forms a homodimer similar to the Commd9 COMM domain, but possesses two additional C-terminal α-helices. C. trachomatis protein CT584 has an identical structure (PDB ID 4MLK) (Barta et al., 2013). (C) Side by side view of Commd9 HN domain, and the N-terminal domain of Cpn0803 (residues 8–98) showing the similarity in the overall secondary structure topology. The chlamydial proteins lack helices corresponding to Commd9 α1 and α5 (D) Comparison of the full-length Commd9 structure determined by SAXS and the Cpn0803 crystal structure, highlighting the similarity in their domains and their inter-domain orientations. (E) Ribbon representation of Cpn0803 showing the dimerization (COMM domain-like) module and the trimerisation (HN domain like) domain.