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Atomic-Resolution Structures of the APC/C Subunits Apc4 and the Apc5 N-Terminal Domain.

Cronin NB, Yang J, Zhang Z, Kulkarni K, Chang L, Yamano H, Barford D - J. Mol. Biol. (2015)

Bottom Line: Apc4 comprises a WD40 domain split by a long α-helical domain, whereas Apc5(N) has an α-helical fold.In a separate study, we had fitted these atomic models to a 3.6-Å-resolution cryo-electron microscopy map of the APC/C.We discuss the complementary approaches of high-resolution electron microscopy and protein crystallography to the structure determination of subunits of multimeric complexes.

View Article: PubMed Central - PubMed

Affiliation: Division of Structural Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom.

No MeSH data available.


Related in: MedlinePlus

Apc5 has an N-terminal helical domain (Apc5N) connected by a disordered linker to a TPR superhelix of 13 TPR motifs (Apc5TPR). (a) Cartoon of EM structure of human Apc5 color-ramped from blue to red from N- to C-termini. The small subunit Apc15 that contacts Apc5 is also shown. (b) Stereoview of a superimposition of Apc5N based on human Apc5N EM coordinates (blue) and Xenopus Apc5N X-ray (yellow) coordinates. Major structural differences involve the α1/α2 and α5/α6 loops that contact Apc4.
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f0035: Apc5 has an N-terminal helical domain (Apc5N) connected by a disordered linker to a TPR superhelix of 13 TPR motifs (Apc5TPR). (a) Cartoon of EM structure of human Apc5 color-ramped from blue to red from N- to C-termini. The small subunit Apc15 that contacts Apc5 is also shown. (b) Stereoview of a superimposition of Apc5N based on human Apc5N EM coordinates (blue) and Xenopus Apc5N X-ray (yellow) coordinates. Major structural differences involve the α1/α2 and α5/α6 loops that contact Apc4.

Mentions: Apc5N [residues 27–161 (human Apc5 numbering)] adopts an all α-helical domain architecture comprising seven α-helices (Fig. 6a and Supplementary Fig. 6). Helices α1–α6 pack to create an antiparallel bundle with α1 at the center of the domain almost completely surrounded by helices α2–α6. This α-helical domain is capped by α7, orientated orthogonally to the α-helical domain. The X-ray structure of X. laevis Apc5N was readily docked into the assigned density of the 3.6-Å-resolution EM density map of human APC/CCdh1.Emi1[44] (Supplementary Fig. 2a). A small shift of the loop connecting α5 with α6 accommodates the Apc4–Apc5 interface within the context of the APC/C (Fig. 6b). A larger 6-Å-conformational change involving the loop connecting α1 with α2 and the N-terminus of α2 results from both packing at the Apc4–Apc5 interface and a two-residue insertion within human Apc5 relative to X. laevis Apc5 (Supplementary Fig. 3). Residues 1–26 of Apc5N, predicted to form two α-helices, are disordered in both the crystal structure and the EM density map. No EM density is visible for the loop (residues 170–205) connecting Apc5N with Apc5TPR, and thus, as predicted, this loop is disordered. In the crystal structure, residues 164–168 from the TEV cleavage site continue the α7 helix, similar in structure to α7 of human Apc5N defined in the EM density map. DALI searches [47] revealed weak structural similarity to the RNP assembly factor (Table 1), although the biological significance of this similarity is unclear.


Atomic-Resolution Structures of the APC/C Subunits Apc4 and the Apc5 N-Terminal Domain.

Cronin NB, Yang J, Zhang Z, Kulkarni K, Chang L, Yamano H, Barford D - J. Mol. Biol. (2015)

Apc5 has an N-terminal helical domain (Apc5N) connected by a disordered linker to a TPR superhelix of 13 TPR motifs (Apc5TPR). (a) Cartoon of EM structure of human Apc5 color-ramped from blue to red from N- to C-termini. The small subunit Apc15 that contacts Apc5 is also shown. (b) Stereoview of a superimposition of Apc5N based on human Apc5N EM coordinates (blue) and Xenopus Apc5N X-ray (yellow) coordinates. Major structural differences involve the α1/α2 and α5/α6 loops that contact Apc4.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4590430&req=5

f0035: Apc5 has an N-terminal helical domain (Apc5N) connected by a disordered linker to a TPR superhelix of 13 TPR motifs (Apc5TPR). (a) Cartoon of EM structure of human Apc5 color-ramped from blue to red from N- to C-termini. The small subunit Apc15 that contacts Apc5 is also shown. (b) Stereoview of a superimposition of Apc5N based on human Apc5N EM coordinates (blue) and Xenopus Apc5N X-ray (yellow) coordinates. Major structural differences involve the α1/α2 and α5/α6 loops that contact Apc4.
Mentions: Apc5N [residues 27–161 (human Apc5 numbering)] adopts an all α-helical domain architecture comprising seven α-helices (Fig. 6a and Supplementary Fig. 6). Helices α1–α6 pack to create an antiparallel bundle with α1 at the center of the domain almost completely surrounded by helices α2–α6. This α-helical domain is capped by α7, orientated orthogonally to the α-helical domain. The X-ray structure of X. laevis Apc5N was readily docked into the assigned density of the 3.6-Å-resolution EM density map of human APC/CCdh1.Emi1[44] (Supplementary Fig. 2a). A small shift of the loop connecting α5 with α6 accommodates the Apc4–Apc5 interface within the context of the APC/C (Fig. 6b). A larger 6-Å-conformational change involving the loop connecting α1 with α2 and the N-terminus of α2 results from both packing at the Apc4–Apc5 interface and a two-residue insertion within human Apc5 relative to X. laevis Apc5 (Supplementary Fig. 3). Residues 1–26 of Apc5N, predicted to form two α-helices, are disordered in both the crystal structure and the EM density map. No EM density is visible for the loop (residues 170–205) connecting Apc5N with Apc5TPR, and thus, as predicted, this loop is disordered. In the crystal structure, residues 164–168 from the TEV cleavage site continue the α7 helix, similar in structure to α7 of human Apc5N defined in the EM density map. DALI searches [47] revealed weak structural similarity to the RNP assembly factor (Table 1), although the biological significance of this similarity is unclear.

Bottom Line: Apc4 comprises a WD40 domain split by a long α-helical domain, whereas Apc5(N) has an α-helical fold.In a separate study, we had fitted these atomic models to a 3.6-Å-resolution cryo-electron microscopy map of the APC/C.We discuss the complementary approaches of high-resolution electron microscopy and protein crystallography to the structure determination of subunits of multimeric complexes.

View Article: PubMed Central - PubMed

Affiliation: Division of Structural Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom.

No MeSH data available.


Related in: MedlinePlus