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. 2013 May 7;21(5):854-60.
doi: 10.1016/j.str.2013.03.001. Epub 2013 Apr 4.

Molecular organization and ATP-induced conformational changes of ABCA4, the photoreceptor-specific ABC transporter

Yaroslav Tsybovsky  1 , Tivadar Orban, Robert S Molday, Derek Taylor, Krzysztof Palczewski
Affiliations

Molecular organization and ATP-induced conformational changes of ABCA4, the photoreceptor-specific ABC transporter

Yaroslav Tsybovsky et al. Structure. .

Abstract

ATP-binding cassette (ABC) transporters use ATP to translocate various substrates across cellular membranes. Several members of subfamily A of mammalian ABC transporters are associated with severe health disorders, but their unusual complexity and large size have so far precluded structural characterization. ABCA4 is localized to the discs of vertebrate photoreceptor outer segments. This protein transports N-retinylidene-phosphatidylethanolamine to the outer side of disc membranes to prevent formation of toxic compounds causing macular degeneration. An 18 Å-resolution structure of ABCA4 isolated from bovine rod outer segments was determined using electron microscopy and single-particle reconstruction. Significant conformational changes in the cytoplasmic and transmembrane regions were observed upon binding of a nonhydrolyzable ATP analog and accompanied by altered hydrogen/deuterium exchange in the Walker A motif of one of the nucleotide-binding domains. These findings provide an initial view of the molecular organization and functional rearrangements for any member of the ABCA subfamily of ABC transporters.

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Figures

Figure 1
Figure 1
Structure of ABCA4 determined by EM. (A) Untilted (left) and 45° tilted (right) EM micrographs of uranyl acetate-stained ABCA4. The tilt axis is marked with an arrow. Examples of ABCA4 particles forming tilt pairs are enclosed in circles and marked with numbers. TMV: tobacco mosaic virus. (B) Examples of two dimensional (2D) class averages generated using untilted particles. (C) Angular views of the RCT model of ABCA4. (D) Angular views of the final ABCA4 structure filtered to 19 Å resolution. A cross-section with the exposed internal cavity (marked with an arrow) is shown for the 135° view. See also Figure S1 in Supplemental Information.
Figure 2
Figure 2
Identification of intradiscal regions of ABCA4. (A) A topological model of ABCA4 based on published evidence (Bungert et al., 2001; Tsybovsky et al., 2011). ATP-binding Walker A motifs located in NBDs are colored red. Glycosylation sites are shown with stars and phosphorylation sites with brown spheres. A disulfide bridge between ECD1 and ECD2 (Bungert et al., 2001) is marked S-S. (B) Examples of ABCA4 particles with one (top row) or two (bottom row) bound molecules of succinylated ConA (53 kDa in size). ConA particles are marked with white arrows. (C) Examples of 2D class averages of the ABCA4-ConA complex. ConA molecules bound exclusively to the ‘handle’ and linker regions of ABCA4, identifying them as ECDs. (D) A 3D reconstruction of the ABCA4-ConA complex illustrating positions of three ConA binding sites (black arrows). (E) The EM model of ABCA4 with assigned ECDs, TMDs and CDs. The proposed Amphipol belt around the TM region is colored in cyan. Grey rectangle represents the anticipated position of the lipid bilayer. See also Figure S2 in Supplemental Information.
Figure 3
Figure 3
Global and local conformational changes in ABCA4 induced by binding of AMPPNP. (A) Angular views of the ABCA4 structure determined in the presence of AMPPNP. The structure was filtered to 19 Å resolution. (B) Views of ligand-free (tan) and AMPPNP-bound (light-blue) EM maps of ABCA4 with the front surface cut away to expose the internal cavity. Lines indicate the suggested position of the membrane. (C) Deuterium uptake by the Walker A ATP-binding motif of NBD1 (left) and NBD2 (right) in the absence (black) and presence (red) of AMPPNP. Addition of AMPPNP decreased the uptake in NBD2, but not NBD1. Data are represented as mean +/− SD. The statistically significant difference (p=5.5·10−7) is marked with an asterisk. (D) In silico models of NBD1 (left) and NBD2 (right) with peptides showing no changes versus significant changes in deuterium uptake upon addition of AMPPNP shown in blue and red, respectively. ATP molecules (pink) were positioned for illustration purposes based on the superimposed crystal structure of a homologous NBD domain (PDB code 3FVQ). See also Figure S3, movie S1 and Table S1 in Supplemental Information.
Figure 4
Figure 4
A hypothetical model of ABCA4 transport composed of four principle stages (marked 1–4). N-retinyidene-PE is shown as a green oval, whereas ATP and ADP are represented with red and yellow circles, respectively. The TM region is colored dark-blue. Binding of ATP by NBD2 (stage 2) induces a tighter contact between the CDs, which is associated with rearrangements in the TM region that lead to substrate translocation. The rectangle encompasses the two stages of the transport cycle visualized in this study, assuming that binding of N-retinyidene-PE by itself does not induce global conformational changes. See also Figure S4 in Supplemental Information.
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