Structure of the transporter associated with antigen processing trapped by herpes simplex virus
- Howard Hughes Medical Institute, The Rockefeller University, United States
- Janelia Research Campus, Howard Hughes Medical Institute, United States
Figures
Figure 1
Cryo-EM reconstruction of the TAP/ICP47 complex.
(A) Stereo views of the overall density map (blue mesh), filtered to 4 Å resolution and sharpened with a B-factor of −150 Å2, for two 180° related views. The TAP/ICP47 model is shown in stick model …
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Figure 1—source data 1
Resolution of the final cryo-EM reconstruction.
FSC values from Frealign between unfiltered reconstructions of two independently refined half data sets indicating the resolution of the reconstruction (FSC).
- https://doi.org/10.7554/eLife.21829.004
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Figure 1—source data 2
Validation of the structure model.
FSC values calculated between the structure model and the half map used for refinement, the other half map, and the full map.
- https://doi.org/10.7554/eLife.21829.005
Figure 2
The structure of TAP trapped by ICP47.
(A) Ribbon representation of the TAP/ICP47 complex. Color code: TAP1 (blue), TAP2 (yellow), ICP47 (magenta) (B) The domain-swapped architecture: TAP1 is shown in ribbon representation, TAP2 and …
Figure 3
The substrate-binding site.
(A) Biochemically identified substrate-binding regions: TAP1 375–420 and 453–487 (blue), TAP2 301–389 and 414–433 (gold). The five residues previously suggested to interact with the substrate (TAP1 …
Figure 4
The interface between TAP and ICP47.
(A) The first 34 residues of ICP47, highlighted in darker magenta, insert into the transmembrane pathway. R34, and the first and last residues of ICP47 resolved in the structure (M1, P55) are …
Figure 5
Sequence alignment of the TAP residues that contact ICP47.
ICP47 inhibits TAP from human, owl monkey, pig, cow and dog (the top five sequences), but not that of rabbit, mouse and rat (the bottom three sequences). Residues contacting ICP47 are colored based …
Figure 6
Structures of three peptide transporters in the ABC family.
(A) Ribbon representations. The two subunits are shown in blue and gold, respectively. ICP47 is colored in magenta. The peptidase domains of PCAT1 observed in the inward-facing conformation are …
Tables
Table 1
Summary of Cryo-EM data.
| Imaging | |
|---|---|
| Microscope | Titan Krios I, 300keV (FEI) |
| Detector | K2 Summit direct electron detector (Gatan) |
| Energy filter | 10 eV (Gatan) |
| Data collection | |
| Pixel size | 1.04 Å |
| Movies | 3875 |
| Frames | 50 |
| Total exposure time | 10 s |
| Exposure time per frame | 0.2 s |
| Total exposure | 74 electrons/Å2 |
| Exposure per frame | 1.48 electrons/Å2/frame |
| Defocus range | −1.5 to −3.5 μm |
| Final reconstruction | |
| Number of particles | 501,973 |
| B-factor correction | −150 Å2 |
Table 2
Reciprocal space refinement statistics
| Space group | P1 |
|---|---|
| Cell dimensions | |
| a, b, c (Å) | 92.5, 116.0, 116.0 |
| α,β,γ (°) | 90.0, 90.0, 90.0 |
| Resolution (Å) | 100.0 - 3.97 |
| Number of residues | |
| TAP1 | 561 |
| TAP2 | 551 |
| ICP47 | 55 |
| R.m.s deviations | |
| Bond lengths (Å) | 0.0070 |
| Bond angles (°) | 0.881 |
| Ramachandran | |
| Favored (%) | 94.3 |
| Allowed (%) | 5.5 |
| Outliers (%) | 0.2 |
