The trimeric structures of PPNDS-bound (A) and PPADS-bound (B) pdP2X7, viewed parallel to the membrane. The PPNDS and PPADS molecules are shown as spheres. Each subunit of the trimers is colored …
(A–B) Representative current traces from patch-clamp recordings of pdP2X7. Effects of 10 µM PPNDS (blue) on the 1 mM ATP-evoked (orange) current of pdP2X7 (A). Effects of 100 µM PPADS (blue) on the …
Numerical data for Figure 1—figure supplement 1C and D.
(A) The gold-standard Fourier shell correlation curves for the PPNDS-bound data. (B) Angular particle distribution. The heat map of particle projections in each viewing angle. (C) The side view, a …
Before applying C3 symmetry, all steps including 3D classification were performed in Relion 3.1. With C3 symmetry, further refinement using cryoSPARC v4.2.1 by non-uniform refinement of this final …
(A) The gold-standard Fourier shell correlation curves for the PPADS-bound data. (B) Angular particle distribution. The heat map of particle projections in each viewing angle. (C) The side view, a …
Before applying C3 symmetry, all steps including 3D classification were performed in Relion 3.1. With C3 symmetry, further refinement using cryoSPARC v4.2.1 by non-uniform refinement of this final …
(A) The P2X7 protomer in cartoon representation. Each structural feature is colored according to the dolphin model. (B, C) Superposition of the …
(A, B) Overall structure (A) and close-up view of the PPNDS binding site (B) in the PPNDS-bound panda P2X7 (pdP2X7) structure. PPNDS molecules are shown by stick models. Water molecules are depicted …
(A, B) Close-up views of the PPNDS (A) and PPADS (B) binding sites. Dotted lines represent hydrogen bonds. The EM density maps for the residues involved in the PPNDS and PPADS interactions are shown …
(A, B) The plots of the root mean square deviations (RMSD) of Cα atoms (A) and the RMSD values of atoms in PPNDS (B).
Numerical data for Figure 2—figure supplement 2A, B.
(A, B) Overall structure (A) and close-up view of the PPADS binding site (B) in the PPADS-bound panda P2X7 (pdP2X7) structure. PPADS molecules are shown by stick models. Water molecules are depicted …
(A) Overall structure and close-up view of the ATP-bound rat P2X7 structure (PDB ID: 6U9W). The cytoplasmic domain is not shown. Dotted black lines indicate hydrogen bonding. (B) Sequence alignment …
(A) Superposition of the ATP-bound rP2X7 structure (red, PDB ID: 6U9W) and the pyridoxal-5'-phosphate-6-(2'-naphthylazo-6'-nitro-4',8'-disulfonate) (PPNDS)-bound panda P2X7 (pdP2X7) structure …
(A) Superimposition of the pyridoxal-5'-phosphate-6-(2'-naphthylazo-6'-nitro-4',8'-disulfonate) (PPNDS)-bound and pyridoxal phosphate-6-azophenyl-2′,5′-disulfonic acid (PPADS)-bound structures in …
Numerical data for Figure 6B–D.
(A–C) Representative current traces from patch-clamp recordings of P2X receptors. Effects of 10 µM PPNDS (blue) on the 1 mM ATP-evoked (orange) current of panda P2X7 (pdP2X7) mutants (A). Effects of …
PdP2X7 w. PPNDS (EMD-36671) (PDB: 8JV8) | PdP2X7 w. PPADS (EMD-36670) (PDB: 8JV7) | |
---|---|---|
Data collection and processing | ||
Magnification | ×29,000 | ×29,000 |
Voltage (kV) | 300 | 300 |
Electron exposure (e–/Å2) | 50 | 50 |
Defocus range (μm) | –1.3 to –2.0 | –1.3 to –2.0 |
Pixel size (Å) | 0.83 | 0.83 |
Symmetry imposed | C3 | C3 |
Initial particle images (no.) | 663,674 | 236,753 |
Final particle images (no.) | 121,008 | 161,188 |
Map resolution (Å) | 3.34 | 3.60 |
FSC threshold | 0.143 | 0.143 |
Map resolution range (Å) | 1.9–40.4 | 2.2–10.2 |
Refinement | ||
Initial model used (PDB code) | This study | This study |
Model resolution (Å) | 3.34 | 3.60 |
FSC threshold | 0.143 | 0.143 |
Model resolution range (Å) | 1.9–40.4 | 2.2–10.2 |
Map sharpening B factor (Å2) | –50 | –150 |
Model composition | ||
Non-hydrogen atoms | 7245 | 7245 |
Protein residues | 963 | 960 |
Ligands | NAG:6, PPNDS:3 | NAG:6, PPADS:3 |
B factors (Å2) | ||
Protein | 148.30 | 117.36 |
Ligand | 189.65 | 146.40 |
R.m.s. deviations | ||
Bond lengths (Å) | 0.014 | 0.003 |
Bond angles (°) | 1.257 | 0.561 |
Validation | ||
MolProbity score | 2.51 | 1.70 |
Clashscore | 13.86 | 9.04 |
Poor rotamers (%) | 3.70 | 1.22 |
Ramachandran plot | ||
Favored (%) | 93.50 | 97.17 |
Allowed (%) | 6.39 | 2.83 |
Disallowed (%) | 0.1 | 0 |