Results for 3j9j
PDB: 3j9j
Gene name: Trpv1
UniProt: TRPV1_RAT
EMD:
emd_5778.gz
EMD-5778
Membrane mimetics: amphipol; DDM, soybean lipids, then prt:amphipols (1:3 ), then detergent was removed and for cryo-EM detergent was replaced by amphiols
EMD-5778
Membrane mimetics: amphipol; DDM, soybean lipids, then prt:amphipols (1:3 ), then detergent was removed and for cryo-EM detergent was replaced by amphiols
Cross-sections at different angles
green: density, gray dots: atoms from the all-atom model, lines: membrane boundaries defined by TMDET
The determined edges at each slice and their comparison to TMDET
dots: edges of the gradient, triangles: outliers,
dashed and solid lines: membrane boundaries defined by TMDET and MemBlob ( mean(Zi) decreased by the thickness of the interface region (8 Å))
[ Download results
Resubmit ]
Manual settings applied
None
Boundary values (averages for MemBlob)
Z (PDBTM) | Z (MemBlob) | Z - 8 | |
End1 | 15.50 | 16.89 | 8.89 |
End0 | -15.50 | -18.44 | -10.44 |
Mapping the results to the structure
You can move/scale/rotate the structure.
Blue: a.a. facing to bulk water;
magenta: interface region;
green: a.a. interacting with the hydrophobic membrane core;
yellow: burried a.a.
red: a.a. with an invisible side chain and non-protein molecules, for which DSSP cannot return SASA
[ Download results
Resubmit ]