Results for 5gjv

PDB: 5gjv Gene name: CACNA2D1 UniProt: CA2D1_RABIT EMD: emd_9513.gz
EMD-9513

Membrane mimetics: micelle; digitonin Note: More manual adjustment needed because of the noise level


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))
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Manual settings applied

* end0 around -20 5
* end1 around 25 5
10 end1 around 28 5
130-210 end1 around 30 5

Boundary values (averages for MemBlob)


Z (PDBTM) Z (MemBlob) Z - 8
End1 13.00 27.33 19.33
End0 -13.00 -22.11 -14.11

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
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