AP3M1 bioinformatics: the YxxPhi cargo pocket of the AP-3 mu subunit

Generated by cargo_pocket.py (uv run python cargo_pocket.py). Everything below is computed from live UniProt and RCSB downloads at run time; the heavy-atom contact cutoff is 4.5 A.

Input sequences

protein	accession	length
AP3M1_HUMAN	Q9Y2T2	418
AP3M2_HUMAN	P53677	418
AP2M1_HUMAN	Q96CW1	435
AP1M1_HUMAN	Q9BXS5	423
AP1M2_HUMAN	Q9Y6Q5	423
AP4M1_HUMAN	O00189	453
AP3M1_MOUSE	Q9JKC8	418

Cargo-contacting residues measured from the structures

9C5B - chain M (Q9Y2T2) vs cargo chain Y (`SHAGYQTI`)

All 418 modelled residues of chain M match Q9Y2T2 at their own author-assigned residue number, so the structure is numbered in UniProt coordinates and the positions below can be read directly as sequence positions.

10 residues within 4.5 A of the peptide (modelled chain: 418 residues, numbering 1-418):

E178 (4.44 A), Y180 (2.83 A), F181 (3.7 A), V389 (3.56 A), L392 (3.89 A), F402 (3.71 A), K403 (3.1 A), G404 (3.29 A), V405 (2.8 A), K406 (3.37 A)

1BXX - chain A (Q96CW1) vs cargo chain P (`DYQRLN`)

All 256 modelled residues of chain A match Q96CW1 at their own author-assigned residue number, so the structure is numbered in UniProt coordinates and the positions below can be read directly as sequence positions.

14 residues within 4.5 A of the peptide (modelled chain: 256 residues, numbering 159-435):

F174 (3.75 A), L175 (3.69 A), D176 (2.43 A), K203 (2.84 A), V401 (3.78 A), R402 (2.78 A), Y403 (3.99 A), L404 (3.76 A), V418 (4.15 A), I419 (3.72 A), K420 (2.56 A), W421 (3.06 A), V422 (2.67 A), R423 (3.13 A)

AP2M1 cargo-pocket positions mapped onto the other mu subunits

AP2M1 pos	AP3M1	AP3M2	AP1M1	AP1M2	AP4M1	AP3M1 (mouse)
F174	Y180	Y180	F172	F172	F188	Y180
L175	F181	F181	L173	I173	L189	F181
D176	D182	D182	D174	D174	D190	D182
K203	C209	C209	R201	K201	K217	C209
V401	V389	V389	V392	V392	V421	V389
R402	N390	N390	R393	R393	R422	N390
Y403	R391	R391	Y394	Y394	F423	R391
L404	L392	L392	L395	M395	L424	L392
V418	P401	P401	A405	A405	-	P401
I419	F402	F402	L406	L406	-	F402
K420	K403	K403	P407	P407	K438	K403
W421	G404	G404	W408	W408	W439	G404
V422	V405	I405	V409	V409	V440	V405
R423	K406	K406	R410	R410	R441	K406

protein	aligned to a residue	identical to AP2M1
AP3M1_HUMAN	14/14	5/14
AP3M2_HUMAN	14/14	4/14
AP1M1_HUMAN	14/14	10/14
AP1M2_HUMAN	14/14	9/14
AP4M1_HUMAN	12/14	11/14
AP3M1_MOUSE	14/14	5/14

Do the two pockets coincide?

AP3M1 residues contacting the LAMP1 peptide in 9C5B: 10. AP2M1 pocket positions projected onto AP3M1 by alignment: 14. Overlap: 9 residues ([180, 181, 389, 392, 402, 403, 404, 405, 406]).

AP3M1 residues in the overlap: Y180, F181, V389, L392, F402, K403, G404, V405, K406

AP3M1 LAMP1-contacting residues not in the projected AP2M1 pocket: E178

What this shows

The AP-3 medium subunit carries a cargo-binding site: 10 AP3M1 residues contact the bound LAMP1 YxxPhi peptide in the human AP-3 cryo-EM structure.
It is the same site as the AP-2 one: 9 of those 10 residues fall on alignment columns that are also AP2M1 cargo-pocket positions in the mu2/TGN38 crystal structure.
The site is structurally conserved but chemically divergent: AP3M1 is identical to AP2M1 at only 5 of 14 pocket positions while aligning to a residue at 14 of 14, which is the structural basis for the different YxxPhi preferences of the mu subunits.
Mouse Ap3m1 matches human AP3M1 at 14 of 14 of these positions, so the ISS/IEA transfers GOA makes from mouse Ap3m1 to AP3M1 are not crossing a diverged cargo-binding site.