TABLE 3.

Proteins co-purifying with cross-linked AP-3 complexes

The table depicts proteins identified by AP-3 immunoaffinity chromatography. ∑ peptides and ∑ Mascot scores corresponds to the sum of all peptides identified and their individual Mascot scores in three MS/MS analyses from two independent purifications. Clathrin binding motifs were identified using gi-defined primary sequences fed into the Eukaryotic Linear Motif (ELM) search engine. Relevant previous proteomes correspond to those of 1) AP-3 microvesicles (18), 2) brain clathrin-coated vesicles (7), 3) HeLa cell clathrin-coated vesicles (8), 4) synaptic vesicles (31), and 5) GTP γS-dependent recruitment of AP-3 to proteoliposomes (30). Clathrin box corresponds to the consensus sequence L(I/V/L/M/F)X(I/V/L/M/F)(D/E).

	Protein	gi no.	∑ peptides	∑ Mascot scores	Clathrin box	Clathrin binding motif WXXW	Previous proteomes
1	Ap3d1 protein	34862288	303	16,302			1, 4, 5
2	Ap3b1 protein	157817716	276	12,454	387LVDVE391		1, 5
					974LLDLD978
					1213LVTVE1217
3	Ap3b2 protein	52317148	247	11,592	228LIDVE232		1, 5
					808LLDLE812
					1046LLTLD1050
4	Ap3m1 protein	1703027	48	2,081	77LFVIE81		3, 5
5	Ap3m2 protein	5803000	23	1,058	77LFVIE81		4, 5
6	Ap3s1 protein	4502861	35	1,659			1, 3, 5
7	Ap3s2 protein	109462206	12	583			4, 5
8	Clathrin heavy chain 1	51491845	27	1,357			2, 3, 5
9	Clathrin light chain a	4502901	2	91			2,3
10	Distrobrevin-binding protein 1	83415179	7	358			1, 3
11	Reduced pigmentation protein	109458315	9	482			3
12	Cappuccino protein	34878563	5	274			3
13	Muted protein	157823988	5	194			1, 3
14	dnaK-type chaperone hsp72/uncoating ATPase	347019	67	3,460	391LLLLD395		1, 2, 4
15	Heat shock protein 1, α/Hsp90	28467005	24	1,270			4
16	Heat shock protein 1, βHsp90	40556608	55	2,741
17	dnaK-type molecular chaperone hst70	92355	13	645	394LLLLD398
18	heat shock 70-kDa protein 5	25742763	6	371	234LLTID238		4
					414LVLLD418
19	Heat shock protein 70	396270	5	254	391LLLLD395
20	Protocadherin 9 isoform 1	62661787	2	66
21	Protocadherin 15	109509982	6	225
22	Phosphatidylinositol 4-kinase type 2 α	16758554	1	46	290LLQFE294	165WTKW168	1, 3, 4
					296LVVLD300
23	ZnT3	8134847	2	86			1, 4
24	Neurotransmitter transporter NTT5	157820661	2	58
25	CKAP4/p63	157823877	6	390
26	Olfactory receptor 598	58801352	2	40
27	Olfactory receptor Olr205	47576839	2	88
28	Annexin II	2143593	6	334			2
29	Tyrosine hydroxylase	6981652	4	176
30	Granuphilin/SYTL4	17385946	1	41		492WTGW495
31	Septin-7	9789726	3	114			2, 4, 5
32	Cytoplasmic dynein intermediate chain 2B	1151093	2	54
33	Dynein, cytoplasmic, light intermediate chain 1	21955134	3	125
34	Dynactin 2	51948450	1	54
35	Dynein, cytoplasmic, heavy polypeptide 1	148491097	33	1,388		2543WSPW2546	2, 4
36	Kinesin family member 21B	157821213	16	262
37	Myosin, heavy polypeptide 9/mFLJ00279 protein	6981236	22	819		825WQWW828
38	Myosin regulatory light chain	228542	6	318
39	Microtubule-associated protein 1B (MAP 1B)	19856246	10	543
40	Intermediate filament protein nestin	2209202	15	527
41	Similar to A-kinase anchor protein 13 isoform 2	157823521	8	184	1435LLCLE1439
42	Casein kinase II, α 1 polypeptide	16758674	8	292			2
43	Calcium/calmodulin-dependent protein kinase II, δ	6978595	4	172
44	Lactate dehydrogenase A	8393706	5	255			2, 4
45	Carbamoyl-phosphate synthetase 2	158534057	10	726
46	Hemoflavoprotein b5/b5r	12007117	7	255
47	Development and differentiation-enhancing factor 2	157823109	7	236
48	Rho guanine nucleotide exchange factor 7	18202066	6	218
49	C9orf86/rbel1/F08G12.1	157819403	23	1,185
50	Hypothetical protein HEAT repeat containing 4	109478489	8	372		687WNDW690
51	E3 ubiquitin-protein ligase NEDD4	32469607	8	392