Table 1

Table 1
Proteins recruited by the SH3 domains of Ruk/CIN85 identified by LC-MS/MS and classified according to modular architectures.
GI	Name	Score	Mr	u.p.	% c.	A	B	C	c.s.	k/n	Modules/domains

1. Proteins with lipid interaction modules

1.a. with lipid and protein interaction modules
gi\|74132096	Tks4	720	101847	21	27	•	•	•	•		PX, SH3, SH3, PR, SH3
gi\|38424073	LL5α	445	152038	8	6	•	•	•	•		FHA, CC, CC, CC, CC, CC, CC, PH
gi\|19923493	PEPP-2	326	128012	8	9			•			WW, WW, PH, CC, CC
gi\|31657094	Anillin	280	125490	9	9	•	•	•	•		CC, PH
gi\|3023207	3BP-2	160	62660	3	10	•			•	•	PH, PR, SH2
gi\|82581557	Lamellipodin	142	141762	3	3	•			•		CC, RA, PH, PR, Paxillin, Paxillin, Paxillin
gi\|84029396	LL5β	128	142812	5	4	•	•	•	•		CC, CC, CC, CC, CC, PH
1.b. with lipid interaction modules and GAP activity
gi\|54860079	RICH1	1153	95776	26	44	•	•	•	•	•	BAR, RhoGAP, PR
gi\|92091600	ARAP1	481	163743	13	10	•	•	•	•		SAM, PR, PH, PH, ArfGAP, PH, PH, RhoGAP, RA, PH
gi\|119370361	ASAP1	202	126363	6	6	•	•	•	•	•	BAR, PH, ArfGAP, Ank, PR, SH3
gi\|21361397	MgcRacGAP	157	71666	3	6			•			RGS, CC, C1, RhoGAP
gi\|42475970	SYDE1	127	80428	2	3			•	•		PR, CaLB, RhoGAP
gi\|4758808	RASAL2	64	129618	2	2			•	•		PH, CaLB, RhoGAP/RasGAP, CC
1.c. with lipid interaction modules and GTPase activity
gi\|56549121	Dynamin 2	1002	98345	13	24	•		•	•		Dynamin GTPase, Dynamin central, PH, GED, PR
gi\|59853099	Dynamin 1	559	97746	9	18	•		•	•		Dynamin GTPase, Dynamin central, PH, GED, PR

2. Proteins with protein interaction modules
2.a. with actin-binding modules
gi\|31324577	MIRab13	494	94352	10	13	•	•	•	•		CH, Znf-LIM, PR, CC, CC
gi\|51702526	N-WASP	411	55192	14	31	•		•	•		EVH1, PBD/CRIB, PR, WH2, WH2
gi\|19923777	GAR22	366	73328	5	10	•			•		CH, GAS2, PR
gi\|60416429	WIP	295	51300	8	20	•		•	•		WH2, PR
gi\|55741671	LIMCH1	271	122788	6	7	•	•		•		CH, CC, CC, CC, Znf-LIM
gi\|18959210	WIRE	196	46317	5	14	•		•	•		WH2, PR
gi\|48428650	Synaptopodin	173	99915	4	6	•		•	•		Synaptopodin, PR
2.b. with MT-binding modules
gi\|20143967	MKLP-1	304	111016	6	8	•	•	•			Kinesin, CC
gi\|20455500	MAP4	284	121457	10	12	•		•			Tau
gi\|4505101	E-MAP-115	152	84116	3	5		•			•	CC, PR, E-MAP-115
gi\|4506039	PRC1	128	72304	4	7	•					MAP65/ASE1
gi\|39963533	MAP7D3	102	90256	2	2		•			•	CC, CC, CC, E-MAP-115
2.c. with modules involved in MT nucleation
gi\|5453660	GCP3	513	104304	10	16	•			•	•	Spc97/Spc98, CC
gi\|5729840	GCP2	275	103096	5	6	•			•	•	CC, Spc97/Spc98
gi\|38454194	GCP4	71	76483	3	4				•		Spc97/Spc98
2.d. with GTP/protein interaction modules
gi\|6683817	Septin 9	1357	65614	22	43	•	•	•	•		Septin
gi\|4758158	Septin 2	711	41679	9	32	•		•			Septin, CC
gi\|8922712	Septin 11	553	49652	8	32	•	•	•			Septin, CC
gi\|57209157	Septin 6	388	49614	3	20	•	•	•			Septin, CC, CC
gi\|21945064	Septin 10	328	53016	8	25	•	•	•			Septin, CC
gi\|67472677	Septin 7	202	50933	6	12	•	•	•	•		Septin, CC, CC
gi\|45645200	Septin 8	173	56234	3	16	•	•	•			Septin, CC, CC
2.e. other with protein interaction modules
gi\|19920317	CKAP4	846	66097	17	35		•	•	•		PR, TM, Spectrin, CC, CC, CC, STAT, CC
gi\|12644198	CDC27	500	92893	10	18		•	•	•		TPR, TPR, TPR, TPR, TPR, TPR, TPR, CC, TPR
gi\|13375926	Vps37B	299	31345	4	22	•	•	•	•		Modr, PR
gi\|38045892	ELKS	296	113964	8	9	•		•			CC, CC, CC, CC, CC, Prf, Prf, CC, CC, CC, CC, CC
gi\|116241251	APC7	278	63720	4	10		•	•			TPR, TPR, TPR, TPR
gi\|46255026	KCTD3	272	89613	7	11	•	•	•			BTB/POZ, WD40, WD40, WD40
gi\|37537859	APC8	239	69040	4	10		•	•			TPR, TPR, TPR, TPR, TPR, TPR
gi\|119577384	Sb1	234	58997	5	11	•	•	•	•	•	WD40, WD40, WD40
gi\|62751805	SH3D19	222	86713	5	7	•	•	•	•		PR, SH3, SH3, SH3, SH3, SH3
gi\|37537862	APC4	215	92789	5	7		•	•			WD40
gi\|63054866	CARMIL	212	148193	4	3	•	•		•		LRR, LRR, CC
gi\|8923243	Palmdelphin	184	62777	3	7	•	•	•	•		CC, CC, CC, Paralemmin
gi\|26454712	SLAIN2	172	62773	3	9	•		•			CC
gi\|24308440	CFBP	165	29107	2	10	•			•	•	PR
gi\|112734870	LOC57648	161	113392	4	6	•		•	•		PR
gi\|6424942	AIP1	154	96646	2	3	•	•		•	•	BRO1, CC, CC, PR
gi\|20127553	APC5	147	85707	3	5			•			TPR, TPR
gi\|31044432	hLEM2	136	57339	3	7		•		•		LEM, TM, TM
gi\|4758116	Dystroglycan 1	134	97862	2	3			•	•		Cadherin, Ig-like, Cadherin, PR, TM, PR
gi\|38173707	BAT2	132	229181	3	2	•		•			BAT2, PR, CC, PR
gi\|83779014	Katanin p80	128	73257	2	5	•		•	•		WD40, WD40, WD40, WD40, WD40, WD40, PR
gi\|14249168	DDA3	127	35725	3	12	•	•	•	•		CC, PR
gi\|13994353	KCTD10	120	35809	2	8		•		•		BTB/POZ
gi\|4503251	Dab2	113	82511	3	4			•	•	•	PTB/PID, PR, PfkB
gi\|116242719	POM121	113	125382	2	3	•		•	•		PR
gi\|6005830	Plakophilin 3	111	87485	2	4	•			•		Arm, Arm, Arm
gi\|115392150	FAM83G	109	91064	3	3		•		•		DUF1669, PR
gi\|10334526	WTAP	107	43557	2	6			•			CC, CC, CC, CC
gi\|5533375	APC6	96	66575	2	4		•				TPR, TPR, TPR
gi\|44917604	srGAP1	94	125099	2	1	•		•	•		CC, FCH, CC, RhoGAP, SH3, CC
gi\|52000732	Atx2	88	140681	2	2	•			•	•	PR, CC, Like-Sm, Atx2, PR, CC, PAM2, PR
gi\|24850113	SHCBP1	72	76669	2	3			•			Pbh1, Pbh1, Pbh1, Pbh1, Pbh1, CC

3. Proteins with nucleic acid interaction modules
3.a. with RNA-binding modules
gi\|118572613	SRm300	602	300179	11	5	•		•	•		Cwf21, PR, atypical RNA-binding motif
gi\|5730027	Sam68	431	48311	8	21	•	•	•	•		PR, KH, PR
gi\|14165437	hnRNPK	236	51281	5	17			•	•		ROK, KH, KH, PR, KH
gi\|4504715	PABPC4	136	71080	3	4	•		•	•		RRM, RRM, RRM, CC, RRM, PABP/HYD
gi\|119612222	PABPC1	136	47647	3	10	•		•			RRM, RRM, RRM, RRM, PABP/HYD
gi\|13937888	hnRNPC	128	33635	3	12	•			•		RRM, CC, CC
gi\|72534660	9G8	118	27578	2	8	•					RRM, Znf-CCHC
3.b. with RNA/DNA-binding modules
gi\|46852388	CARP1	655	133423	8	9	•		•	•		CSP, CC, SAP, CC, CC, CC
gi\|42542379	SRm160	209	102331	6	9	•		•	•		PWI, CC, PR, PR, CC
gi\|23510448	MCM5	150	83301	4	7		•				OB-fold, MCM
gi\|115430211	PHACTR4	127	78391	2	4	•		•	•		RPEL, PR, RPEL, Sigma3/Sigma4, RPEL
gi\|4506583	RP-A	102	68723	2	3		•		•		OB-fold, OB-fold, OB-fold, OB-fold
3.c. with RNA/protein-binding modules
gi\|24638431	Caskin 2	357	127204	10	11	•	•	•	•		ANK, ANK, ANK, ANK, ANK, ANK, SH3, SAM, SAM, PR
gi\|39930517	Atherin	79	56189	2	5			•	•		PR, SAM
gi\|29294627	Liprin β1	61	113680	2	2		•				CC, CC, Intergase, CC, SAM, SAM, SAM
3.d. with DNA-binding modules
gi\|4050036	LEDGF	488	60093	8	19		•	•	•		PWWP, AT-hook, AT-hook, AT-hook, CC, TFS2N
gi\|33872239	C14orf43	138	112905	3	3		•	•	•		PR, ELM2, SANT
gi\|37693995	KLF13	77	31617	2	8			•	•		PR, Znf-C2H2, Znf-C2H2, Znf-C2H2
gi\|42544179	CIZ1	74	101066	2	3			•	•		CC, Znf-C2H2, Znf-C2H2, CC, Znf-C2H2

4. Proteins with enzymatic activities
4.a. with inositol 5'-phosphatase activity
gi\|4755142	SHIP2	726	139297	17	17	•		•	•		SH2, IPP, PR, SAM
gi\|26190608	Synaptojanin 2	697	166575	22	17	•	•	•	•	•	Synaptojanin, IPP, RRM, PR
gi\|8134730	Synaptojanin 1	100	174378	3	2			•	•	•	Synaptojanin, IPP, RRM, PR
4.b. with protein kinase activity
gi\|62362414	c-Abl	241	123595	6	9	•	•	•	•		SH3, SH2, Tyr kinase, F-actin binding
gi\|68303575	CKIa	237	42195	4	14		•				Ser/Tre kinase
gi\|4506735	S6K a4	144	86122	3	5	•			•		Ser/Tre kinase, Ser/Tre kinase
gi\|5453860	PCTAIRE-1	116	55909	3	8		•	•			Ser/Tre kinase
4.c. with E3 ubiquitin ligase activity
gi\|52426745	c-Cbl	353	100881	9	15	•		•	•	•	Cbl N, EF, SH2, Znf-RING, PR, UBA
gi\|116734704	IRF2-BP2	311	61728	5	16	•		•	•		Znf-RING
gi\|862407	Cbl-b	298	110893	8	11	•	•	•	•	•	Cbl N, EF, SH2, Znf-RING, PR, UBA
gi\|24308115	IRF2-BP1	211	62561	3	5	•			•		Znf-RING
4.d. with other ensymatic activities
gi\|4503351	MCMT	286	185388	9	6			•	•		DMAP1, CC, Znf-CXXC, BAH, BAH, DNMT
gi\|47678395	DDX17	269	73138	6	12	•		•	•		Q motif, helicase N, helicase C, PR
gi\|5901990	Katanin p60	148	56214	3	7	•	•	•	•		AAA ATPase, Vps4
gi\|4757810	ATP synthase a	108	59828	3	6		•	•			F1 ATPase N, F1 AAA ATPase, F1 ATPase C
gi\|42476028	ATAD3A	100	71598	3	4		•				CC, CC, CC, CC, AAA ATPase
gi\|8922976	DDX28	88	59743	2	4		•		•		Q motif, helicase N, helicase C

5. Other proteins
gi\|20127556	GTSE-1	176	77081	4	8	•	•		•		none
gi\|47124471	Colligin	113	46525	2	6		•				Serpin, ER-targeting

GI – protein genbank identifier; Name – short protein name; Score – Mascot protein score; Mr – protein molecular weight; u.p. – number of unique peptides matched to protein sequence; % c. – % of protein sequence covered by matched peptides. Dots in columns A, B, or C indicate that protein was recruited by SH3A, SH3B and/or SH3C domains respectively. Dot in column c.s. indicates presence of potential recognition consensus site for the SH3 domains of Ruk/CIN85 in identified protein. Dot in column k/n indicates that identified protein was previously known to interact with Ruk/CIN85 adaptor. The short names of modules found in identified proteins are listed in column Modules/domains. Long names of modules/domain abbreviations are listed in the Additional file 3.
Havrylov et al. Proteome Science 2009 7:21 doi:10.1186/1477-5956-7-21