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Table 1 Proteins recruited by the SH3 domains of Ruk/CIN85 identified by LC-MS/MS and classified according to modular architectures.

From: Proteins recruited by SH3 domains of Ruk/CIN85 adaptor identified by LC-MS/MS

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

  1. 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.