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.