[1] Adams-Cioaba, M.A., Guo, Y., Bian, C., Amaya, M.F., Lam, R., Wasney, G.A., Vedadi, M., Xu, C., and Min, J. (2010). Structural studies of the tandem Tudor domains of fragile X mental retardation related proteins FXR1 and FXR2. PLoS One 5, e13559.21072162
[2] Adams-Cioaba, M.A., and Min, J. (2009). Structure and function of histone methylation binding proteins. Biochemistry and cell biology= Biochimie et biologie cellulaire 87, 93–105 .
[3] Andrade, M.A., Perez-Iratxeta, C., and Ponting, C.P. (2001). Protein repeats: structures, functions, and evolution. J Struct Biol 134, 117–131 .11551174
[4] Ang, X.L., and Wade Harper, J. (2005). SCF-mediated protein degradation and cell cycle control. Oncogene 24, 2860–2870 .15838520
[5] Angers, S., Li, T., Yi, X., MacCoss, M.J., Moon, R.T., and Zheng, N. (2006). Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery. Nature 443, 590–593 .16964240
[6] Bergametti, F., Bianchi, J., and Transy, C. (2002). Interaction of hepatitis B virus X protein with damaged DNA-binding protein p127: structural analysis and identification of antagonists. J Biomed Sci 9, 706–715 .12432237
[7] Brohawn, S.G., Partridge, J.R., Whittle, J.R., and Schwartz, T.U. (2009). The nuclear pore complex has entered the atomic age. Structure 17, 1156–1168 .19748337
[8] Cao, R., Wang, L., Wang, H., Xia, L., Erdjument-Bromage, H., Tempst, P., Jones, R.S., and Zhang, Y. (2002). Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039–1043 .
[9] Cao, R., and Zhang, Y. (2004). The functions of E(Z)/EZH2-mediated methylation of lysine 27 in histone H3. Curr Opin Genet Dev 14, 155–164 .15196462
[10] Cardozo, T., and Pagano, M. (2004). The SCF ubiquitin ligase: insights into a molecular machine. Nat Rev Mol Cell Biol 5, 739–751 .15340381
[11] Chan, D.W., Wang, Y., Wu, M., Wong, J., Qin, J., and Zhao, Y. (2009). Unbiased proteomic screen for binding proteins to modified lysines on histone H3. Proteomics 9, 2343–2354 .19337993
[12] Chen, X., Zhang, Y., Douglas, L., and Zhou, P. (2001). UV-damaged DNA-binding proteins are targets of CUL-4A-mediated ubiquitination and degradation. J Biol Chem 276, 48175–48182 .11673459
[13] Couture, J.F., Collazo, E., and Trievel, R.C. (2006). Molecular recognition of histone H3 by the WD40 protein WDR5. Nat Struct Mol Biol 13, 698–703 .16829960
[14] Czermin, B., Melfi, R., McCabe, D., Seitz, V., Imhof, A., and Pirrotta, V. (2002). Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell 111, 185–196 .12408863
[15] English, C.M., Adkins, M.W., Carson, J.J., Churchill, M.E., and Tyler, J.K. (2006). Structural basis for the histone chaperone activity of Asf1. Cell 127, 495–508 .17081973
[16] Eryilmaz, J., Pan, P., Amaya, M.F., Allali-Hassani, A., Dong, A., Adams-Cioaba, M.A., Mackenzie, F., Vedadi, M., and Min, J. (2009). Structural studies of a four-MBT repeat protein MBTD1. PLoS One 4, e7274.19841675
[17] Feng, Q., and Zhang, Y. (2003). The NuRD complex: linking histone modification to nucleosome remodeling. Curr Top Microbiol Immunol 274, 269–290 .12596911
[18] Fong, H.K., Hurley, J.B., Hopkins, R.S., Miake-Lye, R., Johnson, M.S., Doolittle, R.F., and Simon, M.I. (1986). Repetitive segmental structure of the transducin beta subunit: homology with the CDC4 gene and identification of related mRNAs. Proc Natl Acad Sci U S A 83, 2162–2166 .3083416
[19] Gao, Z., Huang, Z., Olivey, H.E., Gurbuxani, S., Crispino, J.D., and Svensson, E.C. (2010). FOG-1-mediated recruitment of NuRD is required for cell lineage re-enforcement during haematopoiesis. EMBO J 29, 457–468 .20010697
[20] Gaudet, R., Bohm, A., and Sigler, P.B. (1996). Crystal structure at 2.4 angstroms resolution of the complex of transducin betagamma and its regulator, phosducin. Cell 87, 577–588 .8898209
[21] Groisman, R., Polanowska, J., Kuraoka, I., Sawada, J., Saijo, M., Drapkin, R., Kisselev, A.F., Tanaka, K., and Nakatani, Y. (2003). The ubiquitin ligase activity in the DDB2 and CSA complexes is differentially regulated by the COP9 signalosome in response to DNA damage. Cell 113, 357–367 .12732143
[22] Guerrero-Santoro, J., Kapetanaki, M.G., Hsieh, C.L., Gorbachinsky, I., Levine, A.S., and Rapi?-Otrin, V. (2008). The cullin 4B-based UV-damaged DNA-binding protein ligase binds to UV-damaged chromatin and ubiquitinates histone H2A. Cancer Res 68, 5014–5022 .18593899
[23] Guo, Y., Nady, N., Qi, C., Allali-Hassani, A., Zhu, H., Pan, P., Adams-Cioaba, M.A., Amaya, M.F., Dong, A., Vedadi, M., (2009). Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2. Nucleic Acids Res 37, 2204–2210 .19233876
[24] Han, Z., Guo, L., Wang, H., Shen, Y., Deng, X.W., and Chai, J. (2006). Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5. Mol Cell 22, 137–144 .16600877
[25] Hansen, K.H., Bracken, A.P., Pasini, D., Dietrich, N., Gehani, S.S., Monrad, A., Rappsilber, J., Lerdrup, M., and Helin, K. (2008). A model for transmission of the H3K27me3 epigenetic mark. Nat Cell Biol 10, 1291–1300 .18931660
[26] Hao, B., Oehlmann, S., Sowa, M.E., Harper, J.W., and Pavletich, N.P. (2007). Structure of a Fbw7-Skp1-cyclin E complex: multisite-phosphorylated substrate recognition by SCF ubiquitin ligases. Mol Cell 26, 131–143 .17434132
[27] Hardwick, K.G., Johnston, R.C., Smith, D.L., and Murray, A.W. (2000). MAD3 encodes a novel component of the spindle checkpoint which interacts with Bub3p, Cdc20p, and Mad2p. J Cell Biol 148, 871–882 .10704439
[28] Hattendorf, D.A., Andreeva, A., Gangar, A., Brennwald, P.J., and Weis, W.I. (2007). Structure of the yeast polarity protein Sro7 reveals a SNARE regulatory mechanism. Nature 446, 567–571 .17392788
[29] He, Y.J., McCall, C.M., Hu, J., Zeng, Y., and Xiong, Y. (2006). DDB1 functions as a linker to recruit receptor WD40 proteins to CUL4-ROC1 ubiquitin ligases. Genes Dev 20, 2949–2954 .17079684
[30] Higa, L.A., Wu, M., Ye, T., Kobayashi, R., Sun, H., and Zhang, H. (2006). CUL4-DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation. Nat Cell Biol 8, 1277–1283 .17041588
[31] Hu, J., McCall, C.M., Ohta, T., and Xiong, Y. (2004). Targeted ubiquitination of CDT1 by the DDB1-CUL4A-ROC1 ligase in response to DNA damage. Nat Cell Biol 6, 1003–1009 .15448697
[32] Jennings, B.H., Pickles, L.M., Wainwright, S.M., Roe, S.M., Pearl, L.H., and Ish-Horowicz, D. (2006). Molecular recognition of transcriptional repressor motifs by the WD domain of the Groucho/TLE corepressor. Mol Cell 22, 645–655 .16762837
[33] Jin, J., Cardozo, T., Lovering, R.C., Elledge, S.J., Pagano, M., and Harper, J.W. (2004). Systematic analysis and nomenclature of mammalian F-box proteins. Genes Dev 18, 2573–2580 .15520277
[34] Johnston, C.A., Kimple, A.J., Giguère, P.M., and Siderovski, D.P. (2008). Structure of the parathyroid hormone receptor C terminus bound to the G-protein dimer Gbeta1gamma2. Structure 16, 1086–1094 .18611381
[35] Kirchhausen, T., and Harrison, S.C. (1981). Protein organization in clathrin trimers. Cell 23, 755–761 .7226229
[36] Lambright, D.G., Sondek, J., Bohm, A., Skiba, N.P., Hamm, H.E., and Sigler, P.B. (1996). The 2.0 A crystal structure of a heterotrimeric G protein. Nature 379, 311–319 .8552184
[37] Larsen, N.A., Al-Bassam, J., Wei, R.R., and Harrison, S.C. (2007). Structural analysis of Bub3 interactions in the mitotic spindle checkpoint. Proc Natl Acad Sci U S A 104, 1201–1206 .17227844
[38] Lejon, S., Thong, S.Y., Murthy, A., AlQarni, S., Murzina, N.V., Blobel, G.A., Laue, E.D., and Mackay, J.P. (2011). Insights into association of the NuRD complex with FOG-1 from the crystal structure of an RbAp48·FOG-1 complex. J Biol Chem 286, 1196–1203 .21047798
[39] Lens, S.M., Wolthuis, R.M., Klompmaker, R., Kauw, J., Agami, R., Brummelkamp, T., Kops, G., and Medema, R.H. (2003). Survivin is required for a sustained spindle checkpoint arrest in response to lack of tension. EMBO J 22, 2934–2947 .12805209
[40] Letunic, I., Doerks, T., and Bork, P. (2009). SMART 6: recent updates and new developments. Nucleic Acids Res 37, D229–D232 .18978020
[41] Li, D., and Roberts, R. (2001). WD-repeat proteins: structure characteristics, biological function, and their involvement in human diseases. Cell Mol Life Sci 58, 2085–2097 .11814058
[42] Li, T., Chen, X., Garbutt, K.C., Zhou, P., and Zheng, N. (2006). Structure of DDB1 in complex with a paramyxovirus V protein: viral hijack of a propeller cluster in ubiquitin ligase. Cell 124, 105–117 .16413485
[43] Li, T., Robert, E.I., van Breugel, P.C., Strubin, M., and Zheng, N. (2010). A promiscuous α-helical motif anchors viral hijackers and substrate receptors to the CUL4-DDB1 ubiquitin ligase machinery. Nat Struct Mol Biol 17, 105–111 .19966799
[44] Liu, H., Wang, J.Y., Huang, Y., Li, Z., Gong, W., Lehmann, R., and Xu, R.M. (2010a). Structural basis for methylarginine-dependent recognition of Aubergine by Tudor. Genes & Dev 24: 1876–1881
[45] Liu, K., Chen, C., Guo, Y., Lam, R., Bian, C., Xu, C., Zhao, D.Y., Jin, J., MacKenzie, F., Pawson, T., (2010b). Structural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain. Proc Natl Acad Sci U S A 107, 18398–18403 .20937909
[46] Margueron, R., Justin, N., Ohno, K., Sharpe, M.L., Son, J., Drury, W.J. 3rd, Voigt, P., Martin, S.R., Taylor, W.R., De Marco, V., (2009). Role of the polycomb protein EED in the propagation of repressive histone marks. Nature 461, 762–767 .19767730
[47] Michel, J.J., and Xiong, Y. (1998). Human CUL-1, but not other cullin family members, selectively interacts with SKP1 to form a complex with SKP2 and cyclin A. Cell Growth Differ 9, 435–449 .9663463
[48] Min, J., Allali-Hassani, A., Nady, N., Qi, C., Ouyang, H., Liu, Y., MacKenzie, F., Vedadi, M., and Arrowsmith, C.H. (2007). L3MBTL1 recognition of mono- and dimethylated histones. Nat Struct Mol Biol 14, 1229–1230 .18026117
[49] Min, J., Zhang, Y., and Xu, R.M. (2003). Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev 17, 1823–1828 .12897052
[50] Mohri, K., Vorobiev, S., Fedorov, A.A., Almo, S.C., and Ono, S. (2004). Identification of functional residues on Caenorhabditis elegans actin-interacting protein 1 (UNC-78) for disassembly of actin depolymerizing factor/cofilin-bound actin filaments. J Biol Chem 279, 31697–31707 .15150269
[51] Müller, J., Hart, C.M., Francis, N.J., Vargas, M.L., Sengupta, A., Wild, B., Miller, E.L., O’Connor, M.B., Kingston, R.E., and Simon, J.A. (2002). Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell 111, 197–208 .12408864
[52] Murzin, A.G. (1992). Structural principles for the propeller assembly of beta-sheets: the preference for seven-fold symmetry. Proteins 14, 191–201 .1409568
[53] Murzina, N.V., Pei, X.Y., Zhang, W., Sparkes, M., Vicente-Garcia, J., Pratap, J.V., McLaughlin, S.H., Ben-Shahar, T.R., Verreault, A., Luisi, B.F., (2008). Structural basis for the recognition of histone H4 by the histone-chaperone RbAp46. Structure 16, 1077–1085 .18571423
[54] Nash, P., Tang, X., Orlicky, S., Chen, Q., Gertler, F.B., Mendenhall, M.D., Sicheri, F., Pawson, T., and Tyers, M. (2001). Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication. Nature 414, 514–521 .11734846
[55] Neer, E.J., Schmidt, C.J., Nambudripad, R., and Smith, T.F. (1994). The ancient regulatory-protein family of WD-repeat proteins. Nature 371, 297–300 .8090199
[56] Oliver, A.W., Swift, S., Lord, C.J., Ashworth, A., and Pearl, L.H. (2009). Structural basis for recruitment of BRCA2 by PALB2. EMBO Rep 10, 990–996 .19609323
[57] Orlicky, S., Tang, X., Willems, A., Tyers, M., and Sicheri, F. (2003). Structural basis for phosphodependent substrate selection and orientation by the SCFCdc4 ubiquitin ligase. Cell 112, 243–256 .12553912
[58] Paoli, M. (2001). Protein folds propelled by diversity. Prog Biophys Mol Biol 76, 103–130 .11389935
[59] Patel, A., Dharmarajan, V., and Cosgrove, M.S. (2008). Structure of WDR5 bound to mixed lineage leukemia protein-1 peptide. J Biol Chem 283, 32158–32161 .18829459
[60] Ruthenburg, A.J., Wang, W., Graybosch, D.M., Li, H., Allis, C.D., Patel, D.J., and Verdine, G.L. (2006). Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex. Nat Struct Mol Biol 13, 704–712 .16829959
[61] Schuetz, A., Allali-Hassani, A., Martín, F., Loppnau, P., Vedadi, M., Bochkarev, A., Plotnikov, A.N., Arrowsmith, C.H., and Min, J. (2006). Structural basis for molecular recognition and presentation of histone H3 by WDR5. EMBO J 25, 4245–4252 .16946699
[62] Schuster-B?ckler, B., Schultz, J., and Rahmann, S. (2004). HMM Logos for visualization of protein families. BMC Bioinformatics 5, 7.14736340
[63] Shaw, N., Zhao, M., Cheng, C., Xu, H., Saarikettu, J., Li, Y., Da, Y., Yao, Z., Silvennoinen, O., Yang, J., (2007). The multifunctional human p100 protein ‘hooks’ methylated ligands. Nat Struct Mol Biol 14, 779–784 .17632523
[64] Smith, T.F., Gaitatzes, C., Saxena, K., and Neer, E.J. (1999). The WD repeat: a common architecture for diverse functions. Trends Biochem Sci 24, 181–185 .10322433
[65] Song, J.J., Garlick, J.D., and Kingston, R.E. (2008). Structural basis of histone H4 recognition by p55. Genes Dev 22, 1313–1318 .18443147
[66] Song, J.J., and Kingston, R.E. (2008). WDR5 interacts with mixed lineage leukemia (MLL) protein via the histone H3-binding pocket. J Biol Chem 283, 35258–35264 .18840606
[67] Stirnimann, C.U., Petsalaki, E., Russell, R.B., and Müller, C.W. (2010). WD40 proteins propel cellular networks. Trends Biochem Sci 35, 565–574 .20451393
[68] Sy, S.M., Huen, M.S., and Chen, J. (2009). PALB2 is an integral component of the BRCA complex required for homologous recombination repair. Proc Natl Acad Sci U S A 106, 7155–7160 .19369211
[69] ter Haar, E., Harrison, S.C., and Kirchhausen, T. (2000). Peptide-in-groove interactions link target proteins to the beta-propeller of clathrin. Proc Natl Acad Sci U S A 97, 1096–1100 .10655490
[70] Ungewickell, E., and Branton, D. (1981). Assembly units of clathrin coats. Nature 289, 420–422 .7464911
[71] Verreault, A., Kaufman, P.D., Kobayashi, R., and Stillman, B. (1996). Nucleosome assembly by a complex of CAF-1 and acetylated histones H3/H4. Cell 87, 95–104 .8858152
[72] Verreault, A., Kaufman, P.D., Kobayashi, R., and Stillman, B. (1998). Nucleosomal DNA regulates the core-histone-binding subunit of the human Hat1 acetyltransferase. Curr Biol 8, 96–108 .9427644
[73] Voegtli, W.C., Madrona, A.Y., and Wilson, D.K. (2003). The structure of Aip1p, a WD repeat protein that regulates Cofilin-mediated actin depolymerization. J Biol Chem 278, 34373–34379 .12807914
[74] Wall, M.A., Coleman, D.E., Lee, E., I?iguez-Lluhi, J.A., Posner, B.A., Gilman, A.G., and Sprang, S.R. (1995). The structure of the G protein heterotrimer Gi alpha 1 beta 1 gamma 2. Cell 83, 1047–1058 .8521505
[75] Wang, H., Zhai, L., Xu, J., Joo, H.Y., Jackson, S., Erdjument-Bromage, H., Tempst, P., Xiong, Y., and Zhang, Y. (2006). Histone H3 and H4 ubiquitylation by the CUL4-DDB-ROC1 ubiquitin ligase facilitates cellular response to DNA damage. Mol Cell 22, 383–394 .16678110
[76] Wang, L., Brown, J.L., Cao, R., Zhang, Y., Kassis, J.A., and Jones, R.S. (2004). Hierarchical recruitment of polycomb group silencing complexes. Mol Cell 14, 637–646 .15175158
[77] Whittle, J.R., and Schwartz, T.U. (2010). Structure of the Sec13-Sec16 edge element, a template for assembly of the COPII vesicle coat. J Cell Biol 190, 347–361 .20696705
[78] Wittschieben, B.O., Iwai, S., and Wood, R.D. (2005). DDB1-DDB2 (xeroderma pigmentosum group E) protein complex recognizes a cyclobutane pyrimidine dimer, mismatches, apurinic/apyrimidinic sites, and compound lesions in DNA. J Biol Chem 280, 39982–39989 .16223728
[79] Wu, G., Xu, G., Schulman, B.A., Jeffrey, P.D., Harper, J.W., and Pavletich, N.P. (2003). Structure of a beta-TrCP1-Skp1-beta-catenin complex: destruction motif binding and lysine specificity of the SCF(beta-TrCP1) ubiquitin ligase. Mol Cell 11, 1445–1456 .12820959
[80] Wu, X.H., Chen, R.C., Gao, Y., and Wu, Y.D. (2010). The effect of Asp-His-Ser/Thr-Trp tetrad on the thermostability of WD40-repeat proteins. Biochemistry 49, 10237–10245 .20939513
[81] Wysocka, J., Swigut, T., Milne, T.A., Dou, Y., Zhang, X., Burlingame, A.L., Roeder, R.G., Brivanlou, A.H., and Allis, C.D. (2005). WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell 121, 859–872 .15960974
[82] Xu, C., Bian, C., Yang, W., Galka, M., Ouyang, H., Chen, C., Qiu, W., Liu, H., Jones, A.E., MacKenzie, F., (2010). Binding of different histone marks differentially regulates the activity and specificity of polycomb repressive complex 2 (PRC2). Proc Natl Acad Sci U S A 107, 19266–19271 .20974918
