1shf › Citations

Crystal structure of the SH3 domain in human Fyn; comparison of the three-dimensional structures of SH3 domains in tyrosine kinases and spectrin.

Noble ME, Musacchio A, Saraste M, Courtneidge SA, Wierenga RK
EMBO J 12 2617-24 (1993)
Cited: 174 times
EuropePMC logo PMID: 7687536

Abstract

The Src-homology 3 (SH3) region is a protein domain consisting of approximately 60 residues. It occurs in a large number of eukaryotic proteins involved in signal transduction, cell polarization and membrane--cytoskeleton interactions. The function is unknown, but it is probably involved in specific protein--protein interactions. Here we report the crystal structure of the SH3 domain of Fyn (a Src family tyrosine kinase) at 1.9 A resolution. The crystals have two SH3 molecules per asymmetric unit. These two Fyn SH3 domains are not related by a local twofold axis. The crystal structures of spectrin and Fyn SH3 domains as well as the solution structure of the Src SH3 domain show that these all have the same basic fold. A protein domain which has the same topology as SH3 is present in the prokaryotic regulatory enzyme BirA. The comparison between the crystal structures of Fyn and spectrin SH3 domains shows that a conserved surface patch, consisting mainly of aromatic residues, is flanked by two hairpin-like loops (residues 94-104 and 114-118 in Fyn). These loops are different in tyrosine kinase and spectrin SH3 domains. They could modulate the binding properties of the aromatic surface.

Reviews - 1shf mentioned but not cited (4)

  1. Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Igumenova TI, Frederick KK, Wand AJ. Chem Rev 106 1672-1699 (2006)
  2. Noise in cellular signaling pathways: causes and effects. Ladbury JE, Arold ST. Trends Biochem Sci 37 173-178 (2012)
  3. Liaison amid disorder: non-native interactions may underpin long-range coupling in proteins. Chan HS, Zhang Z. J Biol 8 27 (2009)
  4. Reviewing Challenges of Predicting Protein Melting Temperature Change Upon Mutation Through the Full Analysis of a Highly Detailed Dataset with High-Resolution Structures. Louis BBV, Abriata LA. Mol Biotechnol 63 863-884 (2021)

Articles - 1shf mentioned but not cited (50)

  1. Native protein sequences are close to optimal for their structures. Kuhlman B, Baker D. Proc Natl Acad Sci U S A 97 10383-10388 (2000)
  2. Anchor residues in protein-protein interactions. Rajamani D, Thiel S, Vajda S, Camacho CJ. Proc Natl Acad Sci U S A 101 11287-11292 (2004)
  3. Reassessing random-coil statistics in unfolded proteins. Fitzkee NC, Rose GD. Proc Natl Acad Sci U S A 101 12497-12502 (2004)
  4. An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Zhang C, Liu S, Zhou H, Zhou Y. Protein Sci 13 400-411 (2004)
  5. OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing. Lu M, Dousis AD, Ma J. J Mol Biol 376 288-301 (2008)
  6. Solvent accessible surface area approximations for rapid and accurate protein structure prediction. Durham E, Dorr B, Woetzel N, Staritzbichler R, Meiler J. J Mol Model 15 1093-1108 (2009)
  7. Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding. Zarrine-Afsar A, Wallin S, Neculai AM, Neudecker P, Howell PL, Davidson AR, Chan HS. Proc Natl Acad Sci U S A 105 9999-10004 (2008)
  8. FOLD-RATE: prediction of protein folding rates from amino acid sequence. Gromiha MM, Thangakani AM, Selvaraj S. Nucleic Acids Res 34 W70-4 (2006)
  9. A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics. Keasar C, Levitt M. J Mol Biol 329 159-174 (2003)
  10. A new generation of statistical potentials for proteins. Dehouck Y, Gilis D, Rooman M. Biophys J 90 4010-4017 (2006)
  11. Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction. Faraggi E, Yang Y, Zhang S, Zhou Y. Structure 17 1515-1527 (2009)
  12. Dramatic acceleration of protein folding by stabilization of a nonnative backbone conformation. Di Nardo AA, Korzhnev DM, Stogios PJ, Zarrine-Afsar A, Kay LE, Davidson AR. Proc Natl Acad Sci U S A 101 7954-7959 (2004)
  13. A simple model of backbone flexibility improves modeling of side-chain conformational variability. Friedland GD, Linares AJ, Smith CA, Kortemme T. J Mol Biol 380 757-774 (2008)
  14. Approximate protein structural alignment in polynomial time. Kolodny R, Linial N. Proc Natl Acad Sci U S A 101 12201-12206 (2004)
  15. Toward an accurate theoretical framework for describing ensembles for proteins under strongly denaturing conditions. Tran HT, Pappu RV. Biophys J 91 1868-1886 (2006)
  16. Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation. Pokala N, Handel TM. Protein Sci 13 925-936 (2004)
  17. Folding free energy function selects native-like protein sequences in the core but not on the surface. Jaramillo A, Wernisch L, Héry S, Wodak SJ. Proc Natl Acad Sci U S A 99 13554-13559 (2002)
  18. Improved protein structure selection using decoy-dependent discriminatory functions. Wang K, Fain B, Levitt M, Samudrala R. BMC Struct Biol 4 8 (2004)
  19. Sequence variations within protein families are linearly related to structural variations. Koehl P, Levitt M. J Mol Biol 323 551-562 (2002)
  20. Trends in template/fragment-free protein structure prediction. Zhou Y, Duan Y, Yang Y, Faraggi E, Lei H. Theor Chem Acc 128 3-16 (2011)
  21. BCL::Score--knowledge based energy potentials for ranking protein models represented by idealized secondary structure elements. Woetzel N, Karakaş M, Staritzbichler R, Müller R, Weiner BE, Meiler J. PLoS One 7 e49242 (2012)
  22. Calculation of mutational free energy changes in transition states for protein folding. Lindorff-Larsen K, Paci E, Serrano L, Dobson CM, Vendruscolo M. Biophys J 85 1207-1214 (2003)
  23. A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins. Májek P, Elber R. Proteins 76 822-836 (2009)
  24. Guiding conformation space search with an all-atom energy potential. Brunette TJ, Brock O. Proteins 73 958-972 (2008)
  25. The dependence of all-atom statistical potentials on structural training database. Zhang C, Liu S, Zhou H, Zhou Y. Biophys J 86 3349-3358 (2004)
  26. Sparsely populated folding intermediates of the Fyn SH3 domain: matching native-centric essential dynamics and experiment. Ollerenshaw JE, Kaya H, Chan HS, Kay LE. Proc Natl Acad Sci U S A 101 14748-14753 (2004)
  27. The response of internal dynamics to hydrophobic core mutations in the SH3 domain from the Fyn tyrosine kinase. Mittermaier A, Kay LE. Protein Sci 13 1088-1099 (2004)
  28. Protein-protein binding site identification by enumerating the configurations. Guo F, Li SC, Wang L, Zhu D. BMC Bioinformatics 13 158 (2012)
  29. A comprehensive multidimensional-embedded, one-dimensional reaction coordinate for protein unfolding/folding. Toofanny RD, Jonsson AL, Daggett V. Biophys J 98 2671-2681 (2010)
  30. Structure of Stenotrophomonas maltophilia FeoA complexed with zinc: a unique prokaryotic SH3-domain protein that possibly acts as a bacterial ferrous iron-transport activating factor. Su YC, Chin KH, Hung HC, Shen GH, Wang AH, Chou SH. Acta Crystallogr Sect F Struct Biol Cryst Commun 66 636-642 (2010)
  31. H2r: identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments. Merkl R, Zwick M. BMC Bioinformatics 9 151 (2008)
  32. Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation. Arnautova YA, Vorobjev YN, Vila JA, Scheraga HA. Proteins 77 38-51 (2009)
  33. Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions. Potapov V, Cohen M, Inbar Y, Schreiber G. BMC Bioinformatics 11 374 (2010)
  34. Fast search algorithms for computational protein design. Traoré S, Roberts KE, Allouche D, Donald BR, André I, Schiex T, Barbe S. J Comput Chem 37 1048-1058 (2016)
  35. The osmolyte trimethylamine-N-oxide stabilizes the Fyn SH3 domain without altering the structure of its folding transition state. Lin SL, Zarrine-Afsar A, Davidson AR. Protein Sci 18 526-536 (2009)
  36. A pairwise residue contact area-based mean force potential for discrimination of native protein structure. Arab S, Sadeghi M, Eslahchi C, Pezeshk H, Sheari A. BMC Bioinformatics 11 16 (2010)
  37. Protein structure prediction enhanced with evolutionary diversity: SPEED. DeBartolo J, Hocky G, Wilde M, Xu J, Freed KF, Sosnick TR. Protein Sci 19 520-534 (2010)
  38. Bayesian inference of chromatin structure ensembles from population-averaged contact data. Carstens S, Nilges M, Habeck M. Proc Natl Acad Sci U S A 117 7824-7830 (2020)
  39. Explicit orientation dependence in empirical potentials and its significance to side-chain modeling. Ma J. Acc Chem Res 42 1087-1096 (2009)
  40. Scoring predictive models using a reduced representation of proteins: model and energy definition. Fogolari F, Pieri L, Dovier A, Bortolussi L, Giugliarelli G, Corazza A, Esposito G, Viglino P. BMC Struct Biol 7 15 (2007)
  41. A free-rotating and self-avoiding chain model for deriving statistical potentials based on protein structures. Cheng J, Pei J, Lai L. Biophys J 92 3868-3877 (2007)
  42. A knowledge-based structure-discriminating function that requires only main-chain atom coordinates. Makino Y, Itoh N. BMC Struct Biol 8 46 (2008)
  43. Conserved patterns and interactions in the unfolding transition state across SH3 domain structural homologues. Demakis C, Childers MC, Daggett V. Protein Sci 30 391-407 (2021)
  44. Side chain burial and hydrophobic core packing in protein folding transition states. Farber PJ, Mittermaier A. Protein Sci 17 644-651 (2008)
  45. Splitting statistical potentials into meaningful scoring functions: testing the prediction of near-native structures from decoy conformations. Aloy P, Oliva B. BMC Struct Biol 9 71 (2009)
  46. Synergy and allostery in ligand binding by HIV-1 Nef. Aldehaiman A, Momin AA, Restouin A, Wang L, Shi X, Aljedani S, Opi S, Lugari A, Shahul Hameed UF, Ponchon L, Morelli X, Huang M, Dumas C, Collette Y, Arold ST. Biochem J 478 1525-1545 (2021)
  47. Native structure-based modeling and simulation of biomolecular systems per mouse click. Lutz B, Sinner C, Bozic S, Kondov I, Schug A. BMC Bioinformatics 15 292 (2014)
  48. Protposer: The web server that readily proposes protein stabilizing mutations with high PPV. García-Cebollada H, López A, Sancho J. Comput Struct Biotechnol J 20 2415-2433 (2022)
  49. The description of protein internal motions aids selection of ligand binding poses by the INPHARMA method. Stauch B, Orts J, Carlomagno T. J Biomol NMR 54 245-256 (2012)
  50. Module walking using an SH3-like cell-wall-binding domain leads to a new GH184 family of muramidases. Moroz OV, Blagova E, Lebedev AA, Skov LK, Pache RA, Schnorr KM, Kiemer L, Friis EP, Nymand-Grarup S, Ming L, Ye L, Klausen M, Cohn MT, Schmidt EGW, Davies GJ, Wilson KS. Acta Crystallogr D Struct Biol 79 706-720 (2023)


Reviews citing this publication (15)

  1. Regulation, substrates and functions of src. Brown MT, Cooper JA. Biochim Biophys Acta 1287 121-149 (1996)
  2. Structure and regulation of Src family kinases. Boggon TJ, Eck MJ. Oncogene 23 7918-7927 (2004)
  3. Searching protein structure databases has come of age. Holm L, Sander C. Proteins 19 165-173 (1994)
  4. NMR studies of protein structure and dynamics. Kay LE. J Magn Reson 173 193-207 (2005)
  5. An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms. Bartlett AI, Radford SE. Nat Struct Mol Biol 16 582-588 (2009)
  6. SH3 domains and drug design: ligands, structure, and biological function. Dalgarno DC, Botfield MC, Rickles RJ. Biopolymers 43 383-400 (1997)
  7. Structure and function of the SH3 domain. Musacchio A, Wilmanns M, Saraste M. Prog Biophys Mol Biol 61 283-297 (1994)
  8. Structure, regulation and function of phosphoinositide 3-kinases. Fry MJ. Biochim Biophys Acta 1226 237-268 (1994)
  9. Not your average density. Kleywegt GJ, Read RJ. Structure 5 1557-1569 (1997)
  10. SH3 domains: modules of protein-protein interactions. Kurochkina N, Guha U. Biophys Rev 5 29-39 (2013)
  11. Relaxation dispersion NMR spectroscopy as a tool for detailed studies of protein folding. Neudecker P, Lundström P, Kay LE. Biophys J 96 2045-2054 (2009)
  12. SH3 domains. Molecular 'Velcro'. Morton CJ, Campbell ID. Curr Biol 4 615-617 (1994)
  13. In vivo enzymatic protein biotinylation. Chapman-Smith A, Cronan JE. Biomol Eng 16 119-125 (1999)
  14. New insights into protein-tyrosine kinase receptor signaling complexes. Fry MJ, Panayotou G, Booker GW, Waterfield MD. Protein Sci 2 1785-1797 (1993)
  15. Structure and function of phosphatidylinositol-3,4 kinase. Funaki M, Katagiri H, Inukai K, Kikuchi M, Asano T. Cell Signal 12 135-142 (2000)

Articles citing this publication (105)

  1. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Thompson JD, Higgins DG, Gibson TJ. Nucleic Acids Res 22 4673-4680 (1994)
  2. The structure of crystalline profilin-beta-actin. Schutt CE, Myslik JC, Rozycki MD, Goonesekere NC, Lindberg U. Nature 365 810-816 (1993)
  3. Backbone 1H and 15N resonance assignments of the N-terminal SH3 domain of drk in folded and unfolded states using enhanced-sensitivity pulsed field gradient NMR techniques. Zhang O, Kay LE, Olivier JP, Forman-Kay JD. J Biomol NMR 4 845-858 (1994)
  4. Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains. Lim WA, Richards FM, Fox RO. Nature 372 375-379 (1994)
  5. Crystal structure of the conserved core of HIV-1 Nef complexed with a Src family SH3 domain. Lee CH, Saksela K, Mirza UA, Chait BT, Kuriyan J. Cell 85 931-942 (1996)
  6. Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR. Korzhnev DM, Salvatella X, Vendruscolo M, Di Nardo AA, Davidson AR, Dobson CM, Kay LE. Nature 430 586-590 (2004)
  7. UNC-73 activates the Rac GTPase and is required for cell and growth cone migrations in C. elegans. Steven R, Kubiseski TJ, Zheng H, Kulkarni S, Mancillas J, Ruiz Morales A, Hogue CW, Pawson T, Culotti J. Cell 92 785-795 (1998)
  8. High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides. Musacchio A, Saraste M, Wilmanns M. Nat Struct Biol 1 546-551 (1994)
  9. Regulation of Btk function by a major autophosphorylation site within the SH3 domain. Park H, Wahl MI, Afar DE, Turck CW, Rawlings DJ, Tam C, Scharenberg AM, Kinet JP, Witte ON. Immunity 4 515-525 (1996)
  10. SAP couples Fyn to SLAM immune receptors. Chan B, Lanyi A, Song HK, Griesbach J, Simarro-Grande M, Poy F, Howie D, Sumegi J, Terhorst C, Eck MJ. Nat Cell Biol 5 155-160 (2003)
  11. A single amino acid in the SH3 domain of Hck determines its high affinity and specificity in binding to HIV-1 Nef protein. Lee CH, Leung B, Lemmon MA, Zheng J, Cowburn D, Kuriyan J, Saksela K. EMBO J 14 5006-5015 (1995)
  12. Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk. Wu X, Knudsen B, Feller SM, Zheng J, Sali A, Cowburn D, Hanafusa H, Kuriyan J. Structure 3 215-226 (1995)
  13. Proline-rich sequences that bind to Src homology 3 domains with individual specificities. Alexandropoulos K, Cheng G, Baltimore D. Proc Natl Acad Sci U S A 92 3110-3114 (1995)
  14. Identification of Src, Fyn, and Lyn SH3-binding proteins: implications for a function of SH3 domains. Weng Z, Thomas SM, Rickles RJ, Taylor JA, Brauer AW, Seidel-Dugan C, Michael WM, Dreyfuss G, Brugge JS. Mol Cell Biol 14 4509-4521 (1994)
  15. Specific interactions outside the proline-rich core of two classes of Src homology 3 ligands. Feng S, Kasahara C, Rickles RJ, Schreiber SL. Proc Natl Acad Sci U S A 92 12408-12415 (1995)
  16. The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling. Arold S, Franken P, Strub MP, Hoh F, Benichou S, Benarous R, Dumas C. Structure 5 1361-1372 (1997)
  17. The 2.35 A crystal structure of the inactivated form of chicken Src: a dynamic molecule with multiple regulatory interactions. Williams JC, Weijland A, Gonfloni S, Thompson A, Courtneidge SA, Superti-Furga G, Wierenga RK. J Mol Biol 274 757-775 (1997)
  18. NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers. Sekhar A, Kay LE. Proc Natl Acad Sci U S A 110 12867-12874 (2013)
  19. Brain spectrin binding to the NMDA receptor is regulated by phosphorylation, calcium and calmodulin. Wechsler A, Teichberg VI. EMBO J 17 3931-3939 (1998)
  20. Crystal structure of the amphiphysin-2 SH3 domain and its role in the prevention of dynamin ring formation. Owen DJ, Wigge P, Vallis Y, Moore JD, Evans PR, McMahon HT. EMBO J 17 5273-5285 (1998)
  21. Adaptor functions of Cdc42, Ste50, and Sho1 in the yeast osmoregulatory HOG MAPK pathway. Tatebayashi K, Yamamoto K, Tanaka K, Tomida T, Maruoka T, Kasukawa E, Saito H. EMBO J 25 3033-3044 (2006)
  22. SH3 domain recognition of a proline-independent tyrosine-based RKxxYxxY motif in immune cell adaptor SKAP55. Kang H, Freund C, Duke-Cohan JS, Musacchio A, Wagner G, Rudd CE. EMBO J 19 2889-2899 (2000)
  23. Evidence for physical and functional interactions among two Saccharomyces cerevisiae SH3 domain proteins, an adenylyl cyclase-associated protein and the actin cytoskeleton. Lila T, Drubin DG. Mol Biol Cell 8 367-385 (1997)
  24. Mutational analysis of the Src SH3 domain: the same residues of the ligand binding surface are important for intra- and intermolecular interactions. Erpel T, Superti-Furga G, Courtneidge SA. EMBO J 14 963-975 (1995)
  25. Modelling of a voltage-dependent Ca2+ channel beta subunit as a basis for understanding its functional properties. Hanlon MR, Berrow NS, Dolphin AC, Wallace BA. FEBS Lett 445 366-370 (1999)
  26. Solution structure and DNA-binding properties of a thermostable protein from the archaeon Sulfolobus solfataricus. Baumann H, Knapp S, Lundbäck T, Ladenstein R, Härd T. Nat Struct Biol 1 808-819 (1994)
  27. Structural basis for specific binding of the Gads SH3 domain to an RxxK motif-containing SLP-76 peptide: a novel mode of peptide recognition. Liu Q, Berry D, Nash P, Pawson T, McGlade CJ, Li SS. Mol Cell 11 471-481 (2003)
  28. Novel recognition mode between Vav and Grb2 SH3 domains. Nishida M, Nagata K, Hachimori Y, Horiuchi M, Ogura K, Mandiyan V, Schlessinger J, Inagaki F. EMBO J 20 2995-3007 (2001)
  29. Function of a conserved sequence motif in biotin holoenzyme synthetases. Kwon K, Beckett D. Protein Sci 9 1530-1539 (2000)
  30. The crystal structure of a major allergen from plants. Thorn KS, Christensen HE, Shigeta R, Huddler D, Shalaby L, Lindberg U, Chua NH, Schutt CE. Structure 5 19-32 (1997)
  31. Phosphorylation of two regulatory tyrosine residues in the activation of Bruton's tyrosine kinase via alternative receptors. Wahl MI, Fluckiger AC, Kato RM, Park H, Witte ON, Rawlings DJ. Proc Natl Acad Sci U S A 94 11526-11533 (1997)
  32. Structure-function analysis of SH3 domains: SH3 binding specificity altered by single amino acid substitutions. Weng Z, Rickles RJ, Feng S, Richard S, Shaw AS, Schreiber SL, Brugge JS. Mol Cell Biol 15 5627-5634 (1995)
  33. The SH3 domain of Eps8 exists as a novel intertwined dimer. Kishan KV, Scita G, Wong WT, Di Fiore PP, Newcomer ME. Nat Struct Biol 4 739-743 (1997)
  34. Regulation of Btk by Src family tyrosine kinases. Afar DE, Park H, Howell BW, Rawlings DJ, Cooper J, Witte ON. Mol Cell Biol 16 3465-3471 (1996)
  35. Critical residues in an SH3 domain from Sem-5 suggest a mechanism for proline-rich peptide recognition. Lim WA, Richards FM. Nat Struct Biol 1 221-225 (1994)
  36. Solution structure and peptide binding of the SH3 domain from human Fyn. Morton CJ, Pugh DJ, Brown EL, Kahmann JD, Renzoni DA, Campbell ID. Structure 4 705-714 (1996)
  37. NMR structure of the N-terminal SH3 domain of GRB2 and its complex with a proline-rich peptide from Sos. Goudreau N, Cornille F, Duchesne M, Parker F, Tocqué B, Garbay C, Roques BP. Nat Struct Biol 1 898-907 (1994)
  38. Binding of the Grb2 SH2 domain to phosphotyrosine motifs does not change the affinity of its SH3 domains for Sos proline-rich motifs. Cussac D, Frech M, Chardin P. EMBO J 13 4011-4021 (1994)
  39. Structure of the N-terminal SH3 domain of GRB2 complexed with a peptide from the guanine nucleotide releasing factor Sos. Terasawa H, Kohda D, Hatanaka H, Tsuchiya S, Ogura K, Nagata K, Ishii S, Mandiyan V, Ullrich A, Schlessinger J. Nat Struct Biol 1 891-897 (1994)
  40. Letter A tale of two synthetases. Artymiuk PJ, Rice DW, Poirrette AR, Willet P. Nat Struct Biol 1 758-760 (1994)
  41. Grb2 SH3 binding to peptides from Sos: evaluation of a general model for SH3-ligand interactions. Simon JA, Schreiber SL. Chem Biol 2 53-60 (1995)
  42. Identification of a collapsed intermediate with non-native long-range interactions on the folding pathway of a pair of Fyn SH3 domain mutants by NMR relaxation dispersion spectroscopy. Neudecker P, Zarrine-Afsar A, Choy WY, Muhandiram DR, Davidson AR, Kay LE. J Mol Biol 363 958-976 (2006)
  43. Ubiquitin binds to and regulates a subset of SH3 domains. Stamenova SD, French ME, He Y, Francis SA, Kramer ZB, Hicke L. Mol Cell 25 273-284 (2007)
  44. Solution structure of the Grb2 N-terminal SH3 domain complexed with a ten-residue peptide derived from SOS: direct refinement against NOEs, J-couplings and 1H and 13C chemical shifts. Wittekind M, Mapelli C, Lee V, Goldfarb V, Friedrichs MS, Meyers CA, Mueller L. J Mol Biol 267 933-952 (1997)
  45. Hydrophobic complementarity in protein-protein docking. Berchanski A, Shapira B, Eisenstein M. Proteins 56 130-142 (2004)
  46. Protein folding rates estimated from contact predictions. Punta M, Rost B. J Mol Biol 348 507-512 (2005)
  47. The C-terminal domain of biotin protein ligase from E. coli is required for catalytic activity. Chapman-Smith A, Mulhern TD, Whelan F, Cronan JE, Wallace JC. Protein Sci 10 2608-2617 (2001)
  48. Deletion within the Src homology domain 3 of Bruton's tyrosine kinase resulting in X-linked agammaglobulinemia (XLA). Zhu Q, Zhang M, Rawlings DJ, Vihinen M, Hagemann T, Saffran DC, Kwan SP, Nilsson L, Smith CI, Witte ON, Chen SH, Ochs HD. J Exp Med 180 461-470 (1994)
  49. Solution structure and ligand-binding site of the carboxy-terminal SH3 domain of GRB2. Kohda D, Terasawa H, Ichikawa S, Ogura K, Hatanaka H, Mandiyan V, Ullrich A, Schlessinger J, Inagaki F. Structure 2 1029-1040 (1994)
  50. Multiple disordered loops function in corepressor-induced dimerization of the biotin repressor. Kwon K, Streaker ED, Ruparelia S, Beckett D. J Mol Biol 304 821-833 (2000)
  51. Physical and functional interactions between SH2 and SH3 domains of the Src family protein tyrosine kinase p59fyn. Panchamoorthy G, Fukazawa T, Stolz L, Payne G, Reedquist K, Shoelson S, Songyang Z, Cantley L, Walsh C, Band H. Mol Cell Biol 14 6372-6385 (1994)
  52. Replica-exchange Monte Carlo scheme for bayesian data analysis. Habeck M, Nilges M, Rieping W. Phys Rev Lett 94 018105 (2005)
  53. The crystal structure of human CskSH3: structural diversity near the RT-Src and n-Src loop. Borchert TV, Mathieu M, Zeelen JP, Courtneidge SA, Wierenga RK. FEBS Lett 341 79-85 (1994)
  54. Competing protein:protein interactions are proposed to control the biological switch of the E coli biotin repressor. Weaver LH, Kwon K, Beckett D, Matthews BW. Protein Sci 10 2618-2622 (2001)
  55. Identification of a novel proline-rich peptide-binding domain in prolyl 4-hydroxylase. Myllyharju J, Kivirikko KI. EMBO J 18 306-312 (1999)
  56. Thermal unfolding of small proteins with SH3 domain folding pattern. Knapp S, Mattson PT, Christova P, Berndt KD, Karshikoff A, Vihinen M, Smith CI, Ladenstein R. Proteins 31 309-319 (1998)
  57. A comparison of structural and dynamic properties of different simulation methods applied to SH3. van Aalten DM, Amadei A, Bywater R, Findlay JB, Berendsen HJ, Sander C, Stouten PF. Biophys J 70 684-692 (1996)
  58. Protein stabilization by specific binding of guanidinium to a functional arginine-binding surface on an SH3 domain. Zarrine-Afsar A, Mittermaier A, Kay LE, Davidson AR. Protein Sci 15 162-170 (2006)
  59. Stability and peptide binding affinity of an SH3 domain from the Caenorhabditis elegans signaling protein Sem-5. Lim WA, Fox RO, Richards FM. Protein Sci 3 1261-1266 (1994)
  60. Solution structure of GAP SH3 domain by 1H NMR and spatial arrangement of essential Ras signaling-involved sequence. Yang YS, Garbay C, Duchesne M, Cornille F, Jullian N, Fromage N, Tocque B, Roques BP. EMBO J 13 1270-1279 (1994)
  61. Phi-value analysis of a three-state protein folding pathway by NMR relaxation dispersion spectroscopy. Neudecker P, Zarrine-Afsar A, Davidson AR, Kay LE. Proc Natl Acad Sci U S A 104 15717-15722 (2007)
  62. Complete nucleotide sequence, expression, and chromosomal localisation of human mixed-lineage kinase 2. Dorow DS, Devereux L, Tu GF, Price G, Nicholl JK, Sutherland GR, Simpson RJ. Eur J Biochem 234 492-500 (1995)
  63. SH3 in muscles: solution structure of the SH3 domain from nebulin. Politou AS, Millevoi S, Gautel M, Kolmerer B, Pastore A. J Mol Biol 276 189-202 (1998)
  64. The purification and characterization of the catalytic domain of Src expressed in Schizosaccharomyces pombe. Comparison of unphosphorylated and tyrosine phosphorylated species. Weijland A, Neubauer G, Courtneidge SA, Mann M, Wierenga RK, Superti-Furga G. Eur J Biochem 240 756-764 (1996)
  65. The solution structure of Abl SH3, and its relationship to SH2 in the SH(32) construct. Gosser YQ, Zheng J, Overduin M, Mayer BJ, Cowburn D. Structure 3 1075-1086 (1995)
  66. Bergerac-SH3: "frustation" induced by stabilizing the folding nucleus. Viguera AR, Serrano L. J Mol Biol 311 357-371 (2001)
  67. Structural characterization of Staphylococcus aureus biotin protein ligase and interaction partners: an antibiotic target. Pendini NR, Yap MY, Traore DA, Polyak SW, Cowieson NP, Abell A, Booker GW, Wallace JC, Wilce JA, Wilce MC. Protein Sci 22 762-773 (2013)
  68. SH3-SH2 domain orientation in Src kinases: NMR studies of Fyn. Ulmer TS, Werner JM, Campbell ID. Structure 10 901-911 (2002)
  69. Some NMR experiments and a structure determination employing a [15N,2H] enriched protein. Mal TK, Matthews SJ, Kovacs H, Campbell ID, Boyd J. J Biomol NMR 12 259-276 (1998)
  70. Localization of Tec29 to ring canals is mediated by Src64 and PtdIns(3,4,5)P3-dependent mechanisms. Lu N, Guarnieri DJ, Simon MA. EMBO J 23 1089-1100 (2004)
  71. The SH3 domain of postsynaptic density 95 mediates inflammatory pain through phosphatidylinositol-3-kinase recruitment. Arbuckle MI, Komiyama NH, Delaney A, Coba M, Garry EM, Rosie R, Allchorne AJ, Forsyth LH, Bence M, Carlisle HJ, O'Dell TJ, Mitchell R, Fleetwood-Walker SM, Grant SG. EMBO Rep 11 473-478 (2010)
  72. Letter An SH2-SH3 domain hybrid. Russell RB, Russell RB, Barton GJ. Nature 364 765 (1993)
  73. Crystallographic structure of the SH3 domain of the human c-Yes tyrosine kinase: loop flexibility and amyloid aggregation. Martín-García JM, Luque I, Mateo PL, Ruiz-Sanz J, Cámara-Artigas A. FEBS Lett 581 1701-1706 (2007)
  74. Kinetic consequences of native state optimization of surface-exposed electrostatic interactions in the Fyn SH3 domain. Zarrine-Afsar A, Zhang Z, Schweiker KL, Makhatadze GI, Davidson AR, Chan HS. Proteins 80 858-870 (2012)
  75. Alternative splicing of mammalian Intersectin 1: domain associations and tissue specificities. Tsyba L, Skrypkina I, Rynditch A, Nikolaienko O, Ferenets G, Fortna A, Gardiner K. Genomics 84 106-113 (2004)
  76. The Helicobacter pylori cell shape promoting protein Csd5 interacts with the cell wall, MurF, and the bacterial cytoskeleton. Blair KM, Mears KS, Taylor JA, Fero J, Jones LA, Gafken PR, Whitney JC, Salama NR. Mol Microbiol 110 114-127 (2018)
  77. Simulated tempering yields insight into the low-resolution Rosetta scoring functions. Bowman GR, Pande VS. Proteins 74 777-788 (2009)
  78. Stability and folding of the SH3 domain of Bruton's tyrosine kinase. Chen YJ, Lin SC, Tzeng SR, Patel HV, Lyu PC, Cheng JW. Proteins 26 465-471 (1996)
  79. Protein folding while chaperone bound is dependent on weak interactions. Wu K, Stull F, Lee C, Bardwell JCA. Nat Commun 10 4833 (2019)
  80. The promiscuous binding of the Fyn SH3 domain to a peptide from the NS5A protein. Martin-Garcia JM, Luque I, Ruiz-Sanz J, Camara-Artigas A. Acta Crystallogr D Biol Crystallogr 68 1030-1040 (2012)
  81. Fyn Tyrosine Kinase Elicits Amyloid Precursor Protein Tyr682 Phosphorylation in Neurons from Alzheimer's Disease Patients. Iannuzzi F, Sirabella R, Canu N, Maier TJ, Annunziato L, Matrone C. Cells 9 E1807 (2020)
  82. Determination of the solution structure of the SH3 domain of human p56 Lck tyrosine kinase. Hiroaki H, Klaus W, Senn H. J Biomol NMR 8 105-122 (1996)
  83. Predicted structure of the extracellular region of ligand-gated ion-channel receptors shows SH2-like and SH3-like domains forming the ligand-binding site. Gready JE, Ranganathan S, Schofield PR, Matsuo Y, Nishikawa K. Protein Sci 6 983-998 (1997)
  84. Solution structure of N-terminal SH3 domain of Vav and the recognition site for Grb2 C-terminal SH3 domain. Ogura K, Nagata K, Horiuchi M, Ebisui E, Hasuda T, Yuzawa S, Nishida M, Hatanaka H, Inagaki F. J Biomol NMR 22 37-46 (2002)
  85. Homology modeling of the Abl-SH3 domain. Pisabarro MT, Ortiz AR, Serrano L, Wade RC. Proteins 20 203-215 (1994)
  86. SH3 domain of Bruton's tyrosine kinase can bind to proline-rich peptides of TH domain of the kinase and p120cbl. Patel HV, Tzeng SR, Liao CY, Chen SH, Cheng JW. Proteins 29 545-552 (1997)
  87. The SH3 domain of a M7 interacts with its C-terminal proline-rich region. Wang Q, Deloia MA, Kang Y, Litchke C, Zhang N, Titus MA, Walters KJ. Protein Sci 16 189-196 (2007)
  88. A Fyn biosensor reveals pulsatile, spatially localized kinase activity and signaling crosstalk in live mammalian cells. Mukherjee A, Singh R, Udayan S, Biswas S, Reddy PP, Manmadhan S, George G, Kumar S, Das R, Rao BM, Gulyani A. Elife 9 e50571 (2020)
  89. The RabGAP proteins Gyp5p and Gyl1p recruit the BAR domain protein Rvs167p for polarized exocytosis. Prigent M, Boy-Marcotte E, Chesneau L, Gibson K, Dupré-Crochet S, Tisserand H, Verbavatz JM, Cuif MH. Traffic 12 1084-1097 (2011)
  90. Transient helical structure during PI3K and Fyn SH3 domain folding. Matsumura Y, Shinjo M, Kim SJ, Okishio N, Gruebele M, Kihara H. J Phys Chem B 117 4836-4843 (2013)
  91. Insights into the folding and unfolding processes of wild-type and mutated SH3 domain by molecular dynamics and replica exchange molecular dynamics simulations. Chu WT, Zhang JL, Zheng QC, Chen L, Zhang HX. PLoS One 8 e64886 (2013)
  92. SH3 domain regulation of RhoGAP activity: Crosstalk between p120RasGAP and DLC1 RhoGAP. Chau JE, Vish KJ, Boggon TJ, Stiegler AL. Nat Commun 13 4788 (2022)
  93. News Signalling an interest. Yu H, Schreiber SL. Nat Struct Biol 1 417-420 (1994)
  94. Crystal structure of the C-terminal SH3 domain of the adaptor protein GADS in complex with SLP-76 motif peptide reveals a unique SH3-SH3 interaction. Dimasi N. Int J Biochem Cell Biol 39 109-123 (2007)
  95. Folding of the alphaII-spectrin SH3 domain under physiological salt conditions. Petzold K, Ohman A, Backman L. Arch Biochem Biophys 474 39-47 (2008)
  96. Protein alignment using cellulose nanocrystals: practical considerations and range of application. Denisov AY, Kloser E, Gray DG, Mittermaier AK. J Biomol NMR 47 195-204 (2010)
  97. Structural study of hNck2 SH3 domain protein in solution by circular dichroism and X-ray solution scattering. Matsumura Y, Shinjo M, Matsui T, Ichimura K, Song J, Kihara H. Biophys Chem 175-176 39-46 (2013)
  98. The SLE variant Ala71Thr of BLK severely decreases protein abundance and binding to BANK1 through impairment of the SH3 domain function. Díaz-Barreiro A, Bernal-Quirós M, Georg I, Marañón C, Alarcón-Riquelme ME, Castillejo-López C. Genes Immun 17 128-138 (2016)
  99. The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking. Segal D, Eisenstein M. Proteins 59 580-591 (2005)
  100. Comment Helical encounter. Cowburn D. Nat Struct Biol 1 489-491 (1994)
  101. Effects of Topology and Sequence in Protein Folding Linked via Conformational Fluctuations. Trotter D, Wallin S. Biophys J 118 1370-1380 (2020)
  102. Docking and molecular dynamics simulations of the Fyn-SH3 domain with free and phospholipid bilayer-associated 18.5-kDa myelin basic protein (MBP)-Insights into a noncanonical and fuzzy interaction. Bessonov K, Vassall KA, Harauz G. Proteins 85 1336-1350 (2017)
  103. Human Lp(a): regions in sequences of apoproteins similar to domains in signal transduction proteins. Guevara J, Valentinova NV, Davison D, Morrisett JD, Sparrow JT. Endocr Pract 1 440-448 (1995)
  104. Synthesis and evaluation of a (3R,6S,9S)-2-oxo-1-azabicyclo[4.3.0]nonane scaffold as a mimic of Xaa-trans-Pro in poly-L-proline type II helix conformation. Aillard B, Kilburn JD, Blaydes JP, Tizzard GJ, Findlow S, Werner JM, Bloodworth S. Org Biomol Chem 13 4562-4569 (2015)
  105. [Study of the structure and dynamics of a chimeric variant of the SH3 domain (SHA-Bergerac) by NMR spectroscopy]. Prokhorov DA, Timchenko MA, Kudrevatykh IuA, Fediukina DV, Gushchina LV, Khristoforov VS, Filimonov VV, Kutyshenko VP. Bioorg Khim 34 645-653 (2008)


Quick links