anno_start anno_end anno_text entity_type sentence section 0 9 Structure evidence Structure of the GAT domain of the endosomal adapter protein Tom1 TITLE 17 20 GAT structure_element Structure of the GAT domain of the endosomal adapter protein Tom1 TITLE 45 60 adapter protein protein_type Structure of the GAT domain of the endosomal adapter protein Tom1 TITLE 61 65 Tom1 protein Structure of the GAT domain of the endosomal adapter protein Tom1 TITLE 50 71 cell-surface receptor protein_type Cellular homeostasis requires correct delivery of cell-surface receptor proteins (cargo) to their target subcellular compartments. ABSTRACT 4 20 adapter proteins protein_type The adapter proteins Tom1 and Tollip are involved in sorting of ubiquitinated cargo in endosomal compartments. ABSTRACT 21 25 Tom1 protein The adapter proteins Tom1 and Tollip are involved in sorting of ubiquitinated cargo in endosomal compartments. ABSTRACT 30 36 Tollip protein The adapter proteins Tom1 and Tollip are involved in sorting of ubiquitinated cargo in endosomal compartments. ABSTRACT 64 77 ubiquitinated ptm The adapter proteins Tom1 and Tollip are involved in sorting of ubiquitinated cargo in endosomal compartments. ABSTRACT 15 19 Tom1 protein Recruitment of Tom1 to the endosomal compartments is mediated by its GAT domain’s association to Tollip’s Tom1-binding domain (TBD). ABSTRACT 69 72 GAT structure_element Recruitment of Tom1 to the endosomal compartments is mediated by its GAT domain’s association to Tollip’s Tom1-binding domain (TBD). ABSTRACT 97 103 Tollip protein Recruitment of Tom1 to the endosomal compartments is mediated by its GAT domain’s association to Tollip’s Tom1-binding domain (TBD). ABSTRACT 106 125 Tom1-binding domain structure_element Recruitment of Tom1 to the endosomal compartments is mediated by its GAT domain’s association to Tollip’s Tom1-binding domain (TBD). ABSTRACT 127 130 TBD structure_element Recruitment of Tom1 to the endosomal compartments is mediated by its GAT domain’s association to Tollip’s Tom1-binding domain (TBD). ABSTRACT 36 48 solution NMR experimental_method In this data article, we report the solution NMR-derived structure of the Tom1 GAT domain. ABSTRACT 57 66 structure evidence In this data article, we report the solution NMR-derived structure of the Tom1 GAT domain. ABSTRACT 74 78 Tom1 protein In this data article, we report the solution NMR-derived structure of the Tom1 GAT domain. ABSTRACT 79 82 GAT structure_element In this data article, we report the solution NMR-derived structure of the Tom1 GAT domain. ABSTRACT 22 31 structure evidence The estimated protein structure exhibits a bundle of three helical elements. ABSTRACT 3 10 compare experimental_method We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states. ABSTRACT 15 19 Tom1 protein We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states. ABSTRACT 20 23 GAT structure_element We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states. ABSTRACT 24 33 structure evidence We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states. ABSTRACT 45 55 structures evidence We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states. ABSTRACT 77 83 Tollip protein We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states. ABSTRACT 84 88 TBD- protein_state We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states. ABSTRACT 93 108 ubiquitin-bound protein_state We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states. ABSTRACT 141 159 Circular dichroism experimental_method "Subject area Biology More specific subject area Structural biology Type of data Table, text file, graph, figures How data was acquired Circular dichroism and NMR." TABLE 164 167 NMR experimental_method "Subject area Biology More specific subject area Structural biology Type of data Table, text file, graph, figures How data was acquired Circular dichroism and NMR." TABLE 0 3 NMR experimental_method "NMR data was recorded using a Bruker 800 MHz Data format PDB format text file." TABLE 12 22 CS-Rosetta experimental_method "Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol Experimental factors Recombinant human Tom1 GAT domain was purified to homogeneity before use Experimental features Solution structure of Tom1 GAT was determined from NMR chemical shift data Data source location Virginia and Colorado, United States." TABLE 24 59 Protein Structure Validation Server experimental_method "Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol Experimental factors Recombinant human Tom1 GAT domain was purified to homogeneity before use Experimental features Solution structure of Tom1 GAT was determined from NMR chemical shift data Data source location Virginia and Colorado, United States." TABLE 61 65 PSVS experimental_method "Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol Experimental factors Recombinant human Tom1 GAT domain was purified to homogeneity before use Experimental features Solution structure of Tom1 GAT was determined from NMR chemical shift data Data source location Virginia and Colorado, United States." TABLE 68 75 NMRPipe experimental_method "Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol Experimental factors Recombinant human Tom1 GAT domain was purified to homogeneity before use Experimental features Solution structure of Tom1 GAT was determined from NMR chemical shift data Data source location Virginia and Colorado, United States." TABLE 77 84 NMRDraw experimental_method "Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol Experimental factors Recombinant human Tom1 GAT domain was purified to homogeneity before use Experimental features Solution structure of Tom1 GAT was determined from NMR chemical shift data Data source location Virginia and Colorado, United States." TABLE 131 136 human species "Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol Experimental factors Recombinant human Tom1 GAT domain was purified to homogeneity before use Experimental features Solution structure of Tom1 GAT was determined from NMR chemical shift data Data source location Virginia and Colorado, United States." TABLE 137 141 Tom1 protein "Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol Experimental factors Recombinant human Tom1 GAT domain was purified to homogeneity before use Experimental features Solution structure of Tom1 GAT was determined from NMR chemical shift data Data source location Virginia and Colorado, United States." TABLE 142 145 GAT structure_element "Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol Experimental factors Recombinant human Tom1 GAT domain was purified to homogeneity before use Experimental features Solution structure of Tom1 GAT was determined from NMR chemical shift data Data source location Virginia and Colorado, United States." TABLE 216 234 Solution structure evidence "Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol Experimental factors Recombinant human Tom1 GAT domain was purified to homogeneity before use Experimental features Solution structure of Tom1 GAT was determined from NMR chemical shift data Data source location Virginia and Colorado, United States." TABLE 238 242 Tom1 protein "Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol Experimental factors Recombinant human Tom1 GAT domain was purified to homogeneity before use Experimental features Solution structure of Tom1 GAT was determined from NMR chemical shift data Data source location Virginia and Colorado, United States." TABLE 243 246 GAT structure_element "Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol Experimental factors Recombinant human Tom1 GAT domain was purified to homogeneity before use Experimental features Solution structure of Tom1 GAT was determined from NMR chemical shift data Data source location Virginia and Colorado, United States." TABLE 267 270 NMR experimental_method "Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol Experimental factors Recombinant human Tom1 GAT domain was purified to homogeneity before use Experimental features Solution structure of Tom1 GAT was determined from NMR chemical shift data Data source location Virginia and Colorado, United States." TABLE 271 285 chemical shift evidence "Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol Experimental factors Recombinant human Tom1 GAT domain was purified to homogeneity before use Experimental features Solution structure of Tom1 GAT was determined from NMR chemical shift data Data source location Virginia and Colorado, United States." TABLE 5 8 GAT structure_element "Tom1 GAT structural data is publicly available in the RCSB Protein Data Bank (http://www.rscb.org/) under the accession number PDB: 2n9d " TABLE 4 8 Tom1 protein The Tom1 GAT domain solution structure will provide additional tools for modulating its biological function. TABLE 9 12 GAT structure_element The Tom1 GAT domain solution structure will provide additional tools for modulating its biological function. TABLE 20 38 solution structure evidence The Tom1 GAT domain solution structure will provide additional tools for modulating its biological function. TABLE 0 4 Tom1 protein Tom1 GAT can adopt distinct conformations upon ligand binding. TABLE 5 8 GAT structure_element Tom1 GAT can adopt distinct conformations upon ligand binding. TABLE 33 37 Tom1 protein A conformational response of the Tom1 GAT domain upon Tollip TBD binding can serve as an example to explain mutually exclusive ligand binding events. TABLE 38 41 GAT structure_element A conformational response of the Tom1 GAT domain upon Tollip TBD binding can serve as an example to explain mutually exclusive ligand binding events. TABLE 54 60 Tollip protein A conformational response of the Tom1 GAT domain upon Tollip TBD binding can serve as an example to explain mutually exclusive ligand binding events. TABLE 61 64 TBD structure_element A conformational response of the Tom1 GAT domain upon Tollip TBD binding can serve as an example to explain mutually exclusive ligand binding events. TABLE 16 41 far-UV circular dichroism experimental_method Analysis of the far-UV circular dichroism (CD) spectrum of the Tom 1 GAT domain (Fig. 1) predicts 58.7% α-helix, 3% β-strand, 15.5% turn, and 22.8% disordered regions. TABLE 43 45 CD experimental_method Analysis of the far-UV circular dichroism (CD) spectrum of the Tom 1 GAT domain (Fig. 1) predicts 58.7% α-helix, 3% β-strand, 15.5% turn, and 22.8% disordered regions. TABLE 47 55 spectrum evidence Analysis of the far-UV circular dichroism (CD) spectrum of the Tom 1 GAT domain (Fig. 1) predicts 58.7% α-helix, 3% β-strand, 15.5% turn, and 22.8% disordered regions. TABLE 63 68 Tom 1 protein Analysis of the far-UV circular dichroism (CD) spectrum of the Tom 1 GAT domain (Fig. 1) predicts 58.7% α-helix, 3% β-strand, 15.5% turn, and 22.8% disordered regions. TABLE 69 72 GAT structure_element Analysis of the far-UV circular dichroism (CD) spectrum of the Tom 1 GAT domain (Fig. 1) predicts 58.7% α-helix, 3% β-strand, 15.5% turn, and 22.8% disordered regions. TABLE 104 111 α-helix structure_element Analysis of the far-UV circular dichroism (CD) spectrum of the Tom 1 GAT domain (Fig. 1) predicts 58.7% α-helix, 3% β-strand, 15.5% turn, and 22.8% disordered regions. TABLE 116 124 β-strand structure_element Analysis of the far-UV circular dichroism (CD) spectrum of the Tom 1 GAT domain (Fig. 1) predicts 58.7% α-helix, 3% β-strand, 15.5% turn, and 22.8% disordered regions. TABLE 4 8 Tom1 protein The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3). TABLE 9 12 GAT structure_element The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3). TABLE 13 34 structural restraints evidence The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3). TABLE 55 65 structures evidence The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3). TABLE 85 111 root mean square deviation evidence The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3). TABLE 113 117 RMSD evidence The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3). TABLE 243 252 Q216-E240 residue_range The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3). TABLE 254 263 α-helix 1 structure_element The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3). TABLE 266 275 P248-Q274 residue_range The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3). TABLE 277 286 α-helix 2 structure_element The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3). TABLE 293 302 E278-T306 residue_range The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3). TABLE 304 313 α-helix 3 structure_element The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3). TABLE 7 16 ubiquitin chemical Unlike ubiquitin binding, data suggest that conformational changes of the Tom1 GAT α-helices 1 and 2 occur upon Tollip TBD binding (Fig. 3A,B). TABLE 74 78 Tom1 protein Unlike ubiquitin binding, data suggest that conformational changes of the Tom1 GAT α-helices 1 and 2 occur upon Tollip TBD binding (Fig. 3A,B). TABLE 79 82 GAT structure_element Unlike ubiquitin binding, data suggest that conformational changes of the Tom1 GAT α-helices 1 and 2 occur upon Tollip TBD binding (Fig. 3A,B). TABLE 83 100 α-helices 1 and 2 structure_element Unlike ubiquitin binding, data suggest that conformational changes of the Tom1 GAT α-helices 1 and 2 occur upon Tollip TBD binding (Fig. 3A,B). TABLE 112 118 Tollip protein Unlike ubiquitin binding, data suggest that conformational changes of the Tom1 GAT α-helices 1 and 2 occur upon Tollip TBD binding (Fig. 3A,B). TABLE 119 122 TBD structure_element Unlike ubiquitin binding, data suggest that conformational changes of the Tom1 GAT α-helices 1 and 2 occur upon Tollip TBD binding (Fig. 3A,B). TABLE 15 24 far-UV CD experimental_method Representative far-UV CD spectrum of the His-Tom1 GAT domain. FIG 25 33 spectrum evidence Representative far-UV CD spectrum of the His-Tom1 GAT domain. FIG 41 45 His- experimental_method Representative far-UV CD spectrum of the His-Tom1 GAT domain. FIG 45 49 Tom1 protein Representative far-UV CD spectrum of the His-Tom1 GAT domain. FIG 50 53 GAT structure_element Representative far-UV CD spectrum of the His-Tom1 GAT domain. FIG 40 62 backbone superposition experimental_method (A) Stereo view displaying the best-fit backbone superposition of the refined structures for the Tom1 GAT domain. FIG 78 88 structures evidence (A) Stereo view displaying the best-fit backbone superposition of the refined structures for the Tom1 GAT domain. FIG 97 101 Tom1 protein (A) Stereo view displaying the best-fit backbone superposition of the refined structures for the Tom1 GAT domain. FIG 102 105 GAT structure_element (A) Stereo view displaying the best-fit backbone superposition of the refined structures for the Tom1 GAT domain. FIG 96 100 Tom1 protein Helices are shown in orange, whereas loops are colored in green. (B) Ribbon illustration of the Tom1 GAT domain. FIG 101 104 GAT structure_element Helices are shown in orange, whereas loops are colored in green. (B) Ribbon illustration of the Tom1 GAT domain. FIG 21 44 superimposed structures experimental_method (A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green). FIG 52 56 Tom1 protein (A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green). FIG 57 60 GAT structure_element (A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green). FIG 75 79 free protein_state (A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green). FIG 110 116 Tollip protein (A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green). FIG 117 126 TBD-bound protein_state (A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green). FIG 161 184 superimposed structures experimental_method (A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green). FIG 192 196 Tom1 protein (A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green). FIG 197 200 GAT structure_element (A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green). FIG 232 240 Ub-bound protein_state (A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green). FIG 0 3 NMR experimental_method NMR and refinement statistics for the Tom1 GAT domain. TABLE 8 29 refinement statistics evidence NMR and refinement statistics for the Tom1 GAT domain. TABLE 38 42 Tom1 protein NMR and refinement statistics for the Tom1 GAT domain. TABLE 43 46 GAT structure_element NMR and refinement statistics for the Tom1 GAT domain. TABLE 0 3 NMR experimental_method NMR structural statistics for lowest energy conformers of Tom1 GAT using PSVS. TABLE 4 25 structural statistics evidence NMR structural statistics for lowest energy conformers of Tom1 GAT using PSVS. TABLE 58 62 Tom1 protein NMR structural statistics for lowest energy conformers of Tom1 GAT using PSVS. TABLE 63 66 GAT structure_element NMR structural statistics for lowest energy conformers of Tom1 GAT using PSVS. TABLE 73 77 PSVS experimental_method NMR structural statistics for lowest energy conformers of Tom1 GAT using PSVS. TABLE 28 41 superimposing experimental_method deviations were obtained by superimposing residues 215–309 of Tom1 GAT among 10 lowest energy refined structures. TABLE 51 58 215–309 residue_range deviations were obtained by superimposing residues 215–309 of Tom1 GAT among 10 lowest energy refined structures. TABLE 62 66 Tom1 protein deviations were obtained by superimposing residues 215–309 of Tom1 GAT among 10 lowest energy refined structures. TABLE 67 70 GAT structure_element deviations were obtained by superimposing residues 215–309 of Tom1 GAT among 10 lowest energy refined structures. TABLE 102 112 structures evidence deviations were obtained by superimposing residues 215–309 of Tom1 GAT among 10 lowest energy refined structures. TABLE