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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
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