data_11375 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Assigned chemical shifts of the second RNA recognition motif (RRM) of TIA-1 with RNA (UUUUU) ; _BMRB_accession_number 11375 _BMRB_flat_file_name bmr11375.str _Entry_type original _Submission_date 2010-09-08 _Accession_date 2010-09-08 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Takahashi M. . . 2 Kuwasako K. . . 3 Abe C. . . 4 Tsuda K. . . 5 Inoue M. . . 6 Terada T. . . 7 Shirouzu M. . . 8 Kobayashi N. . . 9 Kigawa T. . . 10 Taguchi S. . . 11 Guntert P. . . 12 Hayashizaki Y. . . 13 Tanaka A. . . 14 Muto Y. . . 15 Yokoyama S. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 100 "15N chemical shifts" 100 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-11-30 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 11370 'Assigned chemical shifts of the second RNA recognition motif (RRM) of TIA-1, C terminal truncated' 11371 'Assigned chemical shifts of the second RNA recognition motif (RRM) of TIA-1, D131A mutant' 11372 'Assigned chemical shifts of the second RNA recognition motif (RRM) of TIA-1, K138A mutant' 11373 'Assigned chemical shifts of the second RNA recognition motif (RRM) of TIA-1, T134A mutant' 11374 'Assigned chemical shifts of the second RNA recognition motif (RRM) of TIA-1 with RNA (CCCCC)' 11376 'Assigned chemical shifts of the second RNA recognition motif (RRM) of TIA-1' stop_ _Original_release_date 2010-11-30 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution structure of the second RNA recognition motif (RRM) domain of murine T cell intracellular antigen-1 (TIA-1) and its RNA recognition mode.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18500819 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kuwasako Kanako . . 2 Takahashi Mari . . 3 Tochio Naoya . . 4 Abe Chikage . . 5 Tsuda Kengo . . 6 Inoue Makoto . . 7 Terada Takaho . . 8 Shirouzu Mikako . . 9 Kobayashi Naohiro . . 10 Kigawa Takanori . . 11 Taguchi Seiichi . . 12 Tanaka Akiko . . 13 Hayashizaki Yoshihide . . 14 Guntert Peter . . 15 Muto Yutaka . . 16 Yokoyama Shigeyuki . . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 47 _Journal_issue 24 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 6437 _Page_last 6450 _Year 2008 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Tia1 protein' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RRM domain' $entity_1 'RNA (UUUUU)' $entity_2 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'RRM domain' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 115 _Mol_residue_sequence ; GSSGSSGQKKDTSNHFHVFV GDLSPEITTEDIKAAFAPFG RISDARVVKDMATGKSKGYG FVSFFNKWDAENAIQQMGGQ WLGGRQIRTNWATRKPPAPK STYESNTKQSGPSSG ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 SER 3 SER 4 GLY 5 SER 6 SER 7 GLY 8 GLN 9 LYS 10 LYS 11 ASP 12 THR 13 SER 14 ASN 15 HIS 16 PHE 17 HIS 18 VAL 19 PHE 20 VAL 21 GLY 22 ASP 23 LEU 24 SER 25 PRO 26 GLU 27 ILE 28 THR 29 THR 30 GLU 31 ASP 32 ILE 33 LYS 34 ALA 35 ALA 36 PHE 37 ALA 38 PRO 39 PHE 40 GLY 41 ARG 42 ILE 43 SER 44 ASP 45 ALA 46 ARG 47 VAL 48 VAL 49 LYS 50 ASP 51 MET 52 ALA 53 THR 54 GLY 55 LYS 56 SER 57 LYS 58 GLY 59 TYR 60 GLY 61 PHE 62 VAL 63 SER 64 PHE 65 PHE 66 ASN 67 LYS 68 TRP 69 ASP 70 ALA 71 GLU 72 ASN 73 ALA 74 ILE 75 GLN 76 GLN 77 MET 78 GLY 79 GLY 80 GLN 81 TRP 82 LEU 83 GLY 84 GLY 85 ARG 86 GLN 87 ILE 88 ARG 89 THR 90 ASN 91 TRP 92 ALA 93 THR 94 ARG 95 LYS 96 PRO 97 PRO 98 ALA 99 PRO 100 LYS 101 SER 102 THR 103 TYR 104 GLU 105 SER 106 ASN 107 THR 108 LYS 109 GLN 110 SER 111 GLY 112 PRO 113 SER 114 SER 115 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-10-07 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value BMRB 11370 "RRM domain C terminal truncated" 75.65 87 100.00 100.00 7.29e-57 BMRB 11371 "RRM domain D131A mutant" 89.57 103 99.03 99.03 2.39e-68 BMRB 11372 "RRM domain K138A mutant" 89.57 103 99.03 99.03 1.01e-68 BMRB 11373 "RRM domain T134A mutant" 89.57 103 99.03 99.03 8.77e-69 BMRB 11374 "RRM domain" 100.00 115 100.00 100.00 2.81e-77 BMRB 11376 "RRM domain" 100.00 115 100.00 100.00 2.81e-77 PDB 2DGO "Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1" 100.00 115 100.00 100.00 2.81e-77 PDB 2RNE "Solution Structure Of The Second Rna Recognition Motif (Rrm) Of Tia-1" 100.00 115 100.00 100.00 2.81e-77 GB EAW99825 "TIA1 cytotoxic granule-associated RNA binding protein, isoform CRA_c, partial [Homo sapiens]" 90.43 144 99.04 99.04 2.21e-69 REF XP_005430921 "PREDICTED: nucleolysin TIA-1 isoform p40 [Geospiza fortis]" 90.43 367 98.08 99.04 6.94e-66 stop_ save_ save_entity_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 'RNA (UUUUU)' _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 5 _Mol_residue_sequence UUUUU loop_ _Residue_seq_code _Residue_label 1 U 2 U 3 U 4 U 5 U stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 Mouse 10090 Eukaryota Metazoa Mus musculus stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $entity_1 'cell free synthesis' 'E. coli' Escherichia coli . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details ; 0.583mM RNA, 20mM [U-99% 2H] TRIS, 100mM sodium chloride, 1mM [U-98% 2H] DTT, 0.02% sodium azide, 1mM [U-99% 13C; U-99% 15N] protein, 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM '[U-99% 13C; U-99% 15N]' $entity_2 0.583 mM 'natural abundance' TRIS 20 mM '[U-99% 2H]' 'sodium chloride' 100 mM 'natural abundance' DTT 1 mM '[U-98% 2H]' 'sodium azide' 0.02 % 'natural abundance' H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_OPAL _Saveframe_category software _Name OPAL _Version . loop_ _Vendor _Address _Electronic_address 'Luginbuhl, Guntert, Billeter and Wuthrich' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_3D_1H-15N_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $sample_1 save_ save_3D_1H-13C_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-13C NOESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_condition_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 100 0.1 mM pH 7.0 0.05 pH pressure 1 0.001 atm temperature 298 0.1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_reference_1 _Saveframe_category chemical_shift_reference _Details ; Chemical shift reference of 1H was based on the proton of water (4.784ppm at 298K) and then those of 15N and 13C were calculated based on their gyromagnetic ratios. ; loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DSS C 13 'methyl protons' ppm 0.0 . indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.0 . indirect . . . 1.0 DSS N 15 'methyl protons' ppm 0.0 . indirect . . . 0.101329118 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_chemical_shift_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $OPAL stop_ loop_ _Experiment_label '3D 1H-15N NOESY' '3D 1H-13C NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $condition_1 _Chem_shift_reference_set_label $reference_1 _Mol_system_component_name 'RRM domain' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 8 8 GLN H H 8.161 0.030 1 2 8 8 GLN N N 119.870 0.300 1 3 9 9 LYS H H 8.390 0.030 1 4 9 9 LYS N N 123.239 0.300 1 5 10 10 LYS H H 8.403 0.030 1 6 10 10 LYS N N 123.239 0.300 1 7 11 11 ASP H H 8.421 0.030 1 8 11 11 ASP N N 122.133 0.300 1 9 12 12 THR H H 8.216 0.030 1 10 12 12 THR N N 114.790 0.300 1 11 13 13 SER H H 8.311 0.030 1 12 13 13 SER N N 119.039 0.300 1 13 14 14 ASN H H 8.246 0.030 1 14 14 14 ASN N N 119.162 0.300 1 15 15 15 HIS H H 7.370 0.030 1 16 15 15 HIS N N 119.122 0.300 1 17 16 16 PHE H H 8.488 0.030 1 18 16 16 PHE N N 117.443 0.300 1 19 17 17 HIS H H 9.094 0.030 1 20 17 17 HIS N N 124.835 0.300 1 21 18 18 VAL H H 9.765 0.030 1 22 18 18 VAL N N 126.130 0.300 1 23 19 19 PHE H H 9.040 0.030 1 24 19 19 PHE N N 127.714 0.300 1 25 20 20 VAL H H 7.699 0.030 1 26 20 20 VAL N N 126.758 0.300 1 27 21 21 GLY H H 8.617 0.030 1 28 21 21 GLY N N 111.005 0.300 1 29 22 22 ASP H H 8.395 0.030 1 30 22 22 ASP N N 115.375 0.300 1 31 23 23 LEU H H 7.639 0.030 1 32 23 23 LEU N N 112.424 0.300 1 33 24 24 SER H H 8.950 0.030 1 34 24 24 SER N N 121.344 0.300 1 35 26 26 GLU H H 9.066 0.030 1 36 26 26 GLU N N 116.054 0.300 1 37 27 27 ILE H H 7.369 0.030 1 38 27 27 ILE N N 121.809 0.300 1 39 28 28 THR H H 9.395 0.030 1 40 28 28 THR N N 121.128 0.300 1 41 29 29 THR H H 9.010 0.030 1 42 29 29 THR N N 118.080 0.300 1 43 30 30 GLU H H 8.380 0.030 1 44 30 30 GLU N N 119.903 0.300 1 45 31 31 ASP H H 7.677 0.030 1 46 31 31 ASP N N 119.990 0.300 1 47 32 32 ILE H H 7.872 0.030 1 48 32 32 ILE N N 118.196 0.300 1 49 33 33 LYS H H 8.230 0.030 1 50 33 33 LYS N N 121.254 0.300 1 51 34 34 ALA H H 7.745 0.030 1 52 34 34 ALA N N 118.266 0.300 1 53 35 35 ALA H H 7.832 0.030 1 54 35 35 ALA N N 118.087 0.300 1 55 36 36 PHE H H 7.975 0.030 1 56 36 36 PHE N N 112.069 0.300 1 57 37 37 ALA H H 7.989 0.030 1 58 37 37 ALA N N 125.144 0.300 1 59 39 39 PHE H H 7.719 0.030 1 60 39 39 PHE N N 112.740 0.300 1 61 40 40 GLY H H 7.604 0.030 1 62 40 40 GLY N N 104.806 0.300 1 63 41 41 ARG H H 8.241 0.030 1 64 41 41 ARG N N 117.050 0.300 1 65 42 42 ILE H H 8.472 0.030 1 66 42 42 ILE N N 127.737 0.300 1 67 43 43 SER H H 8.813 0.030 1 68 43 43 SER N N 123.021 0.300 1 69 44 44 ASP H H 7.295 0.030 1 70 44 44 ASP N N 119.575 0.300 1 71 45 45 ALA H H 8.031 0.030 1 72 45 45 ALA N N 120.547 0.300 1 73 46 46 ARG H H 8.838 0.030 1 74 46 46 ARG N N 116.035 0.300 1 75 47 47 VAL H H 7.642 0.030 1 76 47 47 VAL N N 124.088 0.300 1 77 48 48 VAL H H 8.361 0.030 1 78 48 48 VAL N N 130.567 0.300 1 79 49 49 LYS H H 8.101 0.030 1 80 49 49 LYS N N 125.357 0.300 1 81 50 50 ASP H H 8.655 0.030 1 82 50 50 ASP N N 121.840 0.300 1 83 51 51 MET H H 9.040 0.030 1 84 51 51 MET N N 127.153 0.300 1 85 52 52 ALA H H 8.598 0.030 1 86 52 52 ALA N N 120.829 0.300 1 87 53 53 THR H H 7.706 0.030 1 88 53 53 THR N N 104.999 0.300 1 89 54 54 GLY H H 8.491 0.030 1 90 54 54 GLY N N 111.488 0.300 1 91 55 55 LYS H H 7.710 0.030 1 92 55 55 LYS N N 119.224 0.300 1 93 56 56 SER H H 8.707 0.030 1 94 56 56 SER N N 115.239 0.300 1 95 57 57 LYS H H 9.222 0.030 1 96 57 57 LYS N N 125.377 0.300 1 97 58 58 GLY H H 8.931 0.030 1 98 58 58 GLY N N 105.420 0.300 1 99 59 59 TYR H H 6.979 0.030 1 100 59 59 TYR N N 112.750 0.300 1 101 60 60 GLY H H 8.724 0.030 1 102 60 60 GLY N N 106.517 0.300 1 103 61 61 PHE H H 8.494 0.030 1 104 61 61 PHE N N 113.297 0.300 1 105 62 62 VAL H H 8.930 0.030 1 106 62 62 VAL N N 119.804 0.300 1 107 63 63 SER H H 8.654 0.030 1 108 63 63 SER N N 121.903 0.300 1 109 64 64 PHE H H 9.271 0.030 1 110 64 64 PHE N N 121.708 0.300 1 111 65 65 PHE H H 7.710 0.030 1 112 65 65 PHE N N 117.884 0.300 1 113 66 66 ASN H H 8.564 0.030 1 114 66 66 ASN N N 113.918 0.300 1 115 67 67 LYS H H 8.188 0.030 1 116 67 67 LYS N N 126.583 0.300 1 117 68 68 TRP H H 7.578 0.030 1 118 68 68 TRP N N 116.605 0.300 1 119 69 69 ASP H H 6.892 0.030 1 120 69 69 ASP N N 121.216 0.300 1 121 70 70 ALA H H 6.623 0.030 1 122 70 70 ALA N N 119.748 0.300 1 123 71 71 GLU H H 8.373 0.030 1 124 71 71 GLU N N 117.093 0.300 1 125 72 72 ASN H H 7.956 0.030 1 126 72 72 ASN N N 118.013 0.300 1 127 73 73 ALA H H 7.925 0.030 1 128 73 73 ALA N N 121.706 0.300 1 129 74 74 ILE H H 8.058 0.030 1 130 74 74 ILE N N 116.362 0.300 1 131 75 75 GLN H H 7.603 0.030 1 132 75 75 GLN N N 117.023 0.300 1 133 76 76 GLN H H 8.472 0.030 1 134 76 76 GLN N N 114.616 0.300 1 135 77 77 MET H H 7.637 0.030 1 136 77 77 MET N N 112.977 0.300 1 137 78 78 GLY H H 6.984 0.030 1 138 78 78 GLY N N 106.914 0.300 1 139 79 79 GLY H H 8.414 0.030 1 140 79 79 GLY N N 115.380 0.300 1 141 80 80 GLN H H 7.579 0.030 1 142 80 80 GLN N N 118.970 0.300 1 143 81 81 TRP H H 8.626 0.030 1 144 81 81 TRP N N 120.834 0.300 1 145 82 82 LEU H H 8.580 0.030 1 146 82 82 LEU N N 125.912 0.300 1 147 83 83 GLY H H 9.309 0.030 1 148 83 83 GLY N N 115.490 0.300 1 149 84 84 GLY H H 8.713 0.030 1 150 84 84 GLY N N 108.070 0.300 1 151 85 85 ARG H H 7.622 0.030 1 152 85 85 ARG N N 118.385 0.300 1 153 86 86 GLN H H 7.781 0.030 1 154 86 86 GLN N N 121.687 0.300 1 155 87 87 ILE H H 8.144 0.030 1 156 87 87 ILE N N 117.795 0.300 1 157 88 88 ARG H H 7.929 0.030 1 158 88 88 ARG N N 119.474 0.300 1 159 89 89 THR H H 8.416 0.030 1 160 89 89 THR N N 109.928 0.300 1 161 90 90 ASN H H 8.781 0.030 1 162 90 90 ASN N N 115.722 0.300 1 163 91 91 TRP H H 8.505 0.030 1 164 91 91 TRP N N 121.444 0.300 1 165 92 92 ALA H H 8.871 0.030 1 166 92 92 ALA N N 126.392 0.300 1 167 94 94 ARG H H 8.157 0.030 1 168 94 94 ARG N N 122.387 0.300 1 169 95 95 LYS H H 8.230 0.030 1 170 95 95 LYS N N 123.691 0.300 1 171 98 98 ALA H H 8.316 0.030 1 172 98 98 ALA N N 125.602 0.300 1 173 100 100 LYS H H 8.417 0.030 1 174 100 100 LYS N N 121.864 0.300 1 175 101 101 SER H H 8.379 0.030 1 176 101 101 SER N N 116.941 0.300 1 177 102 102 THR H H 8.132 0.030 1 178 102 102 THR N N 115.628 0.300 1 179 103 103 TYR H H 8.126 0.030 1 180 103 103 TYR N N 121.905 0.300 1 181 104 104 GLU H H 8.226 0.030 1 182 104 104 GLU N N 122.689 0.300 1 183 105 105 SER H H 8.279 0.030 1 184 105 105 SER N N 116.823 0.300 1 185 107 107 THR H H 8.080 0.030 1 186 107 107 THR N N 114.229 0.300 1 187 108 108 LYS H H 8.274 0.030 1 188 108 108 LYS N N 123.629 0.300 1 189 109 109 GLN H H 8.388 0.030 1 190 109 109 GLN N N 121.432 0.300 1 191 110 110 SER H H 8.443 0.030 1 192 110 110 SER N N 117.406 0.300 1 193 111 111 GLY H H 8.242 0.030 1 194 111 111 GLY N N 110.755 0.300 1 195 113 113 SER H H 8.527 0.030 1 196 113 113 SER N N 116.727 0.300 1 197 114 114 SER H H 8.306 0.030 1 198 114 114 SER N N 117.833 0.300 1 199 115 115 GLY H H 8.031 0.030 1 200 115 115 GLY N N 116.861 0.300 1 stop_ save_