data_30234 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Representative 1-conformer ensembles of K27-linked Ub2 from RDC data ; _BMRB_accession_number 30234 _BMRB_flat_file_name bmr30234.str _Entry_type original _Submission_date 2017-01-18 _Accession_date 2017-01-18 _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 Castaneda C. A. . 2 Fushman D. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 140 "15N chemical shifts" 140 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-10-20 original BMRB . stop_ _Original_release_date 2017-10-17 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Linkage via K27 Bestows Ubiquitin Chains with Unique Properties among Polyubiquitins. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 26876099 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Castaneda C. A. . 2 Dixon E. K. . 3 Walker O. . . 4 Chaturvedi A. . . 5 Nakasone M. A. . 6 Curtis J. E. . 7 Reed M. R. . 8 Krueger S. . . 9 Cropp T. A. . 10 Fushman D. . . stop_ _Journal_abbreviation Structure _Journal_volume 24 _Journal_issue 3 _Journal_ASTM STRUE6 _Journal_ISSN 1878-4186 _Journal_CSD 2005 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 423 _Page_last 436 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Ubiquitin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'entity_1, 1' $entity_1 'entity_1, 2' $entity_1 stop_ _System_molecular_weight . _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 entity_1 _Molecular_mass 8576.831 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 76 _Mol_residue_sequence ; MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG ; loop_ _Residue_seq_code _Residue_label 1 MET 2 GLN 3 ILE 4 PHE 5 VAL 6 LYS 7 THR 8 LEU 9 THR 10 GLY 11 LYS 12 THR 13 ILE 14 THR 15 LEU 16 GLU 17 VAL 18 GLU 19 PRO 20 SER 21 ASP 22 THR 23 ILE 24 GLU 25 ASN 26 VAL 27 LYS 28 ALA 29 LYS 30 ILE 31 GLN 32 ASP 33 LYS 34 GLU 35 GLY 36 ILE 37 PRO 38 PRO 39 ASP 40 GLN 41 GLN 42 ARG 43 LEU 44 ILE 45 PHE 46 ALA 47 GLY 48 LYS 49 GLN 50 LEU 51 GLU 52 ASP 53 GLY 54 ARG 55 THR 56 LEU 57 SER 58 ASP 59 TYR 60 ASN 61 ILE 62 GLN 63 LYS 64 GLU 65 SER 66 THR 67 LEU 68 HIS 69 LEU 70 VAL 71 LEU 72 ARG 73 LEU 74 ARG 75 GLY 76 GLY 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 _Gene_mnemonic $entity_1 Human 9606 Eukaryota Metazoa Homo sapiens UBB 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 'recombinant technology' . Escherichia coli . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '150 uM [U-99% 15N] K27-diubiquitin, Distal Ub is 15N-labelled Proximal Ub is not enriched, 95% H2O/5% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 150 uM '[U-99% 15N]' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '150 uM [U-99% 15N] K27-diubiquitin, Distal Ub is not enriched Proximal Ub is 15N-labelled, 95% H2O/5% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 150 uM '[U-99% 15N]' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name ARMOR _Version 1.1 loop_ _Vendor _Address _Electronic_address 'Berlin K, Castaneda CA, Fushman D.' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 800 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_2 save_ save_2D_1H-15N_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_2 save_ save_2D_1H-15N_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 20 . mM pH 6.8 . pH pressure 1 . atm temperature 296 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 20 . mM pH 6.8 . pH pressure 1 . atm temperature 296 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . 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 water H 1 protons ppm 4.7 internal direct . . . 1.0 water N 15 protons ppm 4.7 internal indirect . . . 0.10132912 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_assigned_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details 'Chemical shifts are for proximal Ub (chain B in PDB file)' loop_ _Experiment_label '2D 1H-15N HSQC' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_1, 2' _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 2 2 GLN H H 8.846 . . 2 2 2 GLN N N 123.987 . . 3 3 3 ILE H H 8.217 . . 4 3 3 ILE N N 116.067 . . 5 4 4 PHE H H 8.509 . . 6 4 4 PHE N N 119.442 . . 7 5 5 VAL H H 9.185 . . 8 5 5 VAL N N 122.110 . . 9 6 6 LYS H H 8.854 . . 10 6 6 LYS N N 128.852 . . 11 7 7 THR H H 8.658 . . 12 7 7 THR N N 116.331 . . 13 8 8 LEU H H 9.075 . . 14 8 8 LEU N N 122.201 . . 15 9 9 THR H H 7.521 . . 16 9 9 THR N N 106.719 . . 17 10 10 GLY H H 7.723 . . 18 10 10 GLY N N 110.172 . . 19 11 11 LYS H H 7.161 . . 20 11 11 LYS N N 122.776 . . 21 12 12 THR H H 8.552 . . 22 12 12 THR N N 121.525 . . 23 13 13 ILE H H 9.472 . . 24 13 13 ILE N N 128.674 . . 25 14 14 THR H H 8.635 . . 26 14 14 THR N N 122.421 . . 27 15 15 LEU H H 8.633 . . 28 15 15 LEU N N 126.146 . . 29 16 16 GLU H H 8.021 . . 30 16 16 GLU N N 123.374 . . 31 17 17 VAL H H 8.836 . . 32 17 17 VAL N N 118.423 . . 33 18 18 GLU H H 8.533 . . 34 18 18 GLU N N 120.154 . . 35 20 20 SER H H 6.919 . . 36 20 20 SER N N 104.304 . . 37 21 21 ASP H H 7.916 . . 38 21 21 ASP N N 124.756 . . 39 22 22 THR H H 7.813 . . 40 22 22 THR N N 109.795 . . 41 23 23 ILE H H 8.396 . . 42 23 23 ILE N N 121.661 . . 43 24 24 GLU H H 9.513 . . 44 24 24 GLU N N 121.483 . . 45 25 25 ASN H H 7.770 . . 46 25 25 ASN N N 121.628 . . 47 26 26 VAL H H 7.967 . . 48 26 26 VAL N N 122.674 . . 49 28 28 ALA H H 7.880 . . 50 28 28 ALA N N 124.144 . . 51 29 29 LYS H H 7.712 . . 52 29 29 LYS N N 121.063 . . 53 30 30 ILE H H 8.179 . . 54 30 30 ILE N N 122.382 . . 55 31 31 GLN H H 8.435 . . 56 31 31 GLN N N 124.464 . . 57 32 32 ASP H H 7.879 . . 58 32 32 ASP N N 120.569 . . 59 33 33 LYS H H 7.343 . . 60 33 33 LYS N N 116.482 . . 61 34 34 GLU H H 8.635 . . 62 34 34 GLU N N 115.306 . . 63 35 35 GLY H H 8.365 . . 64 35 35 GLY N N 109.813 . . 65 36 36 ILE H H 6.110 . . 66 36 36 ILE N N 121.276 . . 67 39 39 ASP H H 8.253 . . 68 39 39 ASP N N 113.520 . . 69 40 40 GLN H H 7.749 . . 70 40 40 GLN N N 117.647 . . 71 41 41 GLN H H 7.357 . . 72 41 41 GLN N N 119.784 . . 73 42 42 ARG H H 8.167 . . 74 42 42 ARG N N 120.155 . . 75 43 43 LEU H H 8.714 . . 76 43 43 LEU N N 124.885 . . 77 44 44 ILE H H 8.990 . . 78 44 44 ILE N N 122.790 . . 79 45 45 PHE H H 8.703 . . 80 45 45 PHE N N 125.523 . . 81 46 46 ALA H H 9.102 . . 82 46 46 ALA N N 134.427 . . 83 47 47 GLY H H 7.976 . . 84 47 47 GLY N N 103.411 . . 85 48 48 LYS H H 7.889 . . 86 48 48 LYS N N 122.952 . . 87 49 49 GLN H H 8.486 . . 88 49 49 GLN N N 123.799 . . 89 50 50 LEU H H 8.357 . . 90 50 50 LEU N N 126.378 . . 91 51 51 GLU H H 8.050 . . 92 51 51 GLU N N 121.611 . . 93 52 52 ASP H H 8.118 . . 94 52 52 ASP N N 121.442 . . 95 54 54 ARG H H 7.286 . . 96 54 54 ARG N N 120.104 . . 97 55 55 THR H H 8.710 . . 98 55 55 THR N N 110.096 . . 99 56 56 LEU H H 8.091 . . 100 56 56 LEU N N 118.769 . . 101 57 57 SER H H 8.388 . . 102 57 57 SER N N 114.290 . . 103 58 58 ASP H H 7.798 . . 104 58 58 ASP N N 125.354 . . 105 59 59 TYR H H 7.163 . . 106 59 59 TYR N N 116.778 . . 107 60 60 ASN H H 8.031 . . 108 60 60 ASN N N 116.738 . . 109 61 61 ILE H H 7.133 . . 110 61 61 ILE N N 119.961 . . 111 62 62 GLN H H 7.532 . . 112 62 62 GLN N N 125.876 . . 113 63 63 LYS H H 8.376 . . 114 63 63 LYS N N 121.409 . . 115 64 64 GLU H H 9.243 . . 116 64 64 GLU N N 115.742 . . 117 65 65 SER H H 7.626 . . 118 65 65 SER N N 116.019 . . 119 66 66 THR H H 8.623 . . 120 66 66 THR N N 118.232 . . 121 67 67 LEU H H 9.312 . . 122 67 67 LEU N N 128.917 . . 123 68 68 HIS H H 9.150 . . 124 68 68 HIS N N 120.468 . . 125 69 69 LEU H H 8.140 . . 126 69 69 LEU N N 124.353 . . 127 70 70 VAL H H 9.063 . . 128 70 70 VAL N N 126.657 . . 129 71 71 LEU H H 7.922 . . 130 71 71 LEU N N 122.979 . . 131 72 72 ARG H H 8.435 . . 132 72 72 ARG N N 124.464 . . 133 73 73 LEU H H 8.230 . . 134 73 73 LEU N N 125.317 . . 135 74 74 ARG H H 8.350 . . 136 74 74 ARG N N 122.936 . . 137 75 75 GLY H H 8.408 . . 138 75 75 GLY N N 112.023 . . 139 76 76 GLY H H 7.851 . . 140 76 76 GLY N N 115.954 . . stop_ save_ save_assigned_chemical_shifts_2 _Saveframe_category assigned_chemical_shifts _Details 'Chemical shifts are for distal Ub (chain A in PDB file)' loop_ _Experiment_label '2D 1H-15N HSQC' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_1, 1' _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 2 2 GLN H H 8.850 . . 2 2 2 GLN N N 123.695 . . 3 3 3 ILE H H 8.196 . . 4 3 3 ILE N N 115.930 . . 5 4 4 PHE H H 8.505 . . 6 4 4 PHE N N 119.480 . . 7 5 5 VAL H H 9.183 . . 8 5 5 VAL N N 122.105 . . 9 6 6 LYS H H 8.863 . . 10 6 6 LYS N N 128.902 . . 11 7 7 THR H H 8.643 . . 12 7 7 THR N N 116.369 . . 13 8 8 LEU H H 9.043 . . 14 8 8 LEU N N 122.122 . . 15 9 9 THR H H 7.520 . . 16 9 9 THR N N 106.620 . . 17 10 10 GLY H H 7.720 . . 18 10 10 GLY N N 110.150 . . 19 11 11 LYS H H 7.158 . . 20 11 11 LYS N N 122.809 . . 21 12 12 THR H H 8.546 . . 22 12 12 THR N N 121.496 . . 23 13 13 ILE H H 9.457 . . 24 13 13 ILE N N 128.559 . . 25 14 14 THR H H 8.641 . . 26 14 14 THR N N 122.432 . . 27 15 15 LEU H H 8.639 . . 28 15 15 LEU N N 126.056 . . 29 16 16 GLU H H 8.018 . . 30 16 16 GLU N N 123.361 . . 31 17 17 VAL H H 8.838 . . 32 17 17 VAL N N 118.436 . . 33 18 18 GLU H H 8.545 . . 34 18 18 GLU N N 120.162 . . 35 20 20 SER H H 6.922 . . 36 20 20 SER N N 104.271 . . 37 21 21 ASP H H 7.948 . . 38 21 21 ASP N N 124.854 . . 39 22 22 THR H H 7.785 . . 40 22 22 THR N N 109.932 . . 41 23 23 ILE H H 8.414 . . 42 23 23 ILE N N 122.131 . . 43 25 25 ASN H H 7.825 . . 44 25 25 ASN N N 122.373 . . 45 26 26 VAL H H 8.010 . . 46 26 26 VAL N N 123.099 . . 47 27 27 LYS H H 8.454 . . 48 27 27 LYS N N 119.876 . . 49 28 28 ALA H H 7.862 . . 50 28 28 ALA N N 124.385 . . 51 29 29 LYS H H 7.758 . . 52 29 29 LYS N N 121.169 . . 53 30 30 ILE H H 8.185 . . 54 30 30 ILE N N 122.289 . . 55 31 31 GLN H H 8.451 . . 56 31 31 GLN N N 124.473 . . 57 32 32 ASP H H 7.919 . . 58 32 32 ASP N N 120.662 . . 59 33 33 LYS H H 7.319 . . 60 33 33 LYS N N 116.368 . . 61 34 34 GLU H H 8.622 . . 62 34 34 GLU N N 115.220 . . 63 35 35 GLY H H 8.394 . . 64 35 35 GLY N N 109.803 . . 65 36 36 ILE H H 6.045 . . 66 36 36 ILE N N 121.205 . . 67 39 39 ASP H H 8.430 . . 68 39 39 ASP N N 114.555 . . 69 40 40 GLN H H 7.723 . . 70 40 40 GLN N N 117.719 . . 71 41 41 GLN H H 7.388 . . 72 41 41 GLN N N 119.065 . . 73 42 42 ARG H H 8.393 . . 74 42 42 ARG N N 124.101 . . 75 43 43 LEU H H 8.719 . . 76 43 43 LEU N N 125.380 . . 77 44 44 ILE H H 9.023 . . 78 44 44 ILE N N 123.175 . . 79 45 45 PHE H H 8.741 . . 80 45 45 PHE N N 125.744 . . 81 46 46 ALA H H 8.909 . . 82 46 46 ALA N N 133.953 . . 83 47 47 GLY H H 7.998 . . 84 47 47 GLY N N 103.339 . . 85 48 48 LYS H H 7.857 . . 86 48 48 LYS N N 122.911 . . 87 49 49 GLN H H 8.567 . . 88 49 49 GLN N N 124.108 . . 89 50 50 LEU H H 8.457 . . 90 50 50 LEU N N 126.595 . . 91 51 51 GLU H H 8.295 . . 92 51 51 GLU N N 124.017 . . 93 52 52 ASP H H 8.071 . . 94 52 52 ASP N N 121.323 . . 95 54 54 ARG H H 7.359 . . 96 54 54 ARG N N 120.272 . . 97 55 55 THR H H 8.729 . . 98 55 55 THR N N 109.712 . . 99 56 56 LEU H H 8.041 . . 100 56 56 LEU N N 118.916 . . 101 57 57 SER H H 8.384 . . 102 57 57 SER N N 114.409 . . 103 58 58 ASP H H 7.833 . . 104 58 58 ASP N N 125.466 . . 105 59 59 TYR H H 7.150 . . 106 59 59 TYR N N 116.680 . . 107 60 60 ASN H H 8.047 . . 108 60 60 ASN N N 116.907 . . 109 61 61 ILE H H 7.142 . . 110 61 61 ILE N N 119.823 . . 111 62 62 GLN H H 7.519 . . 112 62 62 GLN N N 125.839 . . 113 63 63 LYS H H 8.399 . . 114 63 63 LYS N N 121.502 . . 115 64 64 GLU H H 9.223 . . 116 64 64 GLU N N 115.527 . . 117 65 65 SER H H 7.557 . . 118 65 65 SER N N 115.877 . . 119 66 66 THR H H 8.615 . . 120 66 66 THR N N 118.337 . . 121 67 67 LEU H H 9.304 . . 122 67 67 LEU N N 128.731 . . 123 68 68 HIS H H 9.110 . . 124 68 68 HIS N N 120.477 . . 125 69 69 LEU H H 8.165 . . 126 69 69 LEU N N 124.627 . . 127 70 70 VAL H H 9.055 . . 128 70 70 VAL N N 127.105 . . 129 71 71 LEU H H 8.016 . . 130 71 71 LEU N N 123.833 . . 131 72 72 ARG H H 8.479 . . 132 72 72 ARG N N 124.558 . . 133 73 73 LEU H H 8.317 . . 134 73 73 LEU N N 125.809 . . 135 74 74 ARG H H 8.406 . . 136 74 74 ARG N N 122.926 . . 137 75 75 GLY H H 8.424 . . 138 75 75 GLY N N 111.361 . . 139 76 76 GLY H H 8.379 . . 140 76 76 GLY N N 111.174 . . stop_ save_