data_30340 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structures of REV1 UBM2 domain complex with ubiquitin and with the first small-molecule that inhibits the REV1 UBM2-ubiquitin interaction ; _BMRB_accession_number 30340 _BMRB_flat_file_name bmr30340.str _Entry_type original _Submission_date 2017-09-06 _Accession_date 2017-09-06 _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 Fujii N. . . 2 Vanarotti M. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 99 "13C chemical shifts" 58 "15N chemical shifts" 55 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-09-28 update BMRB 'update entry citation' 2018-06-21 original author 'original release' stop_ _Original_release_date 2017-10-30 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structures of REV1 UBM2 Domain Complex with Ubiquitin and with a Small-Molecule that Inhibits the REV1 UBM2-Ubiquitin Interaction ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 29864443 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Vanarotti Murugendra . . 2 Grace Christy R. . 3 Miller Darcie J. . 4 Actis Marcelo L. . 5 Inoue Akira . . 6 Evison Benjamin J. . 7 Vaithiyalingam Sivaraja . . 8 Singh Aman P. . 9 McDonald Ezelle T. . 10 Fujii Naoaki . . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_name_full 'Journal of molecular biology' _Journal_volume 430 _Journal_issue 17 _Journal_ISSN 1089-8638 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2857 _Page_last 2872 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'DNA repair protein REV1 (E.C.2.7.7.-)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $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 7813.632 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 72 _Mol_residue_sequence ; MGSSHHHHHHHHLNGSSLVP RGSIKSSGLESNSDAGINLI ALPAFSQVDPEVFAALPAEL QRELKAAYDQRQ ; loop_ _Residue_seq_code _Residue_label 1 MET 2 GLY 3 SER 4 SER 5 HIS 6 HIS 7 HIS 8 HIS 9 HIS 10 HIS 11 HIS 12 HIS 13 LEU 14 ASN 15 GLY 16 SER 17 SER 18 LEU 19 VAL 20 PRO 21 ARG 22 GLY 23 SER 24 ILE 25 LYS 26 SER 27 SER 28 GLY 29 LEU 30 GLU 31 SER 32 ASN 33 SER 34 ASP 35 ALA 36 GLY 37 ILE 38 ASN 39 LEU 40 ILE 41 ALA 42 LEU 43 PRO 44 ALA 45 PHE 46 SER 47 GLN 48 VAL 49 ASP 50 PRO 51 GLU 52 VAL 53 PHE 54 ALA 55 ALA 56 LEU 57 PRO 58 ALA 59 GLU 60 LEU 61 GLN 62 ARG 63 GLU 64 LEU 65 LYS 66 ALA 67 ALA 68 TYR 69 ASP 70 GLN 71 ARG 72 GLN 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 'REV1, REV1L' 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' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '0.5 mM [U-13C; U-15N] REV1 UBM2, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.5 mM '[U-13C; U-15N]' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '0.5 mM [U-99% 15N] REV1 UBM2, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.5 mM '[U-99% 15N]' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CARA _Version . loop_ _Vendor _Address _Electronic_address 'Keller and Wuthrich' . . stop_ loop_ _Task 'peak picking' refinement stop_ _Details . save_ save_software_2 _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _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_2 save_ save_3D_HNCA_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCA' _Sample_label $sample_1 save_ save_3D_HNCACB_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCACB' _Sample_label $sample_1 save_ save_3D_HCCH-TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCCH-TOCSY' _Sample_label $sample_1 save_ save_3D_1H-15N_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 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' 0.5 . mM pH 7.0 . pH pressure 1 . mbar temperature 298 . 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 TSP C 12 'methyl carbons' ppm 0 external indirect . . . 1.0 TSP H 1 protons ppm 4.78 external direct . . . 1.0 TSP N 15 nitrogen ppm 0 external indirect . . . 1.0 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 . loop_ _Experiment_label '2D 1H-15N HSQC' '3D HNCA' '3D HNCACB' '3D HCCH-TOCSY' '3D 1H-15N NOESY' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_2 $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_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 12 12 HIS H H 8.233 0.020 . 2 12 12 HIS CA C 53.467 0.300 . 3 12 12 HIS N N 122.374 0.300 . 4 13 13 LEU H H 8.191 0.020 . 5 13 13 LEU CA C 52.453 0.300 . 6 13 13 LEU N N 123.139 0.300 . 7 14 14 ASN H H 8.439 0.020 . 8 14 14 ASN CA C 50.486 0.300 . 9 14 14 ASN N N 119.278 0.300 . 10 15 15 GLY H H 8.329 0.020 . 11 15 15 GLY CA C 42.890 0.300 . 12 15 15 GLY N N 109.412 0.300 . 13 16 16 SER H H 8.115 0.020 . 14 16 16 SER CA C 55.425 0.300 . 15 16 16 SER N N 115.410 0.300 . 16 17 17 SER H H 8.266 0.020 . 17 17 17 SER CA C 55.878 0.300 . 18 17 17 SER N N 117.469 0.300 . 19 18 18 LEU H H 8.140 0.020 . 20 18 18 LEU CA C 52.453 0.300 . 21 18 18 LEU N N 123.652 0.300 . 22 19 19 VAL H H 7.905 0.020 . 23 19 19 VAL CA C 56.944 0.300 . 24 19 19 VAL N N 121.806 0.300 . 25 21 21 ARG H H 8.426 0.020 . 26 21 21 ARG CA C 53.684 0.300 . 27 21 21 ARG N N 122.026 0.300 . 28 22 22 GLY H H 8.415 0.020 . 29 22 22 GLY CA C 42.528 0.300 . 30 22 22 GLY N N 109.952 0.300 . 31 25 25 LYS H H 8.341 0.020 . 32 25 25 LYS CA C 53.354 0.300 . 33 25 25 LYS N N 125.466 0.300 . 34 26 26 SER H H 8.281 0.020 . 35 26 26 SER CA C 55.713 0.300 . 36 26 26 SER N N 117.425 0.300 . 37 27 27 SER H H 8.381 0.020 . 38 27 27 SER CA C 55.713 0.300 . 39 27 27 SER N N 117.846 0.300 . 40 28 28 GLY H H 8.388 0.020 . 41 28 28 GLY CA C 42.487 0.300 . 42 28 28 GLY N N 110.656 0.300 . 43 29 29 LEU H H 8.026 0.020 . 44 29 29 LEU CA C 52.525 0.300 . 45 29 29 LEU N N 121.308 0.300 . 46 30 30 GLU H H 8.461 0.020 . 47 30 30 GLU HA H 4.077 0.020 . 48 30 30 GLU CA C 54.507 0.300 . 49 30 30 GLU N N 121.232 0.300 . 50 31 31 SER H H 8.224 0.020 . 51 31 31 SER HA H 4.179 0.020 . 52 31 31 SER CA C 56.380 0.300 . 53 31 31 SER N N 116.241 0.300 . 54 32 32 ASN H H 8.083 0.020 . 55 32 32 ASN HA H 4.635 0.020 . 56 32 32 ASN CA C 50.444 0.300 . 57 32 32 ASN N N 122.421 0.300 . 58 33 33 SER H H 8.233 0.020 . 59 33 33 SER HA H 4.177 0.020 . 60 33 33 SER CA C 56.205 0.300 . 61 33 33 SER N N 116.129 0.300 . 62 34 34 ASP H H 8.277 0.020 . 63 34 34 ASP HA H 4.543 0.020 . 64 34 34 ASP CA C 51.703 0.300 . 65 34 34 ASP N N 122.355 0.300 . 66 35 35 ALA H H 8.100 0.020 . 67 35 35 ALA HA H 4.213 0.020 . 68 35 35 ALA CA C 50.119 0.300 . 69 35 35 ALA N N 123.894 0.300 . 70 36 36 GLY H H 8.274 0.020 . 71 36 36 GLY HA2 H 3.910 0.020 . 72 36 36 GLY HA3 H 3.856 0.020 . 73 36 36 GLY CA C 42.695 0.300 . 74 36 36 GLY N N 107.403 0.300 . 75 37 37 ILE H H 7.776 0.020 . 76 37 37 ILE HA H 4.081 0.020 . 77 37 37 ILE CA C 58.427 0.300 . 78 37 37 ILE N N 119.314 0.300 . 79 38 38 ASN H H 8.357 0.020 . 80 38 38 ASN HA H 4.632 0.020 . 81 38 38 ASN CA C 50.225 0.300 . 82 38 38 ASN N N 121.967 0.300 . 83 39 39 LEU H H 8.107 0.020 . 84 39 39 LEU HA H 4.282 0.020 . 85 39 39 LEU CA C 52.466 0.300 . 86 39 39 LEU N N 122.695 0.300 . 87 40 40 ILE H H 7.873 0.020 . 88 40 40 ILE HA H 4.035 0.020 . 89 40 40 ILE CA C 58.237 0.300 . 90 40 40 ILE N N 120.082 0.300 . 91 41 41 ALA H H 8.016 0.020 . 92 41 41 ALA HA H 4.282 0.020 . 93 41 41 ALA CA C 49.005 0.300 . 94 41 41 ALA N N 126.891 0.300 . 95 42 42 LEU H H 7.455 0.020 . 96 42 42 LEU HA H 4.463 0.020 . 97 42 42 LEU CA C 50.299 0.300 . 98 42 42 LEU N N 121.067 0.300 . 99 43 43 PRO HA H 4.291 0.020 . 100 43 43 PRO CA C 60.328 0.300 . 101 44 44 ALA H H 8.142 0.020 . 102 44 44 ALA HA H 4.121 0.020 . 103 44 44 ALA CA C 49.940 0.300 . 104 44 44 ALA N N 122.455 0.300 . 105 45 45 PHE H H 8.079 0.020 . 106 45 45 PHE HA H 4.326 0.020 . 107 45 45 PHE CA C 55.959 0.300 . 108 45 45 PHE N N 118.304 0.300 . 109 46 46 SER H H 7.929 0.020 . 110 46 46 SER HA H 4.176 0.020 . 111 46 46 SER CA C 55.900 0.300 . 112 46 46 SER N N 115.090 0.300 . 113 47 47 GLN H H 8.057 0.020 . 114 47 47 GLN HA H 4.245 0.020 . 115 47 47 GLN CA C 53.095 0.300 . 116 47 47 GLN N N 120.500 0.300 . 117 48 48 VAL H H 7.710 0.020 . 118 48 48 VAL HA H 3.988 0.020 . 119 48 48 VAL CA C 58.985 0.300 . 120 48 48 VAL N N 120.128 0.300 . 121 49 49 ASP H H 8.404 0.020 . 122 49 49 ASP HA H 4.641 0.020 . 123 49 49 ASP CA C 50.220 0.300 . 124 49 49 ASP N N 127.253 0.300 . 125 50 50 PRO HA H 4.210 0.020 . 126 50 50 PRO CA C 62.241 0.300 . 127 51 51 GLU H H 8.636 0.020 . 128 51 51 GLU HA H 4.080 0.020 . 129 51 51 GLU CA C 55.832 0.300 . 130 51 51 GLU N N 118.582 0.300 . 131 52 52 VAL H H 7.562 0.020 . 132 52 52 VAL HA H 3.710 0.020 . 133 52 52 VAL CA C 61.798 0.300 . 134 52 52 VAL N N 120.729 0.300 . 135 53 53 PHE H H 8.086 0.020 . 136 53 53 PHE HA H 3.997 0.020 . 137 53 53 PHE CA C 57.536 0.300 . 138 53 53 PHE N N 120.398 0.300 . 139 54 54 ALA H H 7.784 0.020 . 140 54 54 ALA HA H 3.976 0.020 . 141 54 54 ALA CA C 50.695 0.300 . 142 54 54 ALA N N 118.546 0.300 . 143 55 55 ALA H H 7.341 0.020 . 144 55 55 ALA HA H 4.279 0.020 . 145 55 55 ALA CA C 48.941 0.300 . 146 55 55 ALA N N 118.927 0.300 . 147 56 56 LEU H H 7.969 0.020 . 148 56 56 LEU HA H 4.396 0.020 . 149 56 56 LEU CA C 50.291 0.300 . 150 56 56 LEU N N 122.560 0.300 . 151 57 57 PRO HA H 4.351 0.020 . 152 57 57 PRO CA C 60.127 0.300 . 153 58 58 ALA H H 8.720 0.020 . 154 58 58 ALA HA H 3.885 0.020 . 155 58 58 ALA CA C 52.552 0.300 . 156 58 58 ALA N N 126.564 0.300 . 157 59 59 GLU H H 9.211 0.020 . 158 59 59 GLU HA H 3.993 0.020 . 159 59 59 GLU CA C 56.408 0.300 . 160 59 59 GLU N N 116.596 0.300 . 161 60 60 LEU H H 7.200 0.020 . 162 60 60 LEU HA H 4.264 0.020 . 163 60 60 LEU CA C 53.708 0.300 . 164 60 60 LEU N N 120.172 0.300 . 165 61 61 GLN H H 7.941 0.020 . 166 61 61 GLN HA H 3.700 0.020 . 167 61 61 GLN CA C 56.155 0.300 . 168 61 61 GLN N N 118.650 0.300 . 169 62 62 ARG H H 7.831 0.020 . 170 62 62 ARG HA H 4.000 0.020 . 171 62 62 ARG CA C 56.054 0.300 . 172 62 62 ARG N N 117.304 0.300 . 173 63 63 GLU H H 7.718 0.020 . 174 63 63 GLU HA H 4.081 0.020 . 175 63 63 GLU CA C 55.568 0.300 . 176 63 63 GLU N N 119.916 0.300 . 177 64 64 LEU H H 8.245 0.020 . 178 64 64 LEU HA H 4.144 0.020 . 179 64 64 LEU CA C 54.299 0.300 . 180 64 64 LEU N N 120.763 0.300 . 181 65 65 LYS H H 8.079 0.020 . 182 65 65 LYS HA H 3.942 0.020 . 183 65 65 LYS CA C 55.759 0.300 . 184 65 65 LYS N N 119.538 0.300 . 185 66 66 ALA H H 7.883 0.020 . 186 66 66 ALA HA H 4.149 0.020 . 187 66 66 ALA CA C 51.149 0.300 . 188 66 66 ALA N N 121.448 0.300 . 189 67 67 ALA H H 7.746 0.020 . 190 67 67 ALA HA H 4.120 0.020 . 191 67 67 ALA CA C 50.786 0.300 . 192 67 67 ALA N N 120.546 0.300 . 193 68 68 TYR H H 7.867 0.020 . 194 68 68 TYR HA H 4.318 0.020 . 195 68 68 TYR CA C 57.023 0.300 . 196 68 68 TYR N N 118.114 0.300 . 197 69 69 ASP H H 8.182 0.020 . 198 69 69 ASP HA H 4.447 0.020 . 199 69 69 ASP CA C 52.356 0.300 . 200 69 69 ASP N N 120.746 0.300 . 201 70 70 GLN H H 7.851 0.020 . 202 70 70 GLN HA H 4.243 0.020 . 203 70 70 GLN CA C 52.795 0.300 . 204 70 70 GLN N N 118.968 0.300 . 205 71 71 ARG H H 7.934 0.020 . 206 71 71 ARG HA H 4.241 0.020 . 207 71 71 ARG CA C 53.513 0.300 . 208 71 71 ARG N N 121.400 0.300 . 209 72 72 GLN H H 7.835 0.020 . 210 72 72 GLN HA H 4.230 0.020 . 211 72 72 GLN CA C 53.816 0.300 . 212 72 72 GLN N N 125.927 0.300 . stop_ save_