data_26914 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Chemical shifts of 20-mer from UBAP1 ; _BMRB_accession_number 26914 _BMRB_flat_file_name bmr26914.str _Entry_type original _Submission_date 2016-10-03 _Accession_date 2016-10-03 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details '1H and 13C shifts for 20mer peptide from UBAP1 which binds to coiled-coil domain of HD-PTP' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Cliff Matthew J. . 2 Tabernero Lydia . . 3 Gahloth Deepankor . . 4 Heaven Graham . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 58 "13C chemical shifts" 48 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-01-26 update BMRB 'update entry citation' 2016-11-04 original author 'original release' stop_ _Original_release_date 2016-11-04 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural Basis for Selective Interaction between the ESCRT Regulator HD-PTP and UBAP1 ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27839950 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Gahloth Deepankor . . 2 Levy Colin . . 3 Heaven Graham . . 4 Stefani Flavia . . 5 Wunderley Lydia . . 6 Mold Paul . . 7 Cliff Matthew J. . 8 Bella Jordi . . 9 Fielding Alistair J. . 10 Woodman Philip . . 11 Tabernero Lydia . . stop_ _Journal_abbreviation Structure _Journal_volume 24 _Journal_issue 12 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2115 _Page_last 2126 _Year 2016 _Details . loop_ _Keyword 'Endosomal ESCRTs regulation' 'coiled-coil structure' 'mitogenic signalling down-regulation' 'tumour supressor phosphatase' 'ubiquitin-dependent trafficking' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name UBAP1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label UBAP1 $UBAP1 stop_ _System_molecular_weight 2224 _System_physical_state 'intrinsically disordered' _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_UBAP1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common UBAP1 _Molecular_mass . _Mol_thiol_state 'not present' loop_ _Biological_function ; Component of the ESCRT-I complex, a regulator of vesicular trafficking process. Binds to ubiquitinated cargo proteins and is required for the sorting of endocytic ubiquitinated cargos into multivesicular bodies (MVBs). Plays a role in the proteasomal degradation of ubiquitinated cell-surface proteins, such as EGFR and BST2. ; stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 20 _Mol_residue_sequence ; SNIKSLSFPKLDSDDSNQKT ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 261 SER 2 262 ASN 3 263 ILE 4 264 LYS 5 265 SER 6 266 LEU 7 267 SER 8 268 PHE 9 269 PRO 10 270 LYS 11 271 LEU 12 272 ASP 13 273 SER 14 274 ASP 15 275 ASP 16 276 SER 17 277 ASN 18 278 GLN 19 279 LYS 20 280 THR stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . 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 UNP Q9NZ09 UBAP1_HUMAN . . . . . stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $UBAP1 human 9606 Eukaryota Metazoa Homo sapiens 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 $UBAP1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'Peptide dissolved in phosphate buffer pH 6.5 (read) in 99.8% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $UBAP1 3 mg/mL 'natural abundance' D2O 100 v/v '[U-100% 2H]' 'sodium phosphate' 50 mM 'natural abundance' 'sodium azide' 1 mM 'natural abundance' TSP 0.01 v/v 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '90% H2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $UBAP1 3 mg/mL 'natural abundance' D2O 100 v/v [U-2H] 'sodium phosphate' 50 mM 'natural abundance' 'sodium azide' 3 mM 'natural abundance' TSP 0.01 v/v 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 3.2 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_CCPN_Analysis _Saveframe_category software _Name CCPN_Analysis _Version . loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-13C_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC-TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC-TOCSY' _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' 50 . mM pH 6.7 . pH pressure 1 . atm temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_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 13 'methyl protons' ppm 0 internal indirect . . . 0.25 TSP H 1 'methyl protons' ppm 0 internal direct . . . 1 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $CCPN_Analysis stop_ loop_ _Experiment_label '2D 1H-13C HSQC' '2D 1H-1H NOESY' '2D 1H-13C HSQC-TOCSY' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name UBAP1 _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 1 261 1 SER CB C 64.180 0.006 1 2 262 2 ASN HA H 4.742 0.001 1 3 262 2 ASN HB2 H 2.779 0.009 2 4 262 2 ASN HB3 H 2.704 0.006 2 5 262 2 ASN CA C 53.016 0.013 1 6 262 2 ASN CB C 38.763 0.025 1 7 263 3 ILE HA H 4.077 0.002 1 8 263 3 ILE HB H 1.800 0.001 1 9 263 3 ILE HG12 H 1.132 0.003 2 10 263 3 ILE HG13 H 1.392 0.003 2 11 263 3 ILE HG2 H 0.819 0.021 1 12 263 3 ILE HD1 H 0.805 0.018 1 13 263 3 ILE CA C 61.293 0.046 1 14 263 3 ILE CB C 38.517 0.011 1 15 263 3 ILE CG1 C 27.219 0.055 1 16 263 3 ILE CG2 C 17.445 0.010 1 17 263 3 ILE CD1 C 12.779 0.018 1 18 264 4 LYS HA H 4.274 0.002 1 19 264 4 LYS CA C 55.997 0.016 1 20 265 5 SER HA H 4.361 0.025 1 21 265 5 SER CA C 58.101 0.011 1 22 265 5 SER CB C 63.596 0.049 1 23 266 6 LEU HA H 4.283 0.002 1 24 266 6 LEU HB2 H 1.459 0.005 2 25 266 6 LEU HB3 H 1.554 0.002 2 26 266 6 LEU HD1 H 0.801 0.002 2 27 266 6 LEU HD2 H 0.866 0.002 2 28 266 6 LEU CA C 55.069 0.020 1 29 266 6 LEU CB C 42.303 0.023 1 30 266 6 LEU CD1 C 23.291 0.010 2 31 266 6 LEU CD2 C 24.951 0.014 2 32 267 7 SER HA H 4.321 0.001 1 33 267 7 SER HB2 H 3.644 0.004 1 34 267 7 SER CA C 57.885 0.015 1 35 267 7 SER CB C 63.752 0.013 1 36 268 8 PHE HA H 4.827 0.001 1 37 268 8 PHE HB2 H 3.115 0.008 2 38 268 8 PHE HB3 H 2.846 0.010 2 39 268 8 PHE CA C 55.574 0.005 1 40 268 8 PHE CB C 39.035 0.032 1 41 269 9 PRO HA H 4.352 0.002 1 42 269 9 PRO HB2 H 2.204 0.002 2 43 269 9 PRO HB3 H 1.809 0.004 2 44 269 9 PRO HG2 H 1.925 0.001 1 45 269 9 PRO HD2 H 3.682 0.003 2 46 269 9 PRO HD3 H 3.514 0.002 2 47 269 9 PRO CA C 63.139 0.017 1 48 269 9 PRO CB C 32.048 0.028 1 49 269 9 PRO CG C 27.253 0.052 1 50 269 9 PRO CD C 50.556 0.038 1 51 270 10 LYS HA H 4.255 0.000 1 52 270 10 LYS CA C 56.342 0.005 1 53 271 11 LEU HA H 4.343 0.003 1 54 271 11 LEU HB2 H 1.591 0.005 2 55 271 11 LEU HB3 H 1.546 0.010 2 56 271 11 LEU HD1 H 0.861 0.001 2 57 271 11 LEU HD2 H 0.806 0.002 2 58 271 11 LEU CA C 54.906 0.011 1 59 271 11 LEU CB C 42.432 0.014 1 60 271 11 LEU CG C 26.936 0.058 1 61 271 11 LEU CD1 C 24.929 0.028 2 62 271 11 LEU CD2 C 23.313 0.004 2 63 272 12 ASP HA H 4.545 0.003 1 64 272 12 ASP HB2 H 2.554 0.007 2 65 272 12 ASP HB3 H 2.644 0.003 2 66 272 12 ASP CA C 54.311 0.017 1 67 272 12 ASP CB C 41.103 0.057 1 68 273 13 SER HA H 4.359 0.002 1 69 273 13 SER HB2 H 3.839 0.004 2 70 273 13 SER HB3 H 3.757 0.002 2 71 273 13 SER CA C 58.180 0.014 1 72 273 13 SER CB C 63.788 0.007 1 73 274 14 ASP HA H 4.575 0.002 1 74 274 14 ASP HB2 H 2.687 0.000 2 75 274 14 ASP HB3 H 2.609 0.000 2 76 274 14 ASP CA C 54.419 0.015 1 77 274 14 ASP CB C 41.194 0.007 1 78 275 15 ASP HA H 4.551 0.002 1 79 275 15 ASP HB2 H 2.632 0.000 1 80 275 15 ASP CA C 54.413 0.019 1 81 275 15 ASP CB C 41.000 0.027 1 82 276 16 SER HA H 4.277 0.003 1 83 276 16 SER HB2 H 3.871 0.005 2 84 276 16 SER HB3 H 3.830 0.002 2 85 276 16 SER CA C 59.354 0.017 1 86 276 16 SER CB C 63.437 0.027 1 87 277 17 ASN HA H 4.639 0.001 1 88 277 17 ASN HB2 H 2.791 0.010 2 89 277 17 ASN HB3 H 2.729 0.008 2 90 277 17 ASN CA C 53.509 0.016 1 91 277 17 ASN CB C 38.635 0.007 1 92 278 18 GLN HA H 4.236 0.004 1 93 278 18 GLN HB2 H 2.083 0.005 2 94 278 18 GLN HB3 H 1.928 0.006 2 95 278 18 GLN HG2 H 2.302 0.005 1 96 278 18 GLN CA C 56.003 0.016 1 97 278 18 GLN CB C 29.150 0.030 1 98 278 18 GLN CG C 33.700 0.011 1 99 279 19 LYS HA H 4.320 0.003 1 100 279 19 LYS CA C 56.371 0.005 1 101 280 20 THR HA H 4.239 0.004 1 102 280 20 THR HB H 4.179 0.003 1 103 280 20 THR HG2 H 1.139 0.002 1 104 280 20 THR CA C 61.451 0.009 1 105 280 20 THR CB C 69.669 0.016 1 106 280 20 THR CG2 C 21.466 0.014 1 stop_ save_