data_17059 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Identification of a novel ubiquitin binding site of STAM1 VHS domain by NMR spectroscopy ; _BMRB_accession_number 17059 _BMRB_flat_file_name bmr17059.str _Entry_type new _Submission_date 2010-07-13 _Accession_date 2010-07-13 _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 Hong Yoon-Hun . . 2 Ahn Hee-Chul . . 3 Lim Jongsoo . . 4 Kim Hong-Man . . 5 Ji Hye-Young . . 6 Lee Seunga . . 7 Kim Ji-Hun . . 8 Park Eun Y. . 9 Song Hyun K. . 10 Lee Bong-Jin . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count binding_constants 1 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-09-08 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Identification of a novel ubiquitin binding site of STAM1 VHS domain by NMR spectroscopy' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hong Yoon-Hun . . 2 Ahn Hee-Chul . . 3 Lim Jongsoo . . 4 Kim Hong-Man . . 5 Ji Hye-Young . . 6 Lee Seunga . . 7 Kim Ji-Hun . . 8 Park Eun Y. . 9 Song Hyun K. . 10 Lee Bong-Jin . . stop_ _Journal_abbreviation 'FEBS Lett.' _Journal_volume 583 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 287 _Page_last 292 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'STAM1/ubiquitin complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label STAM1 $STAM1 ubiquitin $ubiquitin 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_STAM1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common STAM1 _Molecular_mass . _Mol_thiol_state 'not reported' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 178 _Mol_residue_sequence ; PLFATNPFDQDVEKATSEMN TAEDWGLILDICDKVGQSRT GPKDCLRSIMRRVNHKDPHV AMQALTLLGACVSNCGKIFH LEVCSRDFASEVSNVLNKGH PKVCEKLKALMVEWTDEFKN DPQLSLISAMIKNLKEQGVT FPAIGSQAAEQAKASPALVA KDPGTVANKKEEEDLAKA ; loop_ _Residue_seq_code _Residue_label 1 PRO 2 LEU 3 PHE 4 ALA 5 THR 6 ASN 7 PRO 8 PHE 9 ASP 10 GLN 11 ASP 12 VAL 13 GLU 14 LYS 15 ALA 16 THR 17 SER 18 GLU 19 MET 20 ASN 21 THR 22 ALA 23 GLU 24 ASP 25 TRP 26 GLY 27 LEU 28 ILE 29 LEU 30 ASP 31 ILE 32 CYS 33 ASP 34 LYS 35 VAL 36 GLY 37 GLN 38 SER 39 ARG 40 THR 41 GLY 42 PRO 43 LYS 44 ASP 45 CYS 46 LEU 47 ARG 48 SER 49 ILE 50 MET 51 ARG 52 ARG 53 VAL 54 ASN 55 HIS 56 LYS 57 ASP 58 PRO 59 HIS 60 VAL 61 ALA 62 MET 63 GLN 64 ALA 65 LEU 66 THR 67 LEU 68 LEU 69 GLY 70 ALA 71 CYS 72 VAL 73 SER 74 ASN 75 CYS 76 GLY 77 LYS 78 ILE 79 PHE 80 HIS 81 LEU 82 GLU 83 VAL 84 CYS 85 SER 86 ARG 87 ASP 88 PHE 89 ALA 90 SER 91 GLU 92 VAL 93 SER 94 ASN 95 VAL 96 LEU 97 ASN 98 LYS 99 GLY 100 HIS 101 PRO 102 LYS 103 VAL 104 CYS 105 GLU 106 LYS 107 LEU 108 LYS 109 ALA 110 LEU 111 MET 112 VAL 113 GLU 114 TRP 115 THR 116 ASP 117 GLU 118 PHE 119 LYS 120 ASN 121 ASP 122 PRO 123 GLN 124 LEU 125 SER 126 LEU 127 ILE 128 SER 129 ALA 130 MET 131 ILE 132 LYS 133 ASN 134 LEU 135 LYS 136 GLU 137 GLN 138 GLY 139 VAL 140 THR 141 PHE 142 PRO 143 ALA 144 ILE 145 GLY 146 SER 147 GLN 148 ALA 149 ALA 150 GLU 151 GLN 152 ALA 153 LYS 154 ALA 155 SER 156 PRO 157 ALA 158 LEU 159 VAL 160 ALA 161 LYS 162 ASP 163 PRO 164 GLY 165 THR 166 VAL 167 ALA 168 ASN 169 LYS 170 LYS 171 GLU 172 GLU 173 GLU 174 ASP 175 LEU 176 ALA 177 LYS 178 ALA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-07-08 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 16763 VHS 77.53 138 100.00 100.00 1.26e-97 BMRB 17065 Tandem_ubiquitin_binding_domains_of_STAM1 100.00 191 100.00 100.00 9.98e-128 PDB 3LDZ "Crystal Structure Of Human Stam1 Vhs Domain In Complex With Ubiquitin" 78.65 140 100.00 100.00 2.27e-99 DBJ BAE26170 "unnamed protein product [Mus musculus]" 100.00 553 98.88 99.44 4.21e-124 DBJ BAE28168 "unnamed protein product [Mus musculus]" 100.00 462 98.88 99.44 2.48e-124 DBJ BAE34187 "unnamed protein product [Mus musculus]" 100.00 548 98.88 99.44 1.90e-124 DBJ BAE37536 "unnamed protein product [Mus musculus]" 100.00 548 98.88 99.44 1.90e-124 DBJ BAE40949 "unnamed protein product [Mus musculus]" 100.00 548 98.88 99.44 1.90e-124 GB AAC50734 "STAM [Homo sapiens]" 100.00 540 100.00 100.00 2.38e-125 GB AAC52840 "STAM [Mus musculus]" 100.00 548 98.88 99.44 1.90e-124 GB AAH30586 "STAM protein [Homo sapiens]" 100.00 403 100.00 100.00 1.73e-125 GB AAH44666 "Signal transducing adaptor molecule (SH3 domain and ITAM motif) 1 [Mus musculus]" 100.00 548 98.88 99.44 1.90e-124 GB AAH55326 "Signal transducing adaptor molecule (SH3 domain and ITAM motif) 1 [Mus musculus]" 100.00 548 98.88 99.44 1.90e-124 REF NP_001070310 "signal transducing adapter molecule 1 [Bos taurus]" 100.00 534 99.44 99.44 3.49e-125 REF NP_001102591 "signal transducing adapter molecule 1 [Rattus norvegicus]" 100.00 547 98.88 99.44 3.97e-124 REF NP_003464 "signal transducing adapter molecule 1 [Homo sapiens]" 100.00 540 100.00 100.00 2.38e-125 REF NP_035614 "signal transducing adapter molecule 1 [Mus musculus]" 100.00 548 98.88 99.44 1.90e-124 REF XP_001094352 "PREDICTED: signal transducing adapter molecule 1 [Macaca mulatta]" 72.47 490 99.22 99.22 2.07e-84 SP P70297 "RecName: Full=Signal transducing adapter molecule 1; Short=STAM-1" 100.00 548 98.88 99.44 1.90e-124 SP Q92783 "RecName: Full=Signal transducing adapter molecule 1; Short=STAM-1" 100.00 540 100.00 100.00 2.38e-125 TPG DAA23567 "TPA: signal transducing adaptor molecule 1 [Bos taurus]" 100.00 534 99.44 99.44 3.49e-125 stop_ save_ save_ubiquitin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common ubiquitin _Molecular_mass . _Mol_thiol_state 'not reported' _Details . _Residue_count 156 _Mol_residue_sequence ; MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGGAKKR KKKSYTTPKKNKHKRKKVKL AVLKYYKVDENGKISRLRRE CPSDECGAGVFMASHFDRHY CGKCCLTYCFNKPEDK ; 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 77 ALA 78 LYS 79 LYS 80 ARG 81 LYS 82 LYS 83 LYS 84 SER 85 TYR 86 THR 87 THR 88 PRO 89 LYS 90 LYS 91 ASN 92 LYS 93 HIS 94 LYS 95 ARG 96 LYS 97 LYS 98 VAL 99 LYS 100 LEU 101 ALA 102 VAL 103 LEU 104 LYS 105 TYR 106 TYR 107 LYS 108 VAL 109 ASP 110 GLU 111 ASN 112 GLY 113 LYS 114 ILE 115 SER 116 ARG 117 LEU 118 ARG 119 ARG 120 GLU 121 CYS 122 PRO 123 SER 124 ASP 125 GLU 126 CYS 127 GLY 128 ALA 129 GLY 130 VAL 131 PHE 132 MET 133 ALA 134 SER 135 HIS 136 PHE 137 ASP 138 ARG 139 HIS 140 TYR 141 CYS 142 GLY 143 LYS 144 CYS 145 CYS 146 LEU 147 THR 148 TYR 149 CYS 150 PHE 151 ASN 152 LYS 153 PRO 154 GLU 155 ASP 156 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-30 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 PDB 3J3A "Structure Of The Human 40s Ribosomal Proteins" 51.28 80 100.00 100.00 8.80e-50 PDB 4CXC "Regulation Of The Mammalian Elongation Cycle By 40s Subunit Rolling: A Eukaryotic-specific Ribosome Rearrangement" 100.00 156 100.00 100.00 1.42e-109 PDB 4KZX "Rabbit 40s Ribosomal Subunit In Complex With Eif1." 100.00 156 100.00 100.00 1.42e-109 PDB 4KZY "Rabbit 40s Ribosomal Subunit In Complex With Eif1 And Eif1a." 100.00 156 100.00 100.00 1.42e-109 PDB 4KZZ "Rabbit 40s Ribosomal Subunit In Complex With Mrna, Initiator Trna And Eif1a" 100.00 156 100.00 100.00 1.42e-109 PDB 4UQ4 "Mammalian 80s Hcv-ires Initiation Complex With Eif5b Post-like State" 100.00 156 100.00 100.00 1.42e-109 PDB 4UQ5 "Mammalian 80s Hcv-ires Initiation Complex With Eif5b Pre-like State" 100.00 156 100.00 100.00 1.42e-109 PDB 4W23 "Structure Of The 80s Mammalian Ribosome Bound To Eef2 (this Entry Contains The Small Ribosomal Subunit)" 100.00 156 100.00 100.00 1.42e-109 PDB 4W28 "Structure Of The Translating Mammalian Ribosome-sec61 Complex (this Entry Contains The Small Ribosomal Subunit)" 100.00 156 100.00 100.00 1.42e-109 DBJ BAA04129 "polyubiquitin [Rattus norvegicus]" 50.00 810 97.44 98.72 5.84e-41 DBJ BAA09096 "TI-225 [Mus musculus]" 50.00 126 97.44 98.72 2.25e-45 DBJ BAA11843 "ubiquitin extention protein [Cavia porcellus]" 100.00 156 100.00 100.00 1.42e-109 DBJ BAB27296 "unnamed protein product [Mus musculus]" 50.00 354 97.44 98.72 9.22e-43 DBJ BAB31357 "unnamed protein product [Mus musculus]" 100.00 156 99.36 99.36 9.11e-109 EMBL CAA44911 "ubiquitin [Homo sapiens]" 100.00 156 100.00 100.00 1.42e-109 EMBL CAA57432 "fusion protein: ubiquitin (bases 43_513); ribosomal protein S27a (bases 217_532) [Rattus norvegicus]" 100.00 156 99.36 99.36 9.11e-109 EMBL CAG12343 "unnamed protein product, partial [Tetraodon nigroviridis]" 89.74 140 97.14 97.86 1.57e-94 EMBL CAI73380 "ubiquitin, putative [Theileria annulata]" 50.64 159 97.47 97.47 8.71e-45 EMBL CAJ83451 "ribosomal protein S27a [Xenopus (Silurana) tropicalis]" 100.00 156 100.00 100.00 1.42e-109 GB AAA28997 "ubiquitin [Drosophila melanogaster]" 50.00 231 97.44 98.72 4.75e-44 GB AAA36788 "pro-ubiquitin, partial [Homo sapiens]" 97.44 152 100.00 100.00 6.60e-106 GB AAA53067 "p125 protein, partial [Bovine viral diarrhea virus 1]" 50.00 1054 97.44 98.72 2.65e-40 GB AAA57047 "ubiquitin, partial [synthetic construct]" 100.00 157 100.00 100.00 1.71e-109 GB AAB03872 "polyubiquitin, partial [Manduca sexta]" 50.00 79 97.44 98.72 8.03e-46 PIR UQHUR7 "ubiquitin / ribosomal protein S27a, cytosolic [validated] - human" 100.00 156 100.00 100.00 1.42e-109 REF NP_001013290 "ubiquitin [Danio rerio]" 50.00 610 97.44 98.72 1.51e-41 REF NP_001016172 "ribosomal protein S27a [Xenopus (Silurana) tropicalis]" 100.00 156 100.00 100.00 1.42e-109 REF NP_001029037 "ubiquitin-40S ribosomal protein S27a precursor [Mus musculus]" 100.00 156 99.36 99.36 9.11e-109 REF NP_001086065 "ribosomal protein S27a [Xenopus laevis]" 100.00 156 100.00 100.00 1.42e-109 REF NP_001129064 "ubiquitin-40S ribosomal protein S27a precursor [Homo sapiens]" 100.00 156 100.00 100.00 1.42e-109 SP P0CG50 "RecName: Full=Polyubiquitin-C; Contains: RecName: Full=Ubiquitin; Contains: RecName: Full=Ubiquitin-related 1; Contains: RecNam" 50.00 734 97.44 98.72 3.76e-41 SP P0CG69 "RecName: Full=Polyubiquitin; Contains: RecName: Full=Ubiquitin; Flags: Precursor [Drosophila melanogaster]" 50.00 763 97.44 98.72 4.63e-41 SP P62978 "RecName: Full=Ubiquitin-40S ribosomal protein S27a; AltName: Full=Ubiquitin carboxyl extension protein 80; Contains: RecName: F" 100.00 156 100.00 100.00 1.42e-109 SP P62979 "RecName: Full=Ubiquitin-40S ribosomal protein S27a; AltName: Full=Ubiquitin carboxyl extension protein 80; Contains: RecName: F" 100.00 156 100.00 100.00 1.42e-109 SP P62982 "RecName: Full=Ubiquitin-40S ribosomal protein S27a; AltName: Full=Ubiquitin carboxyl extension protein 80; Contains: RecName: F" 100.00 156 99.36 99.36 9.11e-109 TPG DAA24675 "TPA: 40S ribosomal protein S27a [Bos taurus]" 100.00 156 100.00 100.00 1.42e-109 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $STAM1 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 _Variant _Vector_name $STAM1 'recombinant technology' 'E. coli' . . BL21 DE3 'pET-glutathionse S-transferase' $ubiquitin 'obtained from a vendor' . . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'ubiquitin was titrated into solution' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $STAM1 0.1 mM . . [U-15N] $ubiquitin . mM 0.02 0.5 [U-15N] 'sodium phosphate' 20 mM . . 'natural abundance' DTT 1 mM . . 'natural abundance' 'sodium chloride' 0.1 M . . 'natural abundance' PMSF 0.5 mM . . 'natural abundance' 'sodium azide' 0.05 mM . . 'natural abundance' H2O 95 % . . 'natural abundance' D2O 5 % . . 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details 'STAM1 was titrated into solution' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $STAM1 . mM 0.01 0.2 'natural abundance' $ubiquitin 0.05 mM . . [U-15N] 'sodium phosphate' 20 mM . . 'natural abundance' DTT 1 mM . . 'natural abundance' 'sodium chloride' 0.1 M . . 'natural abundance' PMSF 0.5 mM . . 'natural abundance' 'sodium azide' 0.05 mM . . 'natural abundance' H2O 95 % . . 'natural abundance' D2O 5 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_NMRView _Saveframe_category software _Name NMRView _Version . loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_KaleidaGraph _Saveframe_category software _Name KaleidaGraph _Version 3.5 loop_ _Vendor _Address _Electronic_address 'Synergy Software' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 6.8 . pH pressure 1 . atm stop_ save_