data_17380 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; rbp56 RanBP2 zinc finger backbone chemical shifts ; _BMRB_accession_number 17380 _BMRB_flat_file_name bmr17380.str _Entry_type original _Submission_date 2010-12-23 _Accession_date 2010-12-23 _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 Mansfield Robyn E. . 2 Mackay Joel P. . 3 Nguyen Cuong D. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 32 "13C chemical shifts" 74 "15N chemical shifts" 32 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-03-24 update BMRB 'update entry citation' 2011-01-25 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Characterization of a Family of RanBP2-Type Zinc Fingers that Can Recognize Single-Stranded RNA.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21256132 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Nguyen Cuong D. . 2 Mansfield Robyn E. . 3 Leung Wilfred . . 4 Vaz Paula M. . 5 Loughlin Fionna E. . 6 Grant Richard P. . 7 Mackay Joel P. . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_name_full 'Journal of molecular biology' _Journal_volume 407 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 273 _Page_last 283 _Year 2011 _Details . loop_ _Keyword RanBP2 RNA-binding stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'RBP56 ZnF' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'protein component' $RBP56_ZnF 'zinc ion' $ZN stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . loop_ _Biological_function RNA-binding stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_RBP56_ZnF _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common RBP56_ZnF _Molecular_mass . _Mol_thiol_state 'all other bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 42 _Mol_residue_sequence ; GSRGGDPKSGDWVCPNPSCG NMNFARRNSCNQCNEPRPED SR ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 347 GLY 2 348 SER 3 349 ARG 4 350 GLY 5 351 GLY 6 352 ASP 7 353 PRO 8 354 LYS 9 355 SER 10 356 GLY 11 357 ASP 12 358 TRP 13 359 VAL 14 360 CYS 15 361 PRO 16 362 ASN 17 363 PRO 18 364 SER 19 365 CYS 20 366 GLY 21 367 ASN 22 368 MET 23 369 ASN 24 370 PHE 25 371 ALA 26 372 ARG 27 373 ARG 28 374 ASN 29 375 SER 30 376 CYS 31 377 ASN 32 378 GLN 33 379 CYS 34 380 ASN 35 381 GLU 36 382 PRO 37 383 ARG 38 384 PRO 39 385 GLU 40 386 ASP 41 387 SER 42 388 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-10-28 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 19561 Taf-RRM-RanBP 88.10 162 100.00 100.00 1.14e-17 DBJ BAA33811 "RBP56/hTAFII68 [Homo sapiens]" 88.10 592 100.00 100.00 2.46e-17 DBJ BAA33812 "RBP56/hTAFII68 [Homo sapiens]" 88.10 589 100.00 100.00 3.95e-17 DBJ BAB46889 "hypothetical protein [Macaca fascicularis]" 88.10 397 100.00 100.00 4.60e-17 DBJ BAC34676 "unnamed protein product [Mus musculus]" 88.10 557 97.30 100.00 8.60e-17 DBJ BAE27086 "unnamed protein product [Mus musculus]" 88.10 557 97.30 100.00 8.60e-17 EMBL CAA67398 "hTAFII68 [Homo sapiens]" 88.10 589 100.00 100.00 3.95e-17 GB AAC50932 "putative RNA binding protein RBP56 [Homo sapiens]" 88.10 592 100.00 100.00 2.46e-17 GB AAH46099 "TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa [Homo sapiens]" 88.10 592 100.00 100.00 2.46e-17 GB AAI37592 "TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor [Mus musculus]" 88.10 557 97.30 100.00 8.60e-17 GB AAI66769 "Taf15 protein [Rattus norvegicus]" 88.10 572 97.30 100.00 8.80e-17 GB AAO13485 "TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa [Homo sapiens]" 88.10 589 100.00 100.00 3.95e-17 REF NP_001099294 "TATA-binding protein-associated factor 2N [Rattus norvegicus]" 88.10 394 97.30 100.00 3.59e-17 REF NP_001302693 "TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa [Sus scrofa]" 88.10 602 100.00 100.00 3.46e-17 REF NP_003478 "TATA-binding protein-associated factor 2N isoform 2 [Homo sapiens]" 88.10 589 100.00 100.00 3.95e-17 REF NP_081703 "TATA-binding protein-associated factor 2N [Mus musculus]" 88.10 557 97.30 100.00 8.60e-17 REF NP_631961 "TATA-binding protein-associated factor 2N isoform 1 [Homo sapiens]" 88.10 592 100.00 100.00 2.46e-17 SP Q92804 "RecName: Full=TATA-binding protein-associated factor 2N; AltName: Full=68 kDa TATA-binding protein-associated factor; Short=TAF" 88.10 592 100.00 100.00 2.46e-17 TPG DAA19087 "TPA: TBP-associated factor 15-like [Bos taurus]" 88.10 591 100.00 100.00 5.55e-17 stop_ save_ ############# # Ligands # ############# save_ZN _Saveframe_category ligand _Mol_type non-polymer _Name_common "ZN (ZINC ION)" _BMRB_code . _PDB_code ZN _Molecular_mass 65.409 _Mol_charge 2 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Dec 9 11:09:24 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons ZN ZN ZN . 2 . ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $RBP56_ZnF 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 $RBP56_ZnF 'recombinant technology' . Escherichia coli . pGEX-2T stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RBP56_ZnF 1 mM '[U-100% 13C; U-100% 15N]' DTT 1 mM 'natural abundance' 'sodium phosphate' 25 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' DSS 20 uM 'natural abundance' H2O 93 % 'natural abundance' D2O 7 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _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-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_3D_CBCA(CO)NH_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D CBCA(CO)NH' _Sample_label $sample_1 save_ save_3D_HNCACB_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCACB' _Sample_label $sample_1 save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . 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' 0.125 . M pH 6.5 . 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 _Indirect_shift_ratio_citation_label _Correction_value_citation_label DSS C 13 'methyl protons' ppm 0.00 . indirect . . . 0.251449530 $entry_citation $entry_citation DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 $entry_citation $entry_citation DSS N 15 'methyl protons' ppm 0.00 . indirect . . . 0.101329118 $entry_citation $entry_citation 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_ _Experiment_label '2D 1H-15N HSQC' '3D CBCA(CO)NH' '3D HNCACB' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'protein component' _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 1 350 4 GLY CA C 45.326 0.010 1 2 351 5 GLY H H 8.252 0.005 1 3 351 5 GLY CA C 44.963 0.038 1 4 351 5 GLY N N 108.983 0.031 1 5 352 6 ASP H H 8.411 0.006 1 6 352 6 ASP CA C 52.248 0.000 1 7 352 6 ASP CB C 41.260 0.000 1 8 352 6 ASP N N 121.834 0.026 1 9 353 7 PRO CA C 63.788 0.007 1 10 353 7 PRO CB C 32.175 0.003 1 11 354 8 LYS H H 8.510 0.003 1 12 354 8 LYS CA C 56.512 0.025 1 13 354 8 LYS CB C 32.505 0.010 1 14 354 8 LYS N N 120.446 0.016 1 15 355 9 SER H H 8.139 0.004 1 16 355 9 SER CA C 59.019 0.117 1 17 355 9 SER CB C 64.049 0.013 1 18 355 9 SER N N 115.622 0.057 1 19 356 10 GLY H H 8.420 0.005 1 20 356 10 GLY CA C 45.227 0.012 1 21 356 10 GLY N N 111.260 0.004 1 22 357 11 ASP H H 8.114 0.004 1 23 357 11 ASP CA C 55.715 0.054 1 24 357 11 ASP CB C 40.825 0.015 1 25 357 11 ASP N N 123.514 0.008 1 26 358 12 TRP H H 8.734 0.002 1 27 358 12 TRP CA C 54.041 0.016 1 28 358 12 TRP CB C 31.080 0.008 1 29 358 12 TRP N N 119.263 0.011 1 30 359 13 VAL H H 8.689 0.004 1 31 359 13 VAL CA C 61.457 0.021 1 32 359 13 VAL CB C 32.782 0.034 1 33 359 13 VAL N N 123.937 0.011 1 34 360 14 CYS H H 8.675 0.003 1 35 360 14 CYS CA C 57.853 0.000 1 36 360 14 CYS CB C 32.328 0.000 1 37 360 14 CYS N N 132.779 0.020 1 38 361 15 PRO CA C 63.502 0.016 1 39 361 15 PRO CB C 32.117 0.025 1 40 362 16 ASN H H 8.949 0.001 1 41 362 16 ASN CA C 51.358 0.000 1 42 362 16 ASN CB C 38.741 0.000 1 43 362 16 ASN N N 125.715 0.026 1 44 363 17 PRO CA C 64.581 0.044 1 45 363 17 PRO CB C 32.097 0.001 1 46 364 18 SER H H 7.718 0.001 1 47 364 18 SER CA C 58.903 0.038 1 48 364 18 SER CB C 63.336 0.011 1 49 364 18 SER N N 112.431 0.014 1 50 365 19 CYS H H 8.123 0.002 1 51 365 19 CYS CA C 59.766 0.003 1 52 365 19 CYS CB C 31.846 0.007 1 53 365 19 CYS N N 125.333 0.032 1 54 366 20 GLY H H 7.434 0.002 1 55 366 20 GLY CA C 46.504 0.021 1 56 366 20 GLY N N 104.061 0.039 1 57 367 21 ASN H H 8.499 0.002 1 58 367 21 ASN CA C 54.751 0.029 1 59 367 21 ASN CB C 41.175 0.003 1 60 367 21 ASN N N 120.899 0.031 1 61 368 22 MET H H 8.027 0.005 1 62 368 22 MET CA C 54.807 0.014 1 63 368 22 MET CB C 31.318 0.050 1 64 368 22 MET N N 123.940 0.010 1 65 369 23 ASN H H 8.747 0.002 1 66 369 23 ASN CA C 52.533 0.014 1 67 369 23 ASN CB C 42.988 0.019 1 68 369 23 ASN N N 125.054 0.018 1 69 370 24 PHE H H 7.689 0.002 1 70 370 24 PHE CA C 56.620 0.019 1 71 370 24 PHE CB C 40.112 0.006 1 72 370 24 PHE N N 118.285 0.024 1 73 371 25 ALA H H 8.881 0.002 1 74 371 25 ALA CA C 55.364 0.044 1 75 371 25 ALA CB C 19.541 0.019 1 76 371 25 ALA N N 124.372 0.027 1 77 372 26 ARG H H 7.712 0.012 1 78 372 26 ARG CA C 56.776 0.049 1 79 372 26 ARG CB C 29.412 0.018 1 80 372 26 ARG N N 110.971 0.033 1 81 373 27 ARG H H 8.287 0.002 1 82 373 27 ARG CA C 56.221 0.000 1 83 373 27 ARG CB C 30.940 0.000 1 84 373 27 ARG N N 120.524 0.017 1 85 374 28 ASN CA C 53.862 0.084 1 86 374 28 ASN CB C 39.066 0.019 1 87 375 29 SER H H 7.879 0.001 1 88 375 29 SER CA C 56.727 0.019 1 89 375 29 SER CB C 65.801 0.011 1 90 375 29 SER N N 113.996 0.030 1 91 376 30 CYS H H 9.654 0.003 1 92 376 30 CYS CA C 58.969 0.049 1 93 376 30 CYS CB C 31.146 0.002 1 94 376 30 CYS N N 126.858 0.039 1 95 377 31 ASN H H 8.740 0.001 1 96 377 31 ASN CA C 55.860 0.024 1 97 377 31 ASN CB C 38.879 0.020 1 98 377 31 ASN N N 127.971 0.024 1 99 378 32 GLN H H 9.237 0.003 1 100 378 32 GLN CA C 57.403 0.048 1 101 378 32 GLN CB C 30.397 0.002 1 102 378 32 GLN N N 120.963 0.042 1 103 379 33 CYS H H 8.133 0.002 1 104 379 33 CYS CA C 59.095 0.069 1 105 379 33 CYS CB C 32.005 0.024 1 106 379 33 CYS N N 118.233 0.030 1 107 380 34 ASN H H 7.951 0.001 1 108 380 34 ASN CA C 55.734 0.059 1 109 380 34 ASN CB C 38.465 0.045 1 110 380 34 ASN N N 118.346 0.029 1 111 381 35 GLU H H 8.948 0.002 1 112 381 35 GLU CA C 55.765 0.000 1 113 381 35 GLU CB C 31.531 0.000 1 114 381 35 GLU N N 126.680 0.023 1 115 382 36 PRO CA C 62.927 0.055 1 116 382 36 PRO CB C 32.407 0.014 1 117 383 37 ARG H H 7.449 0.001 1 118 383 37 ARG CA C 54.083 0.000 1 119 383 37 ARG CB C 30.552 0.000 1 120 383 37 ARG N N 123.693 0.007 1 121 384 38 PRO CA C 62.891 0.051 1 122 384 38 PRO CB C 32.208 0.009 1 123 385 39 GLU H H 8.557 0.004 1 124 385 39 GLU CA C 56.844 0.026 1 125 385 39 GLU CB C 30.363 0.014 1 126 385 39 GLU N N 122.789 0.010 1 127 386 40 ASP H H 8.383 0.004 1 128 386 40 ASP CA C 54.309 0.022 1 129 386 40 ASP CB C 41.111 0.004 1 130 386 40 ASP N N 121.046 0.024 1 131 387 41 SER H H 8.168 0.004 1 132 387 41 SER CA C 58.388 0.019 1 133 387 41 SER CB C 63.926 0.010 1 134 387 41 SER N N 116.458 0.013 1 135 388 42 ARG H H 7.918 0.004 1 136 388 42 ARG CA C 57.732 0.000 1 137 388 42 ARG CB C 31.399 0.000 1 138 388 42 ARG N N 128.375 0.016 1 stop_ save_