data_17453 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Oligomeric Structure of the Chemokine CCL5/RANTES from NMR, MS, and SAXS Data ; _BMRB_accession_number 17453 _BMRB_flat_file_name bmr17453.str _Entry_type original _Submission_date 2011-02-09 _Accession_date 2011-02-09 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Tetrameric model of the inflammatory chemokine CCL5/RANTES' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wang Xu . . 2 Watson Caroline M. . 3 Sharp Joshua S. . 4 Handel Tracy M. . 5 Prestegard James H. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 58 "15N chemical shifts" 59 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-08-17 original BMRB . stop_ _Original_release_date 2011-02-18 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Oligomeric Structure of the Chemokine CCL5/RANTES from NMR, MS, and SAXS Data. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21827949 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wang Xu . . 2 Watson Caroline . . 3 Sharp Joshua S. . 4 Handel Tracy M. . 5 Prestegard James H. . stop_ _Journal_abbreviation Structure _Journal_name_full 'Structure (London, England : 1993)' _Journal_volume 19 _Journal_issue 8 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1138 _Page_last 1148 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name ccl5 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label chain_1 $ccl5 chain_2 $ccl5 chain_3 $ccl5 chain_4 $ccl5 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_ccl5 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common ccl5 _Molecular_mass 7774.992 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 68 _Mol_residue_sequence ; SPYSSDTTPCCFAYIARPLP RAHIKEYFYTSGKCSNPAVV FVTRKNRQVCANPEKKWVRE YINSLEMS ; loop_ _Residue_seq_code _Residue_label 1 SER 2 PRO 3 TYR 4 SER 5 SER 6 ASP 7 THR 8 THR 9 PRO 10 CYS 11 CYS 12 PHE 13 ALA 14 TYR 15 ILE 16 ALA 17 ARG 18 PRO 19 LEU 20 PRO 21 ARG 22 ALA 23 HIS 24 ILE 25 LYS 26 GLU 27 TYR 28 PHE 29 TYR 30 THR 31 SER 32 GLY 33 LYS 34 CYS 35 SER 36 ASN 37 PRO 38 ALA 39 VAL 40 VAL 41 PHE 42 VAL 43 THR 44 ARG 45 LYS 46 ASN 47 ARG 48 GLN 49 VAL 50 CYS 51 ALA 52 ASN 53 PRO 54 GLU 55 LYS 56 LYS 57 TRP 58 VAL 59 ARG 60 GLU 61 TYR 62 ILE 63 ASN 64 SER 65 LEU 66 GLU 67 MET 68 SER 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 $ccl5 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 $ccl5 'recombinant technology' . Escherichia coli BL21 pET-23 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'isotropic sample' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $ccl5 1 mM '[U-100% 15N]' 'sodium acetate' 50 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type 'gel solid' _Details 'stretched neutral gel for alignment' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $ccl5 1 mM '[U-100% 15N]' 'sodium acetate' 50 mM 'natural abundance' polyacrylamide 5 % 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NAMD _Saveframe_category software _Name NAMD _Version . loop_ _Vendor _Address _Electronic_address 'Phillips, Braun, Wang, Gumbart, Tajkhorshid, Villa, Chipot, Skeel, Kale, and Schulte' ; NAMD Team Theoretical and Computational Biophysics Group Beckman Institute University of Illinois 405 North Mathews MC-251 Urbana, Illinois 61801 USA ; namd@ks.uiuc.edu stop_ loop_ _Task refinement stop_ _Details 'molecular dynamics simulation' 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_VNMRJ _Saveframe_category software _Name VNMRJ _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_VMD _Saveframe_category software _Name VMD _Version . loop_ _Vendor _Address _Electronic_address 'Humphrey, Dalke & Schulten.' ; VMD Team Theoretical and Computational Biophysics Group Beckman Institute University of Illinois 405 North Mathews MC-251 Urbana, Illinois 61801 USA ; vmd@ks.uiuc.edu stop_ loop_ _Task refinement stop_ _Details 'for constructing structures' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 800 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 900 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_J-mod_TROSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N J-mod TROSY' _Sample_label $sample_1 save_ save_2D_1H-15N_TROSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N TROSY' _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_2 save_ save_2D_1H-15N_J-mod_TROSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N J-mod TROSY' _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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0.05 . M pH 4.4 . pH pressure 1 . atm temperature 297 . 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 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 . indirect . . . 0.101329118 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' 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 chain_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 3 3 TYR H H 8.081 0.03 1 2 3 3 TYR N N 119.535 0.5 1 3 4 4 SER H H 8.299 0.03 1 4 4 4 SER N N 117.688 0.5 1 5 5 5 SER H H 8.123 0.03 1 6 5 5 SER N N 114.930 0.5 1 7 6 6 ASP H H 7.682 0.03 1 8 6 6 ASP N N 122.288 0.5 1 9 7 7 THR H H 7.975 0.03 1 10 7 7 THR N N 110.391 0.5 1 11 8 8 THR H H 9.270 0.03 1 12 8 8 THR N N 117.872 0.5 1 13 10 10 CYS H H 9.116 0.03 1 14 10 10 CYS N N 118.864 0.5 1 15 11 11 CYS H H 9.175 0.03 1 16 11 11 CYS N N 117.401 0.5 1 17 12 12 PHE H H 9.305 0.03 1 18 12 12 PHE N N 120.239 0.5 1 19 13 13 ALA H H 7.636 0.03 1 20 13 13 ALA N N 122.330 0.5 1 21 14 14 TYR H H 8.110 0.03 1 22 14 14 TYR N N 113.347 0.5 1 23 15 15 ILE H H 9.138 0.03 1 24 15 15 ILE N N 123.848 0.5 1 25 16 16 ALA H H 8.567 0.03 1 26 16 16 ALA N N 127.510 0.5 1 27 17 17 ARG H H 7.548 0.03 1 28 17 17 ARG N N 117.356 0.5 1 29 21 21 ARG H H 8.532 0.03 1 30 21 21 ARG N N 128.221 0.5 1 31 22 22 ALA H H 8.647 0.03 1 32 22 22 ALA N N 118.458 0.5 1 33 23 23 HIS H H 7.770 0.03 1 34 23 23 HIS N N 113.436 0.5 1 35 24 24 ILE H H 7.605 0.03 1 36 24 24 ILE N N 119.475 0.5 1 37 25 25 LYS H H 9.401 0.03 1 38 25 25 LYS N N 124.823 0.5 1 39 26 26 GLU H H 7.972 0.03 1 40 26 26 GLU N N 114.965 0.5 1 41 27 27 TYR H H 8.389 0.03 1 42 27 27 TYR N N 117.043 0.5 1 43 28 28 PHE H H 8.528 0.03 1 44 28 28 PHE N N 114.773 0.5 1 45 29 29 TYR H H 8.995 0.03 1 46 29 29 TYR N N 119.398 0.5 1 47 30 30 THR H H 8.083 0.03 1 48 30 30 THR N N 111.130 0.5 1 49 31 31 SER H H 9.753 0.03 1 50 31 31 SER N N 115.139 0.5 1 51 32 32 GLY H H 9.096 0.03 1 52 32 32 GLY N N 118.978 0.5 1 53 33 33 LYS H H 7.991 0.03 1 54 33 33 LYS N N 117.041 0.5 1 55 34 34 CYS H H 7.370 0.03 1 56 34 34 CYS N N 116.415 0.5 1 57 35 35 SER H H 8.771 0.03 1 58 35 35 SER N N 117.817 0.5 1 59 36 36 ASN H H 8.152 0.03 1 60 36 36 ASN N N 118.406 0.5 1 61 38 38 ALA H H 8.179 0.03 1 62 38 38 ALA N N 121.530 0.5 1 63 39 39 VAL H H 8.133 0.03 1 64 39 39 VAL N N 120.393 0.5 1 65 40 40 VAL H H 8.766 0.03 1 66 40 40 VAL N N 126.255 0.5 1 67 41 41 PHE H H 9.084 0.03 1 68 41 41 PHE N N 123.455 0.5 1 69 42 42 VAL H H 8.861 0.03 1 70 42 42 VAL N N 124.027 0.5 1 71 43 43 THR H H 9.364 0.03 1 72 43 43 THR N N 118.255 0.5 1 73 44 44 ARG H H 8.499 0.03 1 74 44 44 ARG N N 118.579 0.5 1 75 45 45 LYS H H 7.632 0.03 1 76 45 45 LYS N N 116.972 0.5 1 77 46 46 ASN H H 8.289 0.03 1 78 46 46 ASN N N 114.914 0.5 1 79 47 47 ARG H H 7.474 0.03 1 80 47 47 ARG N N 118.441 0.5 1 81 48 48 GLN H H 8.820 0.03 1 82 48 48 GLN N N 123.561 0.5 1 83 49 49 VAL H H 8.972 0.03 1 84 49 49 VAL N N 123.147 0.5 1 85 50 50 CYS H H 9.030 0.03 1 86 50 50 CYS N N 125.424 0.5 1 87 51 51 ALA H H 9.806 0.03 1 88 51 51 ALA N N 124.859 0.5 1 89 52 52 ASN H H 8.202 0.03 1 90 52 52 ASN N N 120.149 0.5 1 91 54 54 GLU H H 7.567 0.03 1 92 54 54 GLU N N 113.847 0.5 1 93 55 55 LYS H H 7.237 0.03 1 94 55 55 LYS N N 117.814 0.5 1 95 56 56 LYS H H 8.781 0.03 1 96 56 56 LYS N N 125.069 0.5 1 97 57 57 TRP H H 8.123 0.03 1 98 57 57 TRP N N 115.108 0.5 1 99 59 59 ARG H H 7.213 0.03 1 100 59 59 ARG N N 118.397 0.5 1 101 60 60 GLU H H 8.339 0.03 1 102 60 60 GLU N N 118.527 0.5 1 103 61 61 TYR H H 8.571 0.03 1 104 61 61 TYR N N 122.302 0.5 1 105 62 62 ILE H H 8.384 0.03 1 106 62 62 ILE N N 119.491 0.5 1 107 63 63 ASN H H 7.893 0.03 1 108 63 63 ASN N N 118.212 0.5 1 109 64 64 SER H H 7.909 0.03 1 110 64 64 SER N N 113.936 0.5 1 111 65 65 LEU H H 7.948 0.03 1 112 65 65 LEU N N 122.865 0.5 1 113 66 66 GLU H H 8.076 0.03 1 114 66 66 GLU N N 114.599 0.5 1 115 67 67 MET H H 8.044 0.03 1 116 67 67 MET N N 121.849 0.5 1 117 68 68 SER N N 122.500 0.5 1 stop_ save_