data_30008 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Quantitative characterization of configurational space sampled by HIV-1 nucleocapsid using solution NMR and X-ray scattering ; _BMRB_accession_number 30008 _BMRB_flat_file_name bmr30008.str _Entry_type original _Submission_date 2016-02-05 _Accession_date 2016-02-05 _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 Deshmukh L. . . 2 Schwieters C. D. . 3 Grishaev A. . . 4 Clore G. M. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 42 "13C chemical shifts" 125 "15N chemical shifts" 42 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-06-17 original BMRB . stop_ _Original_release_date 2016-03-28 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Quantitative characterization of configurational space sampled by HIV-1 nucleocapsid using solution NMR, X-ray scattering and protein engineering ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 26946052 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Deshmukh L. . . 2 Schwieters C. D. . 3 Grishaev A. . . 4 Clore G. M. . stop_ _Journal_abbreviation Chemphyschem _Journal_volume 17 _Journal_issue 11 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1548 _Page_last 1552 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Nucleocapsid protein p7' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 entity_ZN $entity_ZN entity_ZN $entity_ZN 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 'Nucleocapsid protein p7' _Molecular_mass 6442.522 _Mol_thiol_state 'all other bound' _Details 'zinc atoms' ############################## # Polymer residue sequence # ############################## _Residue_count 55 _Mol_residue_sequence ; MQRGNFRNQRKIVKCFNCGK EGHTARNCRAPRKKGCWKCG KEGHQMKDCTERQAN ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 378 MET 2 379 GLN 3 380 ARG 4 381 GLY 5 382 ASN 6 383 PHE 7 384 ARG 8 385 ASN 9 386 GLN 10 387 ARG 11 388 LYS 12 389 ILE 13 390 VAL 14 391 LYS 15 392 CYS 16 393 PHE 17 394 ASN 18 395 CYS 19 396 GLY 20 397 LYS 21 398 GLU 22 399 GLY 23 400 HIS 24 401 THR 25 402 ALA 26 403 ARG 27 404 ASN 28 405 CYS 29 406 ARG 30 407 ALA 31 408 PRO 32 409 ARG 33 410 LYS 34 411 LYS 35 412 GLY 36 413 CYS 37 414 TRP 38 415 LYS 39 416 CYS 40 417 GLY 41 418 LYS 42 419 GLU 43 420 GLY 44 421 HIS 45 422 GLN 46 423 MET 47 424 LYS 48 425 ASP 49 426 CYS 50 427 THR 51 428 GLU 52 429 ARG 53 430 GLN 54 431 ALA 55 432 ASN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_ZN _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common 'ZINC ION' _BMRB_code ZN _PDB_code ZN _Molecular_mass 65.409 _Mol_charge 2 _Mol_paramagnetic . _Mol_aromatic no _Details . 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 _Strain _Gene_mnemonic $entity_1 HIV-1 11706 Viruses . Retroviruses HIV-1 'isolate HXB2' gag stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name $entity_1 'recombinant technology' . Escherichia coli . plasmid pET11a stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details ; 0.2 mM [U-13C; U-15N; U-2H] Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1), 50 mM sodium chloride, 20 mM sodium phosphate, 1 mM Dithiothreitol, 0.1 mM zinc chloride, 93% H2O/7% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling Dithiothreitol 1 mM 'natural abundance' $entity_1 0.2 mM '[U-13C; U-15N; U-2H]' 'sodium chloride' 50 mM 'natural abundance' 'sodium phosphate' 20 mM 'natural abundance' 'zinc chloride' 0.1 mM 'natural abundance' H2O 93 % 'natural abundance' D2O 7 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type bicelle _Details ; 0.2 mM [U-13C; U-15N; U-2H] Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1), 50 mM sodium chloride, 20 mM sodium phosphate, 1 mM Dithiothreitol, 0.1 mM zinc chloride, 5 % neutral bicelles, 93% H2O/7% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling Dithiothreitol 1 mM 'natural abundance' $entity_1 0.2 mM '[U-13C; U-15N; U-2H]' 'neutral bicelles' 5 % 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' 'sodium phosphate' 20 mM 'natural abundance' 'zinc chloride' 0.1 mM 'natural abundance' H2O 93 % 'natural abundance' D2O 7 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name Analysis _Version 2.2.2 loop_ _Vendor _Address _Electronic_address 'W. F. Vranken, W. Boucher, T. J. Stevens, R. H. Fogh, A. Pajon, M. Llinas, E. L. Ulrich, J. L. Markley, J. Ionides, E. D. Laue' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name Xplor-NIH _Version 2.41 loop_ _Vendor _Address _Electronic_address 'C. D. Schwieters, J. J. Kuszewski, N. Tjandra, G. M. Clore' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ save_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_1 save_ save_3D_HNCO_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCO' _Sample_label $sample_1 save_ save_3D_HNCA_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCA' _Sample_label $sample_1 save_ save_3D_HNCACB_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCACB' _Sample_label $sample_1 save_ save_2D_ARTSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D ARTSY' _Sample_label $sample_2 save_ save_3D_Quntitaive_HNCO_-_NC'_6 _Saveframe_category NMR_applied_experiment _Experiment_name "3D Quntitaive HNCO - NC'" _Sample_label $sample_2 save_ save_3D_Quntitaive_HNCO_-_CaC'_7 _Saveframe_category NMR_applied_experiment _Experiment_name "3D Quntitaive HNCO - CaC'" _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 'ionic strength' 50 . mM pH 6.5 . pH pressure 1 . atm temperature 308 . 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 water C 13 protons ppm 4.78 internal indirect . . . 0.25144953 water H 1 protons ppm 4.78 internal direct . . . 1 water N 15 protons ppm 4.78 internal indirect . . . 0.25144953 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_ _Software_label $software_1 stop_ loop_ _Experiment_label '2D 1H-15N HSQC' '3D HNCO' '3D HNCA' '3D HNCACB' stop_ loop_ _Sample_label $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 1 387 10 ARG C C 175.936 0.000 . 2 388 11 LYS N N 123.895 0.074 . 3 388 11 LYS H H 8.204 0.001 . 4 388 11 LYS CA C 55.697 0.031 . 5 388 11 LYS CB C 31.963 0.021 . 6 388 11 LYS C C 176.008 0.000 . 7 389 12 ILE N N 124.580 0.012 . 8 389 12 ILE H H 8.078 0.002 . 9 389 12 ILE CA C 60.093 0.002 . 10 389 12 ILE CB C 37.828 0.004 . 11 389 12 ILE C C 175.804 0.000 . 12 390 13 VAL N N 127.022 0.014 . 13 390 13 VAL H H 8.304 0.004 . 14 390 13 VAL CA C 61.281 0.005 . 15 390 13 VAL CB C 31.862 0.011 . 16 390 13 VAL C C 174.167 0.000 . 17 391 14 LYS N N 125.508 0.010 . 18 391 14 LYS H H 8.005 0.004 . 19 391 14 LYS CA C 54.411 0.000 . 20 391 14 LYS CB C 34.412 0.003 . 21 391 14 LYS C C 174.483 0.000 . 22 392 15 CYS N N 127.664 0.043 . 23 392 15 CYS H H 8.131 0.001 . 24 392 15 CYS CA C 58.892 0.043 . 25 392 15 CYS CB C 29.471 0.012 . 26 392 15 CYS C C 178.389 0.000 . 27 393 16 PHE N N 128.792 0.032 . 28 393 16 PHE H H 8.464 0.002 . 29 393 16 PHE CA C 58.695 0.010 . 30 393 16 PHE CB C 37.969 0.010 . 31 393 16 PHE C C 175.741 0.000 . 32 394 17 ASN N N 122.242 0.026 . 33 394 17 ASN H H 9.460 0.001 . 34 394 17 ASN CA C 56.361 0.000 . 35 394 17 ASN CB C 39.567 0.001 . 36 394 17 ASN C C 175.460 0.000 . 37 395 18 CYS N N 117.913 0.018 . 38 395 18 CYS H H 8.822 0.001 . 39 395 18 CYS CA C 58.266 0.013 . 40 395 18 CYS CB C 31.683 0.002 . 41 395 18 CYS C C 176.419 0.000 . 42 396 19 GLY N N 113.818 0.032 . 43 396 19 GLY H H 7.758 0.002 . 44 396 19 GLY CA C 45.803 0.004 . 45 396 19 GLY C C 173.785 0.000 . 46 397 20 LYS N N 121.468 0.029 . 47 397 20 LYS H H 8.021 0.002 . 48 397 20 LYS CA C 55.629 0.005 . 49 397 20 LYS CB C 32.891 0.003 . 50 397 20 LYS C C 175.673 0.000 . 51 398 21 GLU N N 118.462 0.029 . 52 398 21 GLU H H 8.247 0.001 . 53 398 21 GLU CA C 55.521 0.017 . 54 398 21 GLU CB C 30.157 0.009 . 55 398 21 GLU C C 178.557 0.000 . 56 399 22 GLY N N 108.020 0.018 . 57 399 22 GLY H H 8.608 0.002 . 58 399 22 GLY CA C 45.243 0.008 . 59 399 22 GLY C C 173.736 0.000 . 60 400 23 HIS N N 114.682 0.054 . 61 400 23 HIS H H 7.103 0.001 . 62 400 23 HIS CA C 54.862 0.004 . 63 400 23 HIS CB C 29.523 0.000 . 64 401 24 THR N N 106.713 0.029 . 65 401 24 THR H H 8.084 0.003 . 66 401 24 THR CA C 58.940 0.004 . 67 401 24 THR CB C 71.355 0.001 . 68 401 24 THR C C 176.414 0.000 . 69 402 25 ALA N N 123.372 0.039 . 70 402 25 ALA H H 8.708 0.001 . 71 402 25 ALA CA C 55.255 0.024 . 72 402 25 ALA CB C 17.871 0.029 . 73 402 25 ALA C C 180.069 0.000 . 74 403 26 ARG N N 117.150 0.008 . 75 403 26 ARG H H 7.965 0.000 . 76 403 26 ARG CA C 57.946 0.022 . 77 403 26 ARG CB C 28.913 0.020 . 78 403 26 ARG C C 176.744 0.000 . 79 404 27 ASN N N 115.730 0.026 . 80 404 27 ASN H H 7.762 0.003 . 81 404 27 ASN CA C 51.774 0.005 . 82 404 27 ASN CB C 39.334 0.008 . 83 404 27 ASN C C 173.536 0.000 . 84 405 28 CYS N N 124.065 0.030 . 85 405 28 CYS H H 7.381 0.002 . 86 405 28 CYS CA C 61.660 0.000 . 87 405 28 CYS CB C 30.172 0.000 . 88 406 29 ARG CA C 54.982 0.000 . 89 406 29 ARG CB C 29.330 0.000 . 90 406 29 ARG C C 175.951 0.000 . 91 407 30 ALA N N 128.529 0.018 . 92 407 30 ALA H H 8.636 0.002 . 93 407 30 ALA CA C 50.593 0.000 . 94 407 30 ALA CB C 17.338 0.000 . 95 408 31 PRO CA C 62.497 0.000 . 96 408 31 PRO CB C 30.980 0.000 . 97 408 31 PRO C C 176.984 0.000 . 98 409 32 ARG N N 123.246 0.001 . 99 409 32 ARG H H 8.297 0.003 . 100 409 32 ARG CA C 55.608 0.037 . 101 409 32 ARG CB C 29.553 0.002 . 102 409 32 ARG C C 176.896 0.000 . 103 410 33 LYS N N 126.173 0.007 . 104 410 33 LYS H H 8.493 0.005 . 105 410 33 LYS CA C 55.851 0.005 . 106 410 33 LYS CB C 32.233 0.001 . 107 410 33 LYS C C 176.368 0.000 . 108 411 34 LYS N N 123.326 0.011 . 109 411 34 LYS H H 8.273 0.006 . 110 411 34 LYS CA C 55.905 0.026 . 111 411 34 LYS CB C 32.365 0.007 . 112 411 34 LYS C C 176.484 0.000 . 113 412 35 GLY N N 109.471 0.011 . 114 412 35 GLY H H 8.017 0.003 . 115 412 35 GLY CA C 44.003 0.002 . 116 412 35 GLY C C 172.676 0.000 . 117 413 36 CYS N N 124.748 0.038 . 118 413 36 CYS H H 8.059 0.003 . 119 413 36 CYS CA C 59.407 0.021 . 120 413 36 CYS CB C 29.757 0.080 . 121 413 36 CYS C C 178.691 0.000 . 122 414 37 TRP N N 129.789 0.031 . 123 414 37 TRP H H 8.275 0.003 . 124 414 37 TRP CA C 58.134 0.029 . 125 414 37 TRP CB C 28.878 0.008 . 126 414 37 TRP C C 176.463 0.000 . 127 415 38 LYS N N 123.318 0.026 . 128 415 38 LYS H H 9.229 0.002 . 129 415 38 LYS CA C 58.473 0.031 . 130 415 38 LYS CB C 32.750 0.003 . 131 415 38 LYS C C 177.249 0.000 . 132 416 39 CYS N N 117.575 0.024 . 133 416 39 CYS H H 8.403 0.001 . 134 416 39 CYS CA C 58.297 0.022 . 135 416 39 CYS CB C 31.942 0.009 . 136 416 39 CYS C C 176.708 0.000 . 137 417 40 GLY N N 114.141 0.033 . 138 417 40 GLY H H 8.041 0.001 . 139 417 40 GLY CA C 45.797 0.002 . 140 417 40 GLY C C 174.138 0.000 . 141 418 41 LYS N N 122.690 0.030 . 142 418 41 LYS H H 8.325 0.001 . 143 418 41 LYS CA C 56.122 0.037 . 144 418 41 LYS CB C 32.755 0.013 . 145 418 41 LYS C C 176.389 0.000 . 146 419 42 GLU N N 119.157 0.021 . 147 419 42 GLU H H 8.345 0.003 . 148 419 42 GLU CA C 56.260 0.000 . 149 419 42 GLU CB C 30.021 0.000 . 150 420 43 GLY CA C 45.413 0.000 . 151 420 43 GLY C C 173.649 0.000 . 152 421 44 HIS N N 113.525 0.007 . 153 421 44 HIS H H 7.074 0.000 . 154 421 44 HIS CA C 54.952 0.001 . 155 421 44 HIS CB C 29.751 0.073 . 156 422 45 GLN N N 117.421 0.026 . 157 422 45 GLN H H 8.787 0.003 . 158 422 45 GLN CA C 53.796 0.002 . 159 422 45 GLN CB C 30.429 0.032 . 160 422 45 GLN C C 177.774 0.000 . 161 423 46 MET N N 122.206 0.021 . 162 423 46 MET H H 8.729 0.002 . 163 423 46 MET CA C 59.545 0.007 . 164 423 46 MET CB C 31.991 0.002 . 165 423 46 MET C C 178.361 0.000 . 166 424 47 LYS N N 118.826 0.014 . 167 424 47 LYS H H 8.369 0.003 . 168 424 47 LYS CA C 58.116 0.005 . 169 424 47 LYS CB C 30.537 0.061 . 170 424 47 LYS C C 176.175 0.000 . 171 425 48 ASP N N 118.081 0.023 . 172 425 48 ASP H H 7.757 0.002 . 173 425 48 ASP CA C 53.315 0.005 . 174 425 48 ASP CB C 41.963 0.011 . 175 425 48 ASP C C 175.003 0.000 . 176 426 49 CYS N N 123.976 0.030 . 177 426 49 CYS H H 7.484 0.002 . 178 426 49 CYS CA C 62.127 0.012 . 179 426 49 CYS CB C 29.948 0.022 . 180 426 49 CYS C C 177.109 0.000 . 181 427 50 THR N N 120.018 0.009 . 182 427 50 THR H H 8.009 0.005 . 183 427 50 THR CA C 61.264 0.001 . 184 427 50 THR CB C 68.822 0.029 . 185 427 50 THR C C 174.993 0.000 . 186 428 51 GLU N N 125.847 0.006 . 187 428 51 GLU H H 8.524 0.002 . 188 428 51 GLU CA C 56.455 0.015 . 189 428 51 GLU CB C 29.101 0.001 . 190 428 51 GLU C C 176.539 0.000 . 191 429 52 ARG N N 123.045 0.007 . 192 429 52 ARG H H 8.232 0.006 . 193 429 52 ARG CA C 55.541 0.043 . 194 429 52 ARG CB C 29.803 0.056 . 195 429 52 ARG C C 176.138 0.000 . 196 430 53 GLN N N 122.201 0.024 . 197 430 53 GLN H H 8.312 0.004 . 198 430 53 GLN CA C 55.304 0.073 . 199 430 53 GLN CB C 28.683 0.016 . 200 430 53 GLN C C 175.420 0.000 . 201 431 54 ALA N N 126.519 0.014 . 202 431 54 ALA H H 8.239 0.004 . 203 431 54 ALA CA C 51.983 0.010 . 204 431 54 ALA CB C 18.704 0.006 . 205 431 54 ALA C C 176.434 0.000 . 206 432 55 ASN N N 123.920 0.020 . 207 432 55 ASN H H 7.865 0.004 . 208 432 55 ASN CA C 54.421 0.000 . 209 432 55 ASN CB C 39.887 0.000 . stop_ save_