data_15196 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of the HIV-2 nucleocapsid protein ; _BMRB_accession_number 15196 _BMRB_flat_file_name bmr15196.str _Entry_type new _Submission_date 2007-03-21 _Accession_date 2007-03-21 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Matsui T. . . 2 Kodera Y. . . 3 Tanaka H. . . 4 Miyauchi E. . . 5 Komatsu H. . . 6 Tanaka T. . . 7 Kohno T. . . 8 Maeda T. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 151 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-05-06 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_title 'RNA recognition mechanism of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein' _Citation_status published _Citation_type journal _PubMed_ID 17202191 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Matsui T. . . 2 Kodera Y. . . 3 Endoh H. . . 4 Miyauchi E. . . 5 Komatsu H. . . 6 Sato T. . . 7 Tanaka T. . . 8 Kohno T. . . 9 Maeda T. . . stop_ _Journal_abbreviation 'J. Biochem.' _Journal_volume 141 _Journal_issue 2 _Journal_CSD 0353 _Page_first 269 _Page_last 277 _Year 2007 save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name NCp8-f2 loop_ _Mol_system_component_name _Mol_label 'polymer chain' $Gag-Pol_polyprotein_(Pr160Gag-Pol) 'Zinc ion' $ZN stop_ _System_physical_state native _System_oligomer_state ? _System_paramagnetic no save_ ######################## # Monomeric polymers # ######################## save_Gag-Pol_polyprotein_(Pr160Gag-Pol) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Gag-Pol_polyprotein_(Pr160Gag-Pol) _Mol_thiol_state 'all other bound' ############################## # Polymer residue sequence # ############################## _Residue_count 27 _Mol_residue_sequence ; RAPRRQGCWKCGKTGHVMAK CPERQAG ; loop_ _Residue_seq_code _Residue_label 1 ARG 2 ALA 3 PRO 4 ARG 5 ARG 6 GLN 7 GLY 8 CYS 9 TRP 10 LYS 11 CYS 12 GLY 13 LYS 14 THR 15 GLY 16 HIS 17 VAL 18 MET 19 ALA 20 LYS 21 CYS 22 PRO 23 GLU 24 ARG 25 GLN 26 ALA 27 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-02-06 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 15364 Gag_polyprotein_(Pr55Gag) 100.00 49 100.00 100.00 1.50e-09 PDB 2E1X "Nmr Structure Of The Hiv-2 Nucleocapsid Protein" 100.00 27 100.00 100.00 8.69e-10 PDB 2EC7 "Solution Structure Of Human Immunodificiency Virus Type-2 Nucleocapsid Protein" 100.00 49 100.00 100.00 1.50e-09 PDB 2IWJ "Solution Structure Of The Zn Complex Of Hiv-2 Ncp(23-49) Peptide, Encompassing Protein Cchc-Linker, Distal Cchc Zn- Binding Mot" 100.00 27 100.00 100.00 8.69e-10 EMBL CAA32483 "unnamed protein product [Simian immunodeficiency virus]" 100.00 507 100.00 100.00 2.23e-09 GB AAA43932 "gag protein [Human immunodeficiency virus 2]" 100.00 522 100.00 100.00 2.61e-09 GB AAB41427 "gag, partial [Simian immunodeficiency virus]" 100.00 149 100.00 100.00 8.19e-10 GB AAC68655 "Gag [Simian immunodeficiency virus]" 100.00 507 100.00 100.00 2.35e-09 GB AAL18230 "gag polyprotein [Simian immunodeficiency virus]" 51.85 389 100.00 100.00 3.79e+00 GB ADI24350 "gag protein [Simian immunodeficiency virus]" 100.00 507 100.00 100.00 2.42e-09 PRF 1509334A "gag gene" 100.00 507 100.00 100.00 2.23e-09 SP P12496 "RecName: Full=Gag polyprotein; AltName: Full=Pr55Gag; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: RecName: " 100.00 507 100.00 100.00 2.23e-09 SP P12502 "RecName: Full=Gag-Pol polyprotein; AltName: Full=Pr160Gag-Pol; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: " 100.00 1449 100.00 100.00 1.94e-09 SP P18041 "RecName: Full=Gag polyprotein; AltName: Full=Pr55Gag; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: RecName: " 100.00 522 100.00 100.00 2.61e-09 SP P18042 "RecName: Full=Gag-Pol polyprotein; AltName: Full=Pr160Gag-Pol; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: " 100.00 1464 100.00 100.00 1.75e-09 stop_ save_ ############# # Ligands # ############# save_ZN _Saveframe_category ligand _Mol_type non-polymer _Name_common "ZN (ZINC ION)" _PDB_code ZN _Mol_empirical_formula 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 Feb 15 21:22:05 2008 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons ZN ZN ZN N 2 . ? stop_ _Mol_thiol_state . save_ ######################################## # Molecular bond linkage definitions # ######################################## save_crosslink_bonds _Saveframe_category crosslink_bonds loop_ _Bond_order _Bond_type _Atom_one_mol_system_component_name _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_atom_name _Atom_two_mol_system_component_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_atom_name single coordination 'polymer chain' 30 CYS SG 'Zinc ion' . . ZN single coordination 'polymer chain' 33 CYS SG 'Zinc ion' . . ZN single coordination 'polymer chain' 38 HIS NE2 'Zinc ion' . . ZN single coordination 'polymer chain' 43 CYS SG 'Zinc ion' . . ZN stop_ 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 _Details $Gag-Pol_polyprotein_(Pr160Gag-Pol) HIV-2 11709 Viruses . Lentivirus HIV-2 'isolate GH-1' gag 'isolate Ghana-1 subtype A' 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 _Details $Gag-Pol_polyprotein_(Pr160Gag-Pol) 'chemical synthesis' . . . . ? 'This peptide has been chemically synthesized. This sequence occurs naturally in HIV-2.' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample _Saveframe_category sample _Sample_type solution _Details '5mM Protein; 5.5mM ZnCl2; 90% H2O, 10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Gag-Pol_polyprotein_(Pr160Gag-Pol) 5 mM 'natural abundance' $ZN 5.5 mM 'natural abundance' DSS 0.5 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version 2.9.9 loop_ _Vendor _Address _Electronic_address C.D.SCHWIETERS. . . stop_ loop_ _Task 'structure solution' stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 500 save_ ############################# # NMR applied experiments # ############################# save_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample save_ save_2D_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 5.8 . pH temperature 288 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference 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 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 loop_ _Experiment_label '2D TOCSY' stop_ loop_ _Sample_label $sample stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'polymer chain' 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 1 1 ARG HB2 H 1.91 0.02 2 2 1 1 ARG HB3 H 1.91 0.02 2 3 1 1 ARG HG3 H 1.64 0.02 2 4 2 2 ALA H H 8.84 0.02 1 5 2 2 ALA HA H 4.63 0.02 1 6 2 2 ALA HB H 1.39 0.02 1 7 3 3 PRO HB2 H 2.29 0.02 2 8 3 3 PRO HB3 H 1.87 0.02 2 9 3 3 PRO HD2 H 3.83 0.02 2 10 3 3 PRO HD3 H 3.64 0.02 2 11 3 3 PRO HG2 H 2.02 0.02 2 12 3 3 PRO HG3 H 2.02 0.02 2 13 4 4 ARG H H 8.48 0.02 1 14 4 4 ARG HA H 4.27 0.02 1 15 4 4 ARG HB2 H 1.78 0.02 2 16 4 4 ARG HB3 H 1.78 0.02 2 17 4 4 ARG HD2 H 3.14 0.02 2 18 4 4 ARG HD3 H 3.14 0.02 2 19 4 4 ARG HG2 H 1.64 0.02 2 20 4 4 ARG HG3 H 1.64 0.02 2 21 5 5 ARG H H 8.53 0.02 1 22 5 5 ARG HA H 4.31 0.02 1 23 5 5 ARG HB2 H 1.80 0.02 2 24 5 5 ARG HB3 H 1.73 0.02 2 25 5 5 ARG HD2 H 3.05 0.02 2 26 5 5 ARG HD3 H 3.05 0.02 2 27 5 5 ARG HG2 H 1.59 0.02 2 28 5 5 ARG HG3 H 1.56 0.02 2 29 6 6 GLN H H 8.55 0.02 1 30 6 6 GLN HA H 4.37 0.02 1 31 6 6 GLN HB2 H 2.06 0.02 2 32 6 6 GLN HB3 H 1.94 0.02 2 33 6 6 GLN HG2 H 2.34 0.02 2 34 6 6 GLN HG3 H 2.34 0.02 2 35 7 7 GLY H H 8.34 0.02 1 36 7 7 GLY HA2 H 3.55 0.02 2 37 7 7 GLY HA3 H 3.83 0.02 2 38 8 8 CYS H H 8.30 0.02 1 39 8 8 CYS HA H 4.11 0.02 1 40 8 8 CYS HB2 H 2.94 0.02 2 41 8 8 CYS HB3 H 2.20 0.02 2 42 9 9 TRP H H 8.64 0.02 1 43 9 9 TRP HA H 4.52 0.02 1 44 9 9 TRP HB2 H 3.49 0.02 2 45 9 9 TRP HB3 H 3.49 0.02 2 46 9 9 TRP HD1 H 7.36 0.02 1 47 9 9 TRP HE1 H 10.16 0.02 1 48 9 9 TRP HE3 H 7.65 0.02 1 49 9 9 TRP HH2 H 7.26 0.02 1 50 9 9 TRP HZ2 H 7.53 0.02 1 51 9 9 TRP HZ3 H 7.16 0.02 1 52 10 10 LYS H H 9.37 0.02 1 53 10 10 LYS HA H 4.34 0.02 1 54 10 10 LYS HB2 H 2.39 0.02 2 55 10 10 LYS HB3 H 2.39 0.02 2 56 10 10 LYS HD2 H 1.71 0.02 2 57 10 10 LYS HD3 H 1.68 0.02 2 58 10 10 LYS HE2 H 2.95 0.02 2 59 10 10 LYS HE3 H 2.95 0.02 2 60 10 10 LYS HG2 H 1.31 0.02 2 61 10 10 LYS HG3 H 1.31 0.02 2 62 11 11 CYS H H 8.53 0.02 1 63 11 11 CYS HA H 5.01 0.02 1 64 11 11 CYS HB2 H 3.28 0.02 2 65 11 11 CYS HB3 H 2.54 0.02 2 66 12 12 GLY H H 8.25 0.02 1 67 12 12 GLY HA2 H 4.36 0.02 2 68 12 12 GLY HA3 H 3.76 0.02 2 69 13 13 LYS H H 8.46 0.02 1 70 13 13 LYS HA H 4.55 0.02 1 71 13 13 LYS HB2 H 2.02 0.02 2 72 13 13 LYS HB3 H 1.88 0.02 2 73 13 13 LYS HD2 H 1.79 0.02 2 74 13 13 LYS HD3 H 1.68 0.02 2 75 13 13 LYS HE2 H 3.07 0.02 2 76 13 13 LYS HE3 H 3.07 0.02 2 77 13 13 LYS HG2 H 1.49 0.02 2 78 13 13 LYS HG3 H 1.49 0.02 2 79 14 14 THR H H 8.29 0.02 1 80 14 14 THR HA H 4.35 0.02 1 81 14 14 THR HB H 4.25 0.02 1 82 14 14 THR HG2 H 1.18 0.02 1 83 15 15 GLY H H 8.64 0.02 1 84 15 15 GLY HA2 H 4.36 0.02 2 85 15 15 GLY HA3 H 3.76 0.02 2 86 16 16 HIS H H 7.17 0.02 1 87 16 16 HIS HA H 4.97 0.02 1 88 16 16 HIS HB2 H 3.22 0.02 2 89 16 16 HIS HB3 H 3.12 0.02 2 90 16 16 HIS HD2 H 6.91 0.02 1 91 16 16 HIS HE1 H 7.59 0.02 1 92 17 17 VAL H H 8.03 0.02 1 93 17 17 VAL HA H 4.65 0.02 1 94 17 17 VAL HB H 2.42 0.02 1 95 17 17 VAL HG1 H 0.94 0.02 2 96 17 17 VAL HG2 H 0.94 0.02 2 97 18 18 MET H H 8.88 0.02 1 98 18 18 MET HA H 4.79 0.02 1 99 18 18 MET HB2 H 2.21 0.02 2 100 18 18 MET HB3 H 2.21 0.02 2 101 18 18 MET HG2 H 2.61 0.02 2 102 18 18 MET HG3 H 2.61 0.02 2 103 19 19 ALA H H 8.60 0.02 1 104 19 19 ALA HA H 4.15 0.02 1 105 19 19 ALA HB H 1.44 0.02 1 106 20 20 LYS H H 7.95 0.02 1 107 20 20 LYS HA H 4.51 0.02 1 108 20 20 LYS HB2 H 2.14 0.02 2 109 20 20 LYS HB3 H 1.69 0.02 2 110 20 20 LYS HD2 H 1.43 0.02 2 111 20 20 LYS HD3 H 1.43 0.02 2 112 20 20 LYS HE2 H 2.96 0.02 2 113 20 20 LYS HE3 H 2.96 0.02 2 114 20 20 LYS HG2 H 1.26 0.02 2 115 20 20 LYS HG3 H 1.26 0.02 2 116 21 21 CYS H H 7.61 0.02 1 117 21 21 CYS HA H 4.07 0.02 1 118 21 21 CYS HB2 H 3.34 0.02 2 119 21 21 CYS HB3 H 2.85 0.02 2 120 22 22 PRO HB2 H 2.18 0.02 2 121 22 22 PRO HB3 H 1.98 0.02 2 122 22 22 PRO HD2 H 3.68 0.02 2 123 22 22 PRO HD3 H 3.05 0.02 2 124 22 22 PRO HG2 H 1.88 0.02 2 125 22 22 PRO HG3 H 1.82 0.02 2 126 23 23 GLU H H 8.74 0.02 1 127 23 23 GLU HA H 4.29 0.02 1 128 23 23 GLU HB2 H 2.15 0.02 2 129 23 23 GLU HB3 H 1.99 0.02 2 130 23 23 GLU HG2 H 2.35 0.02 2 131 23 23 GLU HG3 H 2.22 0.02 2 132 24 24 ARG H H 8.07 0.02 1 133 24 24 ARG HA H 4.27 0.02 1 134 24 24 ARG HB2 H 1.88 0.02 2 135 24 24 ARG HB3 H 1.82 0.02 2 136 24 24 ARG HD2 H 3.24 0.02 2 137 24 24 ARG HD3 H 3.21 0.02 2 138 24 24 ARG HG2 H 1.62 0.02 2 139 24 24 ARG HG3 H 1.62 0.02 2 140 25 25 GLN H H 8.44 0.02 1 141 25 25 GLN HA H 4.32 0.02 1 142 25 25 GLN HB2 H 2.14 0.02 2 143 25 25 GLN HB3 H 1.99 0.02 2 144 25 25 GLN HG2 H 2.37 0.02 2 145 25 25 GLN HG3 H 2.37 0.02 2 146 26 26 ALA H H 8.42 0.02 1 147 26 26 ALA HA H 4.36 0.02 1 148 26 26 ALA HB H 1.41 0.02 1 149 27 27 GLY H H 8.08 0.02 1 150 27 27 GLY HA2 H 3.77 0.02 2 151 27 27 GLY HA3 H 3.77 0.02 2 stop_ save_