data_18822 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Structure of the trans-membrane domain of the NS2A of dengue virus ; _BMRB_accession_number 18822 _BMRB_flat_file_name bmr18822.str _Entry_type original _Submission_date 2012-11-05 _Accession_date 2012-11-05 _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 Gayen Shovanlal . . 2 Kang Congbao . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 133 "13C chemical shifts" 26 "15N chemical shifts" 26 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-04-12 update BMRB 'update entry citation' 2013-02-21 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'Membrane Topology and Function of Dengue Virus NS2A Protein.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23408612 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Xie Xuping . . 2 Gayen Shovanlal . . 3 Kang Congbao . . 4 Yuan Zhiming . . 5 Shi Pei-Yong . . stop_ _Journal_abbreviation 'J. Virol.' _Journal_name_full 'Journal of virology' _Journal_volume 87 _Journal_issue 8 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4609 _Page_last 4622 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'trans-membrane domain of the NS2A' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'trans-membrane domain of the NS2A' $entity 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_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity _Molecular_mass 2981.647 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 28 _Mol_residue_sequence ; DIGMGVTYLALLAAFKVRPT FAAGLLLR ; loop_ _Residue_seq_code _Residue_label 1 ASP 2 ILE 3 GLY 4 MET 5 GLY 6 VAL 7 THR 8 TYR 9 LEU 10 ALA 11 LEU 12 LEU 13 ALA 14 ALA 15 PHE 16 LYS 17 VAL 18 ARG 19 PRO 20 THR 21 PHE 22 ALA 23 ALA 24 GLY 25 LEU 26 LEU 27 LEU 28 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-10-14 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 2M0S "Solution Structure Of The Trans-membrane Domain Of The Ns2a Of Dengue Virus" 100.00 28 100.00 100.00 9.64e-09 DBJ BAD36758 "polyprotein [Dengue virus 2]" 100.00 3391 100.00 100.00 1.27e-08 DBJ BAD36759 "polyprotein [Dengue virus 2]" 100.00 3391 100.00 100.00 1.27e-08 DBJ BAD36760 "polyprotein [Dengue virus 2]" 100.00 3391 100.00 100.00 1.27e-08 DBJ BAD42415 "polyprotein [Dengue virus 2]" 100.00 3391 100.00 100.00 1.27e-08 DBJ BAD42416 "polyprotein [Dengue virus 2]" 100.00 3391 100.00 100.00 1.27e-08 EMBL CAD31751 "DEN2 polyprotein [Dengue virus 2]" 100.00 3391 100.00 100.00 1.27e-08 EMBL CAI92123 "polyprotein [Dengue virus 2]" 100.00 3391 100.00 100.00 1.27e-08 EMBL CAR65133 "polyprotein [Dengue virus 2]" 100.00 3391 100.00 100.00 1.27e-08 EMBL CAR65134 "polyprotein [Dengue virus 2]" 100.00 3391 100.00 100.00 1.27e-08 EMBL CAR65135 "polyprotein [Dengue virus 2]" 100.00 3391 100.00 100.00 1.27e-08 GB AAA42941 "viral polyprotein [Dengue virus 2]" 100.00 3391 100.00 100.00 1.27e-08 GB AAA42942 "polyprotein [Dengue virus 2]" 100.00 3391 100.00 100.00 1.27e-08 GB AAA42962 "polyprotein [Dengue virus 2]" 100.00 3388 100.00 100.00 1.27e-08 GB AAA66406 "nonstructural protein 1, partial [Dengue virus 2]" 100.00 886 100.00 100.00 5.37e-08 GB AAA73185 "nonstructural protein 5 [Dengue virus 2]" 100.00 3391 100.00 100.00 1.27e-08 PRF 1301272A "protein 1 [Dengue virus 2]" 100.00 885 100.00 100.00 5.27e-08 REF NP_056776 "flavivirus polyprotein [Dengue virus 2]" 100.00 3391 100.00 100.00 1.27e-08 REF NP_739585 "Nonstructural protein NS2A [Dengue virus 2]" 100.00 218 100.00 100.00 9.44e-09 SP P07564 "RecName: Full=Genome polyprotein; Contains: RecName: Full=Capsid protein C; AltName: Full=Core protein; Contains: RecName: Full" 100.00 3391 100.00 100.00 1.27e-08 SP P12823 "RecName: Full=Genome polyprotein; Contains: RecName: Full=Capsid protein C; AltName: Full=Core protein; Contains: RecName: Full" 100.00 3388 100.00 100.00 1.27e-08 SP P14337 "RecName: Full=Genome polyprotein; Contains: RecName: Full=Capsid protein C; AltName: Full=Core protein; Contains: RecName: Full" 100.00 3391 100.00 100.00 1.27e-08 SP P14340 "RecName: Full=Genome polyprotein; Contains: RecName: Full=Capsid protein C; AltName: Full=Core protein; Contains: RecName: Full" 100.00 3391 100.00 100.00 1.27e-08 SP P29990 "RecName: Full=Genome polyprotein; Contains: RecName: Full=Capsid protein C; AltName: Full=Core protein; Contains: RecName: Full" 100.00 3391 100.00 100.00 1.27e-08 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity 'Dengue virus' 12637 Viruses . Flavivirus 'Dengue virus' 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 $entity 'chemical synthesis' . . . . . 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 $entity 3 mg/mL 'natural abundance' chloroform 44.4 % [U-2H] methanol 44.4 % [U-2H] H2O 11.2 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.1 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_ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_Bruker_700 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _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-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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 temperature 298 . K pressure 1 . atm 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 internal direct . . . 1 DSS C 13 'methyl protons' ppm 0 internal indirect . . . 0.251 DSS N 15 'methyl protons' ppm 0 internal indirect . . . 0.101 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' '2D 1H-1H TOCSY' '2D 1H-1H NOESY' 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 'trans-membrane domain of the NS2A' _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 1 1 ASP HA H 4.734 0.02 1 2 1 1 ASP HB2 H 2.929 0.02 2 3 1 1 ASP HB3 H 2.834 0.02 2 4 1 1 ASP H H 8.138 0.02 1 5 1 1 ASP N N 123.280 0.20 1 6 2 2 ILE H H 8.372 0.02 1 7 2 2 ILE HA H 3.987 0.02 1 8 2 2 ILE HB H 1.931 0.02 1 9 2 2 ILE HG12 H 1.311 0.02 2 10 2 2 ILE HG13 H 1.612 0.02 2 11 2 2 ILE CA C 63.570 0.20 1 12 3 3 GLY H H 8.410 0.02 1 13 3 3 GLY HA2 H 3.871 0.02 2 14 3 3 GLY HA3 H 3.894 0.02 2 15 3 3 GLY CA C 46.820 0.20 1 16 3 3 GLY N N 107.813 0.20 1 17 4 4 MET H H 8.039 0.02 1 18 4 4 MET HA H 4.237 0.02 1 19 4 4 MET HB2 H 2.146 0.02 2 20 4 4 MET HB3 H 2.146 0.02 2 21 4 4 MET HG2 H 2.668 0.02 2 22 4 4 MET HG3 H 2.552 0.02 2 23 4 4 MET CA C 57.960 0.20 1 24 4 4 MET N N 120.990 0.20 1 25 5 5 GLY H H 8.199 0.02 1 26 5 5 GLY HA2 H 3.920 0.02 2 27 5 5 GLY HA3 H 3.920 0.02 2 28 5 5 GLY CA C 47.690 0.20 1 29 5 5 GLY N N 106.894 0.20 1 30 6 6 VAL H H 8.268 0.02 1 31 6 6 VAL HA H 3.754 0.02 1 32 6 6 VAL HB H 2.197 0.02 1 33 6 6 VAL HG1 H 1.031 0.02 2 34 6 6 VAL HG2 H 1.126 0.02 2 35 6 6 VAL CA C 66.470 0.20 1 36 6 6 VAL N N 115.379 0.20 1 37 7 7 THR H H 7.706 0.02 1 38 7 7 THR HA H 3.964 0.02 1 39 7 7 THR HB H 3.936 0.02 1 40 7 7 THR HG2 H 1.269 0.02 1 41 7 7 THR CA C 68.370 0.20 1 42 7 7 THR N N 115.692 0.20 1 43 8 8 TYR H H 8.100 0.02 1 44 8 8 TYR HA H 4.209 0.02 1 45 8 8 TYR HB2 H 3.211 0.02 2 46 8 8 TYR HB3 H 3.211 0.02 2 47 8 8 TYR CA C 61.670 0.20 1 48 8 8 TYR N N 120.854 0.20 1 49 9 9 LEU H H 8.006 0.02 1 50 9 9 LEU HA H 3.965 0.02 1 51 9 9 LEU HB2 H 1.987 0.02 2 52 9 9 LEU HB3 H 1.609 0.02 2 53 9 9 LEU HG H 1.580 0.02 1 54 9 9 LEU HD1 H 0.980 0.02 2 55 9 9 LEU HD2 H 0.980 0.02 2 56 9 9 LEU CA C 58.090 0.20 1 57 9 9 LEU N N 117.686 0.20 1 58 10 10 ALA H H 8.320 0.02 1 59 10 10 ALA HA H 4.072 0.02 1 60 10 10 ALA HB H 1.574 0.02 1 61 10 10 ALA CA C 55.460 0.20 1 62 10 10 ALA N N 121.286 0.20 1 63 11 11 LEU H H 8.158 0.02 1 64 11 11 LEU HA H 4.053 0.02 1 65 11 11 LEU HB2 H 1.929 0.02 2 66 11 11 LEU HB3 H 1.868 0.02 2 67 11 11 LEU HG H 1.578 0.02 1 68 11 11 LEU HD1 H 0.924 0.02 2 69 11 11 LEU HD2 H 0.924 0.02 2 70 11 11 LEU CA C 61.490 0.20 1 71 11 11 LEU N N 119.311 0.20 1 72 12 12 LEU H H 8.211 0.02 1 73 12 12 LEU HA H 3.979 0.02 1 74 12 12 LEU HB2 H 1.735 0.02 2 75 12 12 LEU HB3 H 1.567 0.02 2 76 12 12 LEU HD1 H 0.822 0.02 2 77 12 12 LEU HD2 H 0.822 0.02 2 78 12 12 LEU CA C 58.090 0.20 1 79 12 12 LEU N N 119.405 0.20 1 80 13 13 ALA H H 8.353 0.02 1 81 13 13 ALA HA H 3.996 0.02 1 82 13 13 ALA HB H 1.544 0.02 1 83 13 13 ALA CA C 55.060 0.20 1 84 13 13 ALA N N 120.690 0.20 1 85 14 14 ALA H H 8.140 0.02 1 86 14 14 ALA HA H 4.007 0.02 1 87 14 14 ALA HB H 1.447 0.02 1 88 14 14 ALA CA C 55.070 0.20 1 89 14 14 ALA N N 119.292 0.20 1 90 15 15 PHE H H 8.272 0.02 1 91 15 15 PHE HA H 4.352 0.02 1 92 15 15 PHE HB2 H 3.262 0.02 2 93 15 15 PHE HB3 H 3.200 0.02 2 94 15 15 PHE CA C 60.070 0.20 1 95 15 15 PHE N N 119.448 0.20 1 96 16 16 LYS H H 7.959 0.02 1 97 16 16 LYS HA H 4.262 0.02 1 98 16 16 LYS HB2 H 1.997 0.02 2 99 16 16 LYS HB3 H 1.997 0.02 2 100 16 16 LYS HD2 H 1.624 0.02 2 101 16 16 LYS HD3 H 1.704 0.02 2 102 16 16 LYS HE2 H 2.931 0.02 2 103 16 16 LYS HE3 H 2.931 0.02 2 104 16 16 LYS CA C 55.890 0.20 1 105 16 16 LYS N N 116.153 0.20 1 106 17 17 VAL H H 7.991 0.02 1 107 17 17 VAL HA H 4.001 0.02 1 108 17 17 VAL HB H 2.239 0.02 1 109 17 17 VAL HG1 H 0.974 0.02 2 110 17 17 VAL HG2 H 1.063 0.02 2 111 17 17 VAL CA C 63.540 0.20 1 112 17 17 VAL N N 116.676 0.20 1 113 18 18 ARG H H 8.075 0.02 1 114 18 18 ARG HA H 4.414 0.02 1 115 18 18 ARG HB2 H 1.938 0.02 2 116 18 18 ARG HB3 H 1.938 0.02 2 117 18 18 ARG HG2 H 1.767 0.02 2 118 18 18 ARG HG3 H 1.634 0.02 2 119 18 18 ARG HD2 H 3.169 0.02 2 120 18 18 ARG HD3 H 3.169 0.02 2 121 18 18 ARG HE H 7.477 0.02 1 122 18 18 ARG CA C 58.030 0.20 1 123 18 18 ARG N N 120.422 0.20 1 124 19 19 PRO HA H 4.370 0.02 1 125 19 19 PRO HB2 H 2.129 0.02 2 126 19 19 PRO HB3 H 2.291 0.02 2 127 19 19 PRO HG3 H 1.917 0.02 2 128 19 19 PRO HD2 H 3.689 0.02 2 129 19 19 PRO HD3 H 3.642 0.02 2 130 19 19 PRO CA C 65.240 0.20 1 131 20 20 THR H H 7.520 0.02 1 132 20 20 THR HA H 4.254 0.02 1 133 20 20 THR HB H 4.020 0.02 1 134 20 20 THR HG2 H 1.244 0.02 1 135 20 20 THR CA C 63.960 0.20 1 136 20 20 THR N N 111.614 0.20 1 137 21 21 PHE H H 8.065 0.02 1 138 21 21 PHE HA H 4.381 0.02 1 139 21 21 PHE HB2 H 3.200 0.02 2 140 21 21 PHE HB3 H 3.171 0.02 2 141 21 21 PHE CA C 59.890 0.20 1 142 21 21 PHE N N 121.158 0.20 1 143 22 22 ALA H H 8.161 0.02 1 144 22 22 ALA HA H 4.027 0.02 1 145 22 22 ALA HB H 1.483 0.02 1 146 22 22 ALA CA C 54.630 0.20 1 147 22 22 ALA N N 120.586 0.20 1 148 23 23 ALA H H 7.955 0.02 1 149 23 23 ALA HA H 4.036 0.02 1 150 23 23 ALA HB H 1.516 0.02 1 151 23 23 ALA CA C 54.720 0.20 1 152 23 23 ALA N N 118.530 0.20 1 153 24 24 GLY H H 7.990 0.02 1 154 24 24 GLY HA2 H 3.816 0.02 2 155 24 24 GLY HA3 H 3.816 0.02 2 156 24 24 GLY CA C 46.650 0.20 1 157 24 24 GLY N N 103.400 0.20 1 158 25 25 LEU H H 7.650 0.02 1 159 25 25 LEU HA H 4.154 0.02 1 160 25 25 LEU HB2 H 1.821 0.02 2 161 25 25 LEU HB3 H 1.821 0.02 2 162 25 25 LEU HG H 1.529 0.02 1 163 25 25 LEU HD1 H 0.847 0.02 2 164 25 25 LEU HD2 H 0.847 0.02 2 165 25 25 LEU CA C 56.550 0.20 1 166 25 25 LEU N N 118.196 0.20 1 167 26 26 LEU H H 7.638 0.02 1 168 26 26 LEU HA H 4.256 0.02 1 169 26 26 LEU HB2 H 1.774 0.02 2 170 26 26 LEU HB3 H 1.627 0.02 2 171 26 26 LEU HD1 H 0.884 0.02 2 172 26 26 LEU HD2 H 0.927 0.02 2 173 26 26 LEU CA C 55.730 0.20 1 174 26 26 LEU N N 116.901 0.20 1 175 27 27 LEU H H 7.673 0.02 1 176 27 27 LEU HA H 4.338 0.02 1 177 27 27 LEU HB2 H 1.752 0.02 2 178 27 27 LEU HB3 H 1.642 0.02 2 179 27 27 LEU HD1 H 0.900 0.02 2 180 27 27 LEU HD2 H 0.916 0.02 2 181 27 27 LEU CA C 54.950 0.20 1 182 27 27 LEU N N 117.617 0.20 1 183 28 28 ARG H H 7.653 0.02 1 184 28 28 ARG HB3 H 1.948 0.02 2 185 28 28 ARG N N 119.190 0.20 1 stop_ save_