data_17929 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of the influenza AM2-BM2 chimeric channel bound to rimantadine ; _BMRB_accession_number 17929 _BMRB_flat_file_name bmr17929.str _Entry_type original _Submission_date 2011-09-10 _Accession_date 2011-09-10 _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 Pielak Rafal M. . 2 Oxenoid Kirill . . 3 Chou James J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 24 "13C chemical shifts" 14 "15N chemical shifts" 24 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-12-05 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 17928 'influenza AM2-BM2 chimeric channel' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural investigation of rimantadine inhibition of the AM2-BM2 chimera channel of influenza viruses' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22078564 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Pielak Rafal M. . 2 Oxenoid Kirill . . 3 Chou James J. . stop_ _Journal_abbreviation Structure _Journal_volume 19 _Journal_issue 11 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1655 _Page_last 1663 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name AM2-BM2 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label AM2-BM2_1 $AM2-BM2 AM2-BM2_2 $AM2-BM2 AM2-BM2_3 $AM2-BM2 AM2-BM2_4 $AM2-BM2 RIMANTADINE $RIM 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_AM2-BM2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common AM2-BM2 _Molecular_mass 3244.864 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 35 _Mol_residue_sequence ; RSNDSSDPLVVAASIIGILH FIAWTIGHLNQIKRG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 18 ARG 2 19 SER 3 20 ASN 4 21 ASP 5 22 SER 6 23 SER 7 24 ASP 8 25 PRO 9 26 LEU 10 27 VAL 11 28 VAL 12 29 ALA 13 30 ALA 14 31 SER 15 32 ILE 16 33 ILE 17 34 GLY 18 35 ILE 19 36 LEU 20 37 HIS 21 38 PHE 22 39 ILE 23 40 ALA 24 41 TRP 25 42 THR 26 43 ILE 27 44 GLY 28 45 HIS 29 46 LEU 30 47 ASN 31 48 GLN 32 49 ILE 33 50 LYS 34 51 ARG 35 52 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-11-10 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 17928 influenza_AM2-BM2_chimeric_channel 100.00 35 100.00 100.00 3.30e-15 PDB 2LJB "Structure Of The Influenza Am2-Bm2 Chimeric Channel" 100.00 35 100.00 100.00 3.30e-15 PDB 2LJC "Structure Of The Influenza Am2-Bm2 Chimeric Channel Bound To Rimantadine" 100.00 35 100.00 100.00 3.30e-15 stop_ save_ ############# # Ligands # ############# save_RIM _Saveframe_category ligand _Mol_type non-polymer _Name_common "RIM (RIMANTADINE)" _BMRB_code . _PDB_code RIM _Molecular_mass 179.302 _Mol_charge 0 _Mol_paramagnetic no _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Sep 22 17:20:39 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons CA CA C . 0 . ? CB CB C . 0 . ? NC NC N . 0 . ? CD CD C . 0 . ? CE1 CE1 C . 0 . ? CE2 CE2 C . 0 . ? CE3 CE3 C . 0 . ? CF1 CF1 C . 0 . ? CF2 CF2 C . 0 . ? CF3 CF3 C . 0 . ? CG1 CG1 C . 0 . ? CG2 CG2 C . 0 . ? CG3 CG3 C . 0 . ? HA1 HA1 H . 0 . ? HA2 HA2 H . 0 . ? HA3 HA3 H . 0 . ? HB HB H . 0 . ? HNC1 HNC1 H . 0 . ? HNC2 HNC2 H . 0 . ? HE11 HE11 H . 0 . ? HE12 HE12 H . 0 . ? HE21 HE21 H . 0 . ? HE22 HE22 H . 0 . ? HE31 HE31 H . 0 . ? HE32 HE32 H . 0 . ? HF1 HF1 H . 0 . ? HF2 HF2 H . 0 . ? HF3 HF3 H . 0 . ? HG11 HG11 H . 0 . ? HG12 HG12 H . 0 . ? HG21 HG21 H . 0 . ? HG22 HG22 H . 0 . ? HG31 HG31 H . 0 . ? HG32 HG32 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING CA CB ? ? SING CA HA1 ? ? SING CA HA2 ? ? SING CA HA3 ? ? SING CB CD ? ? SING CB NC ? ? SING CB HB ? ? SING NC HNC1 ? ? SING NC HNC2 ? ? SING CD CE2 ? ? SING CD CE1 ? ? SING CD CE3 ? ? SING CE1 CF1 ? ? SING CE1 HE11 ? ? SING CE1 HE12 ? ? SING CE2 CF2 ? ? SING CE2 HE21 ? ? SING CE2 HE22 ? ? SING CE3 CF3 ? ? SING CE3 HE31 ? ? SING CE3 HE32 ? ? SING CF1 CG1 ? ? SING CF1 CG3 ? ? SING CF1 HF1 ? ? SING CF2 CG1 ? ? SING CF2 CG2 ? ? SING CF2 HF2 ? ? SING CF3 CG2 ? ? SING CF3 CG3 ? ? SING CF3 HF3 ? ? SING CG1 HG11 ? ? SING CG1 HG12 ? ? SING CG2 HG21 ? ? SING CG2 HG22 ? ? SING CG3 HG31 ? ? SING CG3 HG32 ? ? stop_ _Mol_thiol_state 'not present' _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 $AM2-BM2 'Influenzavirus A and B' 197911 Viruses . 'Influenzavirus A and B' . 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 $AM2-BM2 'recombinant technology' . . . BL21(DE3) trpLE-fusion $RIM 'obtained from a vendor' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'triple labeled protein for assignment' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $AM2-BM2 1.2 mM '[U-100% 13C; U-100% 15N; U-80% 2H]' DHPC 300 mM 'natural abundance' 'sodium phosphate' 40 mM 'natural abundance' $RIM 50 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details 'double labeled protein for NOE experiments' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $AM2-BM2 1.5 mM '[U-100% 13C; U-100% 15N]' DHPC 300 mM '[U-99% 2H]' 'sodium phosphate' 40 mM 'natural abundance' $RIM 50 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details 'perdeuterated sample for protein-drug NOEs' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $AM2-BM2 1.5 mM '[U-100% 15N; U-99% 2H]' DHPC 300 mM '[U-99% 2H]' 'sodium phosphate' 40 mM 'natural abundance' $RIM 50 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type solution _Details 'mixed sample for inter-monomer NOEs' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $AM2-BM2 0.9 mM '[U-100% 15N; U-99% 2H]' $AM2-BM2 0.9 mM '[U-10% 13C]' DHPC 300 mM '[U-99% 2H]' 'sodium phosphate' 40 mM 'natural abundance' $RIM 50 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ save_sample_5 _Saveframe_category sample _Sample_type solution _Details '15% 13C labeled sample for assigning stereospecific methyl groups' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $AM2-BM2 1.4 mM '[U-15% 13C]' DHPC 300 mM '[U-99% 2H]' 'sodium phosphate' 40 mM 'natural abundance' $RIM 50 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ save_sample_6 _Saveframe_category sample _Sample_type solution _Details 'aligned sample for RDC measurement' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $AM2-BM2 0.5 mM '[U-100% 13C; U-100% 15N; U-80% 2H]' DHPC 300 mM 'natural abundance' 'sodium phosphate' 40 mM 'natural abundance' $RIM 50 mM 'natural abundance' 'DNA nanotube' 5.4 mg 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_xwinnmr _Saveframe_category software _Name xwinnmr _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ save_CARA _Saveframe_category software _Name CARA _Version . loop_ _Vendor _Address _Electronic_address 'Keller and Wuthrich' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _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_2 save_ save_3D_HNCA_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCA' _Sample_label $sample_1 save_ save_3D_1H-15N_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $sample_2 save_ save_3D_1H-13C_NOESY_aliphatic_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-13C NOESY aliphatic' _Sample_label $sample_2 save_ save_3D_1H-13C_NOESY_aromatic_6 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-13C NOESY aromatic' _Sample_label $sample_2 save_ save_3D_1H-15N_NOESY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $sample_3 save_ save_3D_1H-15N_NOESY_8 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $sample_4 save_ save_2D_1H-13C_HSQC_(28m_CT)_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC (28m CT)' _Sample_label $sample_5 save_ save_Interleaved_HSQC-TROSY_10 _Saveframe_category NMR_applied_experiment _Experiment_name 'Interleaved HSQC-TROSY' _Sample_label $sample_1 save_ save_Interleaved_HSQC-TROSY_11 _Saveframe_category NMR_applied_experiment _Experiment_name 'Interleaved HSQC-TROSY' _Sample_label $sample_6 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 273 . K pH 7.5 . pH pressure 1 . atm 'ionic strength' 100 . mM 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 TMS H 1 'methyl protons' ppm 0 external direct . . . 1 TMS C 13 'methyl carbon' ppm 0 external direct . . . 1 urea N 15 nitrogen ppm 0 external 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 _Details . loop_ _Experiment_label '3D HNCA' '3D 1H-15N NOESY' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name AM2-BM2_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 24 7 ASP H H 8.429 0.25 1 2 24 7 ASP CA C 53.33 0.25 1 3 24 7 ASP N N 125.566 0.25 1 4 26 9 LEU H H 8.19 0.25 1 5 26 9 LEU CA C 58.488 0.25 1 6 26 9 LEU N N 119.147 0.25 1 7 27 10 VAL H H 7.255 0.25 1 8 27 10 VAL CA C 65.487 0.25 1 9 27 10 VAL N N 121.008 0.25 1 10 28 11 VAL H H 8.171 0.25 1 11 28 11 VAL CA C 67.586 0.25 1 12 28 11 VAL N N 123.961 0.25 1 13 29 12 ALA H H 8.418 0.25 1 14 29 12 ALA CA C 55.896 0.25 1 15 29 12 ALA N N 121.779 0.25 1 16 30 13 ALA H H 8.636 0.25 1 17 30 13 ALA CA C 55.481 0.25 1 18 30 13 ALA N N 118.633 0.25 1 19 31 14 SER H H 8.267 0.25 1 20 31 14 SER CA C 63.672 0.25 1 21 31 14 SER N N 119.981 0.25 1 22 32 15 ILE H H 7.797 0.25 1 23 32 15 ILE CA C 65.616 0.25 1 24 32 15 ILE N N 122.292 0.25 1 25 33 16 ILE H H 7.996 0.25 1 26 33 16 ILE CA C 65.538 0.25 1 27 33 16 ILE N N 121.008 0.25 1 28 34 17 GLY H H 8.061 0.25 1 29 34 17 GLY CA C 47.264 0.25 1 30 34 17 GLY N N 123.769 0.25 1 31 36 19 LEU H H 8.113 0.25 1 32 36 19 LEU N N 120.377 0.25 1 33 37 20 HIS H H 9.052 0.25 1 34 37 20 HIS N N 118.796 0.25 1 35 39 22 ILE H H 8.2 0.25 1 36 39 22 ILE N N 121.245 0.25 1 37 40 23 ALA H H 8.835 0.25 1 38 40 23 ALA N N 121.33 0.25 1 39 41 24 TRP H H 8.52 0.25 1 40 41 24 TRP N N 119.054 0.25 1 41 42 25 THR H H 8.068 0.25 1 42 42 25 THR N N 117.474 0.25 1 43 43 26 ILE H H 8.02 0.25 1 44 43 26 ILE N N 120.749 0.25 1 45 44 27 GLY H H 8.067 0.25 1 46 44 27 GLY N N 107.156 0.25 1 47 45 28 HIS H H 7.815 0.25 1 48 45 28 HIS CA C 59.466 0.25 1 49 45 28 HIS N N 121.329 0.25 1 50 46 29 LEU H H 8.075 0.25 1 51 46 29 LEU CA C 57.258 0.25 1 52 46 29 LEU N N 119.724 0.25 1 53 47 30 ASN H H 7.995 0.25 1 54 47 30 ASN CA C 54.911 0.25 1 55 47 30 ASN N N 117.028 0.25 1 56 48 31 GLN H H 7.672 0.25 1 57 48 31 GLN CA C 56.985 0.25 1 58 48 31 GLN N N 118.954 0.25 1 59 49 32 ILE H H 7.679 0.25 1 60 49 32 ILE N N 119.836 0.25 1 61 50 33 LYS H H 8.018 0.25 1 62 50 33 LYS N N 124.429 0.25 1 stop_ save_