data_16477 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of the transmembrane proximal region of the hepatis C virus E1 glycoprotein. ; _BMRB_accession_number 16477 _BMRB_flat_file_name bmr16477.str _Entry_type new _Submission_date 2009-09-04 _Accession_date 2009-09-04 _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 Spadaccini Roberta . . 2 D'Errico Gerardino . . 3 D'Alessio Viviana . . 4 Notomista Eugenio . . 5 Bianchi Alessia . . 6 Merola Marcello . . 7 Picone Delia . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 169 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-03-18 update BMRB 'complete entry citation' 2009-12-11 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural characterization of the transmembrane proximal region of the hepatitis C virus E1 glycoprotein.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19891955 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Spadaccini Roberta . . 2 Notomista Gerardino . . 3 Bianchi Viviana . . 4 Merola Eugenio . . 5 Picone Alessia . . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta' _Journal_name_full 'Biochimica et biophysica acta' _Journal_volume 1798 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 344 _Page_last 353 _Year 2010 _Details . loop_ _Keyword NMR HCV glycoprotein pretransmembrane ESR stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'e1 peptide' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label e1 $e1 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_e1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common e1_peptide _Molecular_mass 3328.988 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 29 _Mol_residue_sequence ; TGHRMAWDMMMNWSPTAALV VAQLLRIPQ ; loop_ _Residue_seq_code _Residue_label 1 THR 2 GLY 3 HIS 4 ARG 5 MET 6 ALA 7 TRP 8 ASP 9 MET 10 MET 11 MET 12 ASN 13 TRP 14 SER 15 PRO 16 THR 17 ALA 18 ALA 19 LEU 20 VAL 21 VAL 22 ALA 23 GLN 24 LEU 25 LEU 26 ARG 27 ILE 28 PRO 29 GLN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-18 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 2KNU "Solution Structure Of The Transmembrane Proximal Region Of The Hepatis C Virus E1 Glycoprotein" 100.00 29 100.00 100.00 4.58e-11 DBJ BAC41283 "polyprotein, partial [Hepatitis C virus]" 100.00 488 100.00 100.00 8.40e-10 DBJ BAC41284 "polyprotein, partial [Hepatitis C virus]" 100.00 488 100.00 100.00 7.92e-10 DBJ BAN91312 "polyprotein, partial [Hepatitis C virus]" 100.00 195 100.00 100.00 6.14e-11 EMBL CAA37292 "unnamed protein product, partial [Hepatitis C virus]" 100.00 309 100.00 100.00 1.99e-10 EMBL CAD53863 "polyprotein, partial [Hepatitis C virus]" 51.72 88 100.00 100.00 7.04e+00 EMBL CAD53864 "polyprotein, partial [Hepatitis C virus]" 51.72 88 100.00 100.00 6.83e+00 EMBL CAD53866 "polyprotein, partial [Hepatitis C virus]" 51.72 88 100.00 100.00 6.97e+00 EMBL CAD53867 "polyprotein, partial [Hepatitis C virus]" 51.72 88 100.00 100.00 7.78e+00 GB AAA45563 "envelope protein E1, partial [Hepatitis C virus]" 100.00 192 100.00 100.00 9.20e-11 GB AAB02127 "polyprotein, partial [Hepatitis C virus]" 100.00 778 100.00 100.00 1.09e-09 GB AAB02128 "largest ORF, partial [Hepatitis C virus]" 100.00 778 100.00 100.00 1.15e-09 GB AAB66324 "polyprotein [Hepatitis C virus subtype 1a]" 100.00 3011 100.00 100.00 7.98e-10 GB AAB67036 "polyprotein [Hepatitis C virus (isolate H77)]" 100.00 3011 100.00 100.00 8.29e-10 REF NP_671491 "polyprotein [Hepatitis C virus]" 100.00 3011 100.00 100.00 7.98e-10 REF NP_751920 "E1 protein [Hepatitis C virus]" 100.00 192 100.00 100.00 9.02e-11 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $e1 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 $e1 '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 $e1 1 mM 'natural abundance' D2O 20 % 'natural abundance' hexafluoroisopropanol 80 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $e1 1 mM 'natural abundance' H2O 20 % 'natural abundance' hexafluoroisopropanol 80 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task refinement 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_ 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_ save_NMRView _Saveframe_category software _Name NMRView _Version . loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-1H_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_COSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 300 . K pH 4.5 . pH 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 . . . 1.0 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-1H TOCSY' '2D 1H-1H COSY' '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_2 $sample_1 stop_ _Sample_conditions_label $sample_conditions _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name e1 _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 THR HB H 4.185 0.000 1 2 1 1 THR HG2 H 1.316 0.000 1 3 2 2 GLY H H 8.221 0.000 1 4 2 2 GLY HA2 H 3.885 0.000 2 5 2 2 GLY HA3 H 3.980 0.000 2 6 3 3 HIS H H 7.889 0.000 1 7 3 3 HIS HA H 4.671 0.000 1 8 3 3 HIS HB2 H 3.092 0.000 2 9 3 3 HIS HB3 H 3.274 0.000 2 10 4 4 ARG H H 7.955 0.000 1 11 4 4 ARG HA H 4.295 0.000 1 12 4 4 ARG HB2 H 1.763 0.000 2 13 4 4 ARG HB3 H 1.854 0.000 2 14 4 4 ARG HD2 H 3.113 0.000 1 15 4 4 ARG HD3 H 3.113 0.000 1 16 4 4 ARG HE H 6.904 0.000 1 17 4 4 ARG HG2 H 1.642 0.000 1 18 4 4 ARG HG3 H 1.642 0.000 1 19 5 5 MET H H 7.900 0.000 1 20 5 5 MET HA H 4.432 0.000 1 21 5 5 MET HB2 H 2.479 0.000 1 22 5 5 MET HB3 H 2.479 0.000 1 23 5 5 MET HG2 H 1.630 0.000 1 24 5 5 MET HG3 H 1.630 0.000 1 25 6 6 ALA H H 7.534 0.000 1 26 6 6 ALA HA H 4.131 0.000 1 27 6 6 ALA HB H 1.377 0.000 1 28 7 7 TRP H H 7.157 0.000 1 29 7 7 TRP HA H 4.526 0.000 1 30 7 7 TRP HB2 H 3.310 0.000 1 31 7 7 TRP HB3 H 3.310 0.000 1 32 7 7 TRP HD1 H 7.111 0.000 1 33 7 7 TRP HE1 H 9.147 0.000 1 34 7 7 TRP HE3 H 7.558 0.000 1 35 7 7 TRP HH2 H 7.205 0.000 1 36 7 7 TRP HZ2 H 7.411 0.000 1 37 7 7 TRP HZ3 H 7.131 0.000 1 38 8 8 ASP H H 7.651 0.000 1 39 8 8 ASP HA H 4.514 0.000 1 40 8 8 ASP HB2 H 2.709 0.000 2 41 8 8 ASP HB3 H 2.791 0.000 2 42 9 9 MET H H 7.768 0.000 1 43 9 9 MET HA H 4.350 0.000 1 44 9 9 MET HB2 H 2.381 0.000 1 45 9 9 MET HB3 H 2.381 0.000 1 46 9 9 MET HG2 H 1.943 0.000 1 47 9 9 MET HG3 H 1.943 0.000 1 48 10 10 MET H H 7.728 0.000 1 49 10 10 MET HA H 4.268 0.000 1 50 10 10 MET HB2 H 2.571 0.000 1 51 10 10 MET HB3 H 2.571 0.000 1 52 10 10 MET HG2 H 2.107 0.000 1 53 10 10 MET HG3 H 2.107 0.000 1 54 11 11 MET H H 7.856 0.000 1 55 11 11 MET HA H 4.295 0.000 1 56 11 11 MET HB2 H 2.080 0.000 1 57 11 11 MET HB3 H 2.080 0.000 1 58 11 11 MET HG2 H 2.490 0.000 2 59 11 11 MET HG3 H 2.600 0.000 2 60 12 12 ASN H H 7.757 0.000 1 61 12 12 ASN HA H 4.695 0.000 1 62 12 12 ASN HB2 H 2.736 0.000 1 63 12 12 ASN HB3 H 2.736 0.000 1 64 12 12 ASN HD21 H 6.962 0.000 1 65 12 12 ASN HD22 H 6.231 0.000 1 66 13 13 TRP H H 7.729 0.000 1 67 13 13 TRP HA H 4.514 0.000 1 68 13 13 TRP HB2 H 3.283 0.000 1 69 13 13 TRP HB3 H 3.283 0.000 1 70 13 13 TRP HD1 H 7.166 0.000 1 71 13 13 TRP HE1 H 8.988 0.000 1 72 13 13 TRP HE3 H 7.513 0.000 1 73 13 13 TRP HH2 H 7.156 0.000 1 74 13 13 TRP HZ2 H 7.371 0.000 1 75 13 13 TRP HZ3 H 7.079 0.000 1 76 14 14 SER H H 6.898 0.000 1 77 14 14 SER HA H 4.541 0.000 1 78 14 14 SER HB2 H 3.748 0.000 2 79 14 14 SER HB3 H 3.912 0.000 2 80 15 15 PRO HA H 4.218 0.000 1 81 15 15 PRO HB2 H 2.331 0.000 1 82 15 15 PRO HB3 H 2.331 0.000 1 83 15 15 PRO HD2 H 3.551 0.000 2 84 15 15 PRO HD3 H 3.659 0.000 2 85 15 15 PRO HG2 H 1.975 0.000 2 86 15 15 PRO HG3 H 2.065 0.000 2 87 16 16 THR H H 7.284 0.000 1 88 16 16 THR HA H 4.022 0.000 1 89 16 16 THR HB H 4.212 0.000 1 90 16 16 THR HG2 H 1.205 0.000 1 91 17 17 ALA H H 7.510 0.000 1 92 17 17 ALA HA H 4.008 0.000 1 93 17 17 ALA HB H 1.370 0.000 1 94 18 18 ALA H H 7.415 0.000 1 95 18 18 ALA HA H 4.027 0.000 1 96 18 18 ALA HB H 1.478 0.000 1 97 19 19 LEU H H 7.432 0.000 1 98 19 19 LEU HA H 4.159 0.000 1 99 19 19 LEU HB2 H 1.889 0.000 1 100 19 19 LEU HB3 H 1.889 0.000 1 101 19 19 LEU HD1 H 0.911 0.000 2 102 19 19 LEU HD2 H 0.851 0.000 2 103 19 19 LEU HG H 1.588 0.000 1 104 20 20 VAL H H 7.599 0.000 1 105 20 20 VAL HA H 3.666 0.000 1 106 20 20 VAL HB H 2.217 0.000 1 107 20 20 VAL HG1 H 0.931 0.000 2 108 20 20 VAL HG2 H 0.986 0.000 2 109 21 21 VAL H H 8.112 0.000 1 110 21 21 VAL HA H 3.557 0.000 1 111 21 21 VAL HB H 2.080 0.000 1 112 21 21 VAL HG1 H 0.951 0.000 2 113 21 21 VAL HG2 H 1.051 0.000 2 114 22 22 ALA H H 7.830 0.000 1 115 22 22 ALA HA H 4.013 0.000 1 116 22 22 ALA HB H 1.520 0.000 1 117 23 23 GLN H H 7.585 0.000 1 118 23 23 GLN HA H 4.131 0.000 1 119 23 23 GLN HB2 H 2.326 0.000 1 120 23 23 GLN HB3 H 2.326 0.000 1 121 23 23 GLN HE21 H 7.022 0.000 1 122 23 23 GLN HE22 H 6.056 0.000 1 123 23 23 GLN HG2 H 2.408 0.000 2 124 23 23 GLN HG3 H 2.600 0.000 2 125 24 24 LEU H H 8.312 0.000 1 126 24 24 LEU HA H 4.159 0.000 1 127 24 24 LEU HB2 H 1.533 0.000 2 128 24 24 LEU HB3 H 1.946 0.000 2 129 24 24 LEU HD1 H 0.839 0.000 1 130 24 24 LEU HD2 H 0.839 0.000 1 131 24 24 LEU HG H 1.856 0.000 1 132 25 25 LEU H H 8.178 0.000 1 133 25 25 LEU HA H 4.213 0.000 1 134 25 25 LEU HB2 H 1.779 0.000 1 135 25 25 LEU HB3 H 1.779 0.000 1 136 25 25 LEU HD1 H 0.839 0.000 1 137 25 25 LEU HD2 H 0.839 0.000 1 138 25 25 LEU HG H 1.560 0.000 1 139 26 26 ARG H H 7.453 0.000 1 140 26 26 ARG HA H 4.159 0.000 1 141 26 26 ARG HB2 H 1.946 0.000 1 142 26 26 ARG HB3 H 1.946 0.000 1 143 26 26 ARG HD2 H 3.201 0.000 1 144 26 26 ARG HD3 H 3.201 0.000 1 145 26 26 ARG HE H 6.884 0.000 1 146 26 26 ARG HG2 H 1.672 0.000 2 147 26 26 ARG HG3 H 1.756 0.000 2 148 27 27 ILE H H 7.527 0.000 1 149 27 27 ILE HA H 4.350 0.000 1 150 27 27 ILE HB H 1.916 0.000 1 151 27 27 ILE HD1 H 0.885 0.000 1 152 27 27 ILE HG12 H 1.175 0.000 1 153 27 27 ILE HG13 H 1.175 0.000 1 154 27 27 ILE HG2 H 0.977 0.000 1 155 28 28 PRO HA H 4.388 0.000 1 156 28 28 PRO HB2 H 2.194 0.000 1 157 28 28 PRO HB3 H 2.194 0.000 1 158 28 28 PRO HD2 H 3.640 0.000 2 159 28 28 PRO HD3 H 3.949 0.000 2 160 28 28 PRO HG2 H 1.975 0.000 2 161 28 28 PRO HG3 H 2.056 0.000 2 162 29 29 GLN H H 7.486 0.000 1 163 29 29 GLN HA H 4.405 0.000 1 164 29 29 GLN HB2 H 1.956 0.000 2 165 29 29 GLN HB3 H 2.217 0.000 2 166 29 29 GLN HE21 H 7.094 0.000 1 167 29 29 GLN HE22 H 6.071 0.000 1 168 29 29 GLN HG2 H 2.381 0.000 1 169 29 29 GLN HG3 H 2.381 0.000 1 stop_ save_