data_30795 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; SARS-CoV-2 Envelope Protein Transmembrane Domain: Pentameric Structure Determined by Solid-State NMR ; _BMRB_accession_number 30795 _BMRB_flat_file_name bmr30795.str _Entry_type original _Submission_date 2020-09-11 _Accession_date 2020-09-11 _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 Mandala V. S. . 2 Hong M. . . 3 McKay M. J. . 4 Shcherbakov A. S. . 5 Dregni A. J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 133 "15N chemical shifts" 28 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-12-18 update BMRB 'update entry citation' 2020-09-28 original author 'original release' stop_ _Original_release_date 2020-09-22 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure and drug binding of the SARS-CoV-2 envelope protein transmembrane domain in lipid bilayers ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 33177698 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Mandala Venkata S. . 2 McKay Matthew J. . 3 Shcherbakov Alexander A. . 4 Dregni Aurelio J. . 5 Kolocouris Antonios . . 6 Hong Mei . . stop_ _Journal_abbreviation 'Nat. Struct. Mol. Biol.' _Journal_name_full 'Nature structural & molecular biology' _Journal_volume 27 _Journal_issue 12 _Journal_ISSN 1545-9985 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1202 _Page_last 1208 _Year 2020 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Envelope small membrane protein' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label unit_1 $entity_1 unit_2 $entity_1 unit_3 $entity_1 unit_4 $entity_1 unit_5 $entity_1 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 entity_1 _Molecular_mass 3362.115 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 31 _Mol_residue_sequence ; ETGTLIVNSVLLFLAFVVFL LVTLAILTALR ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 8 GLU 2 9 THR 3 10 GLY 4 11 THR 5 12 LEU 6 13 ILE 7 14 VAL 8 15 ASN 9 16 SER 10 17 VAL 11 18 LEU 12 19 LEU 13 20 PHE 14 21 LEU 15 22 ALA 16 23 PHE 17 24 VAL 18 25 VAL 19 26 PHE 20 27 LEU 21 28 LEU 22 29 VAL 23 30 THR 24 31 LEU 25 32 ALA 26 33 ILE 27 34 LEU 28 35 THR 29 36 ALA 30 37 LEU 31 38 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_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 2019-nCoV 2697049 Viruses . Betacoronavirus HCoV-SARS 2019-nCoV 'E, 4' 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_1 'recombinant technology' . . . BL21(DE3) . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type membrane _Details ; 0.1 mg/uL [U-13C; U-15N] SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.23 mg/uL POPC, 0.1 mg/uL POPE, 0.08 mg/uL bovine PI, 0.04 mg/uL POPS, 0.04 mg/uL Cholesterol, aqueous buffer. ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.1 mg/uL '[U-13C; U-15N]' POPC 0.23 mg/uL 'natural abundance' POPE 0.1 mg/uL 'natural abundance' 'bovine PI' 0.08 mg/uL 'natural abundance' POPS 0.04 mg/uL 'natural abundance' Cholesterol 0.04 mg/uL 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type membrane _Details ; 0.1 mg/uL [U-13C; U-15N] SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.1 mg/uL [4-19F-Phe] fluoro SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.23 mg/uL POPC, 0.1 mg/uL POPE, 0.08 mg/uL bovine PI, 0.04 mg/uL POPS, 0.04 mg/uL Cholesterol, aqueous buffer. ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.1 mg/uL '[U-13C; U-15N]' POPC 0.23 mg/uL 'natural abundance' POPE 0.1 mg/uL 'natural abundance' 'bovine PI' 0.08 mg/uL 'natural abundance' POPS 0.04 mg/uL 'natural abundance' Cholesterol 0.04 mg/uL 'natural abundance' $entity_1 0.1 mg/uL [4-19F-Phe] stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type membrane _Details ; 0.1 mg/uL [U-15N] 15N SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.1 mg/uL [U-13C] 13C SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.23 mg/uL POPC, 0.1 mg/uL POPE, 0.08 mg/uL bovine PI, 0.04 mg/uL POPS, 0.04 mg/uL Cholesterol, aqueous buffer. ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling POPC 0.23 mg/uL 'natural abundance' POPE 0.1 mg/uL 'natural abundance' 'bovine PI' 0.08 mg/uL 'natural abundance' POPS 0.04 mg/uL 'natural abundance' Cholesterol 0.04 mg/uL 'natural abundance' $entity_1 0.1 mg/uL [U-15N] $entity_1 0.1 mg/uL [U-13C] stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name NMRFAM-SPARKY _Version . loop_ _Vendor _Address _Electronic_address NMRFAM . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name TopSpin _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_3 _Saveframe_category software _Name 'X-PLOR NIH' _Version 2.47 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'AVANCE NEO' _Field_strength 900 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'AVANCE II' _Field_strength 800 _Details . save_ save_NMR_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'AVANCE III HD' _Field_strength 60 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_CC_CORD_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D CC CORD' _Sample_label $sample_1 save_ save_2D_NCA/NCO_SPEC-CP_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NCA/NCO SPEC-CP' _Sample_label $sample_1 save_ save_3D_NCACX/NCOCX/CONCA_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D NCACX/NCOCX/CONCA' _Sample_label $sample_1 save_ save_1D/2D_13C-19F_REDOR_4 _Saveframe_category NMR_applied_experiment _Experiment_name '1D/2D 13C-19F REDOR' _Sample_label $sample_2 save_ save_2D_13C-19F_SPEC-CP_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-19F SPEC-CP' _Sample_label $sample_2 save_ save_2D_NHHC_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NHHC' _Sample_label $sample_3 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' 20 . mM pH 7.5 0.2 pH pressure 1 . atm temperature 293 . 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 DSS C 13 'methyl carbons' ppm 0 external direct . . . 1.0 'liquid anhydrous ammonia' N 15 nitrogen ppm 0 external 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D CC CORD' '2D NCA/NCO SPEC-CP' '3D NCACX/NCOCX/CONCA' '1D/2D 13C-19F REDOR' '2D 13C-19F SPEC-CP' '2D NHHC' stop_ loop_ _Sample_label $sample_1 $sample_2 $sample_3 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name unit_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 9 2 THR CA C 63.56 0.000 . 2 9 2 THR CB C 69.18 0.000 . 3 10 3 GLY C C 174.71 0.000 . 4 10 3 GLY CA C 46.78 0.042 . 5 10 3 GLY N N 110.69 0.000 . 6 11 4 THR C C 175.42 0.000 . 7 11 4 THR CA C 64.47 0.179 . 8 11 4 THR CB C 68.42 0.016 . 9 11 4 THR CG2 C 22.41 0.000 . 10 13 6 ILE C C 177.16 0.093 . 11 13 6 ILE CA C 64.17 0.112 . 12 13 6 ILE CB C 37.41 0.045 . 13 13 6 ILE CG1 C 29.05 0.014 . 14 13 6 ILE CG2 C 17.89 0.000 . 15 13 6 ILE CD1 C 12.93 0.001 . 16 13 6 ILE N N 119.92 0.000 . 17 14 7 VAL C C 176.74 0.116 . 18 14 7 VAL CA C 66.86 0.094 . 19 14 7 VAL CB C 31.26 0.083 . 20 14 7 VAL CG1 C 23.31 0.068 . 21 14 7 VAL CG2 C 20.84 0.098 . 22 14 7 VAL N N 119.51 0.204 . 23 15 8 ASN C C 177.40 0.032 . 24 15 8 ASN CA C 56.00 0.092 . 25 15 8 ASN CB C 37.43 0.007 . 26 15 8 ASN CG C 174.22 0.035 . 27 15 8 ASN N N 117.07 0.159 . 28 15 8 ASN ND2 N 107.66 0.000 . 29 16 9 SER C C 175.25 0.115 . 30 16 9 SER CA C 62.86 0.154 . 31 16 9 SER CB C 63.00 0.045 . 32 16 9 SER N N 116.35 0.101 . 33 17 10 VAL C C 177.42 0.128 . 34 17 10 VAL CA C 66.66 0.102 . 35 17 10 VAL CB C 31.22 0.034 . 36 17 10 VAL CG1 C 23.37 0.033 . 37 17 10 VAL CG2 C 21.38 0.017 . 38 17 10 VAL N N 121.06 0.123 . 39 18 11 LEU C C 178.68 0.047 . 40 18 11 LEU CA C 57.59 0.114 . 41 18 11 LEU CB C 40.98 0.095 . 42 18 11 LEU CG C 26.80 0.000 . 43 18 11 LEU CD1 C 25.43 0.000 . 44 18 11 LEU CD2 C 20.27 0.079 . 45 18 11 LEU N N 118.65 0.158 . 46 19 12 LEU C C 178.03 0.008 . 47 19 12 LEU CA C 58.13 0.071 . 48 19 12 LEU CB C 41.89 0.020 . 49 19 12 LEU CG C 26.86 0.000 . 50 19 12 LEU N N 120.47 0.098 . 51 20 13 PHE C C 176.50 0.071 . 52 20 13 PHE CA C 61.47 0.067 . 53 20 13 PHE CB C 39.40 0.019 . 54 20 13 PHE CG C 138.40 0.000 . 55 20 13 PHE N N 118.84 0.127 . 56 21 14 LEU C C 178.57 0.036 . 57 21 14 LEU CA C 57.46 0.053 . 58 21 14 LEU CB C 42.76 0.027 . 59 21 14 LEU CG C 26.88 0.000 . 60 21 14 LEU CD1 C 25.62 0.000 . 61 21 14 LEU CD2 C 22.22 0.049 . 62 21 14 LEU N N 118.77 0.216 . 63 22 15 ALA C C 178.50 0.141 . 64 22 15 ALA CA C 55.92 0.059 . 65 22 15 ALA CB C 18.57 0.022 . 66 22 15 ALA N N 123.47 0.112 . 67 23 16 PHE C C 176.30 0.180 . 68 23 16 PHE CA C 61.43 0.076 . 69 23 16 PHE CB C 39.35 0.024 . 70 23 16 PHE CG C 139.24 0.133 . 71 23 16 PHE N N 118.92 0.139 . 72 24 17 VAL C C 177.69 0.051 . 73 24 17 VAL CA C 67.38 0.086 . 74 24 17 VAL CB C 31.68 0.059 . 75 24 17 VAL CG1 C 22.96 0.112 . 76 24 17 VAL CG2 C 20.79 0.047 . 77 24 17 VAL N N 118.31 0.186 . 78 25 18 VAL C C 176.81 0.080 . 79 25 18 VAL CA C 67.63 0.048 . 80 25 18 VAL CB C 31.11 0.087 . 81 25 18 VAL CG1 C 23.10 0.031 . 82 25 18 VAL CG2 C 21.57 0.024 . 83 25 18 VAL N N 118.92 0.117 . 84 26 19 PHE C C 177.69 0.102 . 85 26 19 PHE CA C 62.24 0.089 . 86 26 19 PHE CB C 39.05 0.054 . 87 26 19 PHE CG C 139.04 0.000 . 88 26 19 PHE N N 119.68 0.063 . 89 27 20 LEU C C 177.88 0.106 . 90 27 20 LEU CA C 57.62 0.059 . 91 27 20 LEU CB C 41.79 0.009 . 92 27 20 LEU CG C 27.54 0.000 . 93 27 20 LEU CD1 C 25.81 0.000 . 94 27 20 LEU CD2 C 20.60 0.039 . 95 27 20 LEU N N 120.78 0.122 . 96 28 21 LEU C C 178.63 0.064 . 97 28 21 LEU CA C 57.47 0.082 . 98 28 21 LEU CB C 41.15 0.075 . 99 28 21 LEU CG C 25.48 0.000 . 100 28 21 LEU CD1 C 25.42 0.000 . 101 28 21 LEU CD2 C 20.79 0.026 . 102 28 21 LEU N N 118.36 0.148 . 103 29 22 VAL C C 176.98 0.051 . 104 29 22 VAL CA C 66.29 0.072 . 105 29 22 VAL CB C 30.70 0.027 . 106 29 22 VAL CG1 C 24.21 0.032 . 107 29 22 VAL CG2 C 21.46 0.046 . 108 29 22 VAL N N 119.37 0.180 . 109 30 23 THR C C 175.51 0.079 . 110 30 23 THR CA C 68.87 0.040 . 111 30 23 THR CB C 66.39 0.041 . 112 30 23 THR CG2 C 20.18 0.023 . 113 30 23 THR N N 119.19 0.111 . 114 31 24 LEU C C 178.06 0.091 . 115 31 24 LEU CA C 58.49 0.056 . 116 31 24 LEU CB C 41.43 0.051 . 117 31 24 LEU CG C 27.29 0.043 . 118 31 24 LEU CD1 C 27.25 0.008 . 119 31 24 LEU CD2 C 24.38 0.004 . 120 31 24 LEU N N 121.69 0.099 . 121 32 25 ALA C C 178.98 0.035 . 122 32 25 ALA CA C 55.33 0.056 . 123 32 25 ALA CB C 18.55 0.048 . 124 32 25 ALA N N 123.62 0.107 . 125 33 26 ILE C C 176.97 0.058 . 126 33 26 ILE CA C 65.67 0.064 . 127 33 26 ILE CB C 38.08 0.011 . 128 33 26 ILE CG1 C 31.00 0.000 . 129 33 26 ILE CG2 C 19.08 0.004 . 130 33 26 ILE CD1 C 14.28 0.055 . 131 33 26 ILE N N 117.29 0.097 . 132 34 27 LEU C C 178.54 0.067 . 133 34 27 LEU CA C 57.98 0.055 . 134 34 27 LEU CB C 40.79 0.044 . 135 34 27 LEU CG C 27.65 0.050 . 136 34 27 LEU CD1 C 27.60 0.033 . 137 34 27 LEU CD2 C 23.59 0.017 . 138 34 27 LEU N N 116.90 0.047 . 139 35 28 THR C C 175.60 0.065 . 140 35 28 THR CA C 62.97 0.077 . 141 35 28 THR CB C 69.50 0.089 . 142 35 28 THR CG2 C 21.89 0.052 . 143 35 28 THR N N 102.20 0.081 . 144 36 29 ALA C C 179.00 0.062 . 145 36 29 ALA CA C 53.62 0.069 . 146 36 29 ALA CB C 19.68 0.035 . 147 36 29 ALA N N 123.08 0.078 . 148 37 30 LEU C C 172.99 0.042 . 149 37 30 LEU CA C 53.29 0.062 . 150 37 30 LEU CB C 38.57 0.070 . 151 37 30 LEU CG C 26.44 0.014 . 152 37 30 LEU CD1 C 25.20 0.046 . 153 37 30 LEU CD2 C 21.94 0.016 . 154 37 30 LEU N N 119.38 0.114 . 155 38 31 ARG C C 180.93 0.000 . 156 38 31 ARG CA C 53.87 0.058 . 157 38 31 ARG CB C 29.89 0.021 . 158 38 31 ARG CG C 25.55 0.000 . 159 38 31 ARG CD C 41.70 0.009 . 160 38 31 ARG CZ C 159.43 0.023 . 161 38 31 ARG N N 124.43 0.215 . stop_ save_