1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 0000-0003-3532-4390 Medeiros-Silva, J. 0000-0003-3422-4734 Dregni, A.J. 0000-0002-5222-0334 Somberg, N.H. 0000-0001-5255-5858 Hong, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N C N 65 N O N 66 N O N 67 N O N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N N N 78 N C N 79 N C N 80 N O N 81 N O N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N N N 88 S C N 89 N C N 90 N O N 91 S C N 92 N C N 93 N C N 94 N C N 95 N O N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N N N 110 S C N 111 N C N 112 N O N 113 N C N 114 N C N 115 N C N 116 N C N 117 N O N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N N N 132 S C N 133 N C N 134 N O N 135 N C Y 136 N C Y 137 N C Y 138 N C Y 139 N C Y 140 N C Y 141 N C N 142 N O N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N N N 155 S C N 156 N C N 157 N O N 158 N C N 159 N O N 160 N O N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N N N 169 S C N 170 N C N 171 N O N 172 R C N 173 N O N 174 N C N 175 N O N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N N N 186 S C N 187 N C N 188 N O N 189 N C N 190 N C N 191 N C N 192 N O N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N doub N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N doub N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N doub N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N doub N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N doub N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N doub N 131 N sing N 132 N sing N 133 N sing N 134 N sing Y 135 N doub Y 136 N sing Y 137 N sing N 138 N sing Y 139 N doub N 140 N sing Y 141 N doub N 142 N sing Y 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N doub N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N doub N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N doub N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing US Sci Adv 2375-2548 9 eadi9007 eadi9007 10.1126/sciadv.adi9007 37831764 Atomic structure of the open SARS-CoV-2 E viroporin. 2023 0000-0003-3532-4390 0000-0003-3422-4734 0000-0002-5222-0334 0000-0002-7395-4353 0000-0001-5255-5858 10.2210/pdb8suz/pdb pdb_00008suz 10.13018/BMR31085 3362.115 Envelope small membrane protein 5 man polymer sM protein no no ETGTLIVNSVLLFLAFVVFLLVTLAILTALR ETGTLIVNSVLLFLAFVVFLLVTLAILTALR A,B,C,D,E polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n sample 1 31 E, 4 2697049 Severe acute respiratory syndrome coronavirus 2 Wuhan-Hu-1 469008 Escherichia coli BL21(DE3) Biological sequence Champion pET-SUMO database_2 repository Initial release Database references 1 0 2023-10-25 1 1 2024-05-15 _database_2.pdbx_DOI United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) GM088204 Netherlands Netherlands Organisation for Scientific Research (NWO) 452020132 meihong@mit.edu 0000-0001-5255-5858 Mei Hong principal investigator/group leader Open State of the SARS-CoV-2 Envelope Protein Transmembrane Domain, Determined by Solid-State NMR N RCSB Y RCSB 2023-05-14 REL REL REL REL structures with the lowest energy 3000 10 isotropic 2 2D 15N-13C isotropic 2 2D 13C-detected CORD isotropic 2 2D 1H-15N CP HETCOR isotropic 1 2D 15N-13C PSD isotropic 2 3D HNCA isotropic 3 3D HN(CO)CA isotropic 3 1D 19F 13C-detected REDOR isotropic 3 2D 19F 1H-15N 1H-detected CP HETCOR isotropic 2 3D NCa-filtered 13C-detected DIPSHIFT 15.5 % w/w [U-99% 13C; U-99% 15N] 23 % w/w natural abundance 3.5 % w/w natural abundance 10 % w/w natural abundance 8 % w/w natural abundance 4 % w/w natural abundance 36 % w/w natural abundance 30 mM natural abundance 30 mM natural abundance 10 mM natural abundance 7.5 % w/w [U-99% 15N; U-80% 2H] 8 % w/w [U-100% 13C] 23 % w/w natural abundance 3.5 % w/w natural abundance 10 % w/w natural abundance 8 % w/w natural abundance 4 % w/w natural abundance 36 % w/w natural abundance 30 mM natural abundance 30 mM natural abundance 10 mM natural abundance 7.5 % w/w [U-100% 13C; U-100% 15N; U-80% 2H] 8 % w/w natural abundance 23 % w/w natural abundance 11 % w/w natural abundance 10 % w/w natural abundance 4.5 % w/w natural abundance 36 % w/w natural abundance 30 mM natural abundance 30 mM natural abundance 10 mM natural abundance 4.5 % w/w [U-99% 13C; U-99% 15N] 4 % w/w natural abundance 36.5 % w/w natural abundance 16 % w/w natural abundance 39 % w/w natural abundance 30 mM natural abundance 30 mM natural abundance 10 mM natural abundance 8.5 % w/w [U-99% 13C; U-99% 15N] 35 % w/w natural abundance 15.5 % w/w natural abundance 59 % w/w natural abundance 30 mM natural abundance 30 mM natural abundance 10 mM natural abundance Sample Under Magic Angle Spinning 1 M 1 4.5 pH 1 atm 283 2 K Sample Under Magic Angle Spinning 1 M 2 4.5 pH 1 atm 273 2 K Sample Under Magic Angle Spinning 1 M 5 4.5 pH 1 atm 331 2 K simulated annealing 1 medoid 15.5 % w/w [U-99% 13C; U-99% 15N] ETM, 23 % w/w POPC, 3.5 % w/w POPS, 10 % w/w POPE, 8 % w/w PI, 4 % w/w Cholesterol, 36 % w/w Water, 30 mM sodium acetate, 30 mM calcium chloride, 10 mM sodium chloride, 95% H2O/5% D2O ETM reconstituted in liposomes based on the lipid composition of the ER-Golgi Intermediate Compartment, reconstituted in acidic pH and calcium [13C/15N] ETM ERGIC 95% H2O/5% D2O liposome 7.5 % w/w [U-99% 15N; U-80% 2H] ETM, 8 % w/w [U-100% 13C] ETM, 23 % w/w POPC, 3.5 % w/w POPS, 10 % w/w POPE, 8 % w/w PI, 4 % w/w Cholesterol, 36 % w/w Water, 30 mM sodium acetate, 30 mM calcium chloride, 10 mM sodium chloride, 95% H2O/5% D2O ETM reconstituted in liposomes based on the lipid composition of the ER-Golgi Intermediate Compartment, reconstituted in acidic pH and calcium [13C]+[15N] Mix ETM ERGIC 95% H2O/5% D2O liposome 7.5 % w/w [U-100% 13C; U-100% 15N; U-80% 2H] ETM, 8 % w/w 4-19F-Phe20-ETM, 23 % w/w POPC, 11 % w/w POPS, 10 % w/w POPE, 4.5 % w/w Cholesterol, 36 % w/w Water, 30 mM sodium acetate, 30 mM calcium chloride, 10 mM sodium chloride, 95% H2O/5% D2O ETM reconstituted in liposomes based on the lipid composition of the ER-Golgi Intermediate Compartment, reconstituted in acidic pH and calcium. PI lipids were excluded [13C]+[19F-Phe20] Mix ETM ERGIC 95% H2O/5% D2O liposome 4.5 % w/w [U-99% 13C; U-99% 15N] ETM, 4 % w/w 4-19F-Phe20-ETM, 36.5 % w/w DMPC, 16 % w/w DMPG, 39 % w/w Water, 30 mM sodium acetate, 30 mM calcium chloride, 10 mM sodium chloride, 95% H2O/5% D2O ETM reconstituted in DMPC/DMPG liposomes, reconstituted in acidic pH and calcium [13C/5N/(2H/1H)]+[19F-Phe20] Mix ETM DMPX 95% H2O/5% D2O liposome 8.5 % w/w [U-99% 13C; U-99% 15N] ETM, 35 % w/w POPC, 15.5 % w/w POPG, 59 % w/w Water, 30 mM sodium acetate, 30 mM calcium chloride, 10 mM sodium chloride, 95% H2O/5% D2O ETM reconstituted in liposomes POPC/POPG, reconstituted in acidic pH and calcium [13C/15N] ETM POPX 95% H2O/5% D2O liposome Bruker Biospin collection TopSpin Bruker Biospin data analysis TopSpin CCPN chemical shift assignment CcpNmr Analysis Schwieters, Kuszewski, Tjandra and Clore refinement X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore structure calculation X-PLOR NIH 900 Bruker AVANCE II 800 Bruker AVANCE III 600 Bruker AVANCE NEO GLU 8 n 1 GLU 8 A THR 9 n 2 THR 9 A GLY 10 n 3 GLY 10 A THR 11 n 4 THR 11 A LEU 12 n 5 LEU 12 A ILE 13 n 6 ILE 13 A VAL 14 n 7 VAL 14 A ASN 15 n 8 ASN 15 A SER 16 n 9 SER 16 A VAL 17 n 10 VAL 17 A LEU 18 n 11 LEU 18 A LEU 19 n 12 LEU 19 A PHE 20 n 13 PHE 20 A LEU 21 n 14 LEU 21 A ALA 22 n 15 ALA 22 A PHE 23 n 16 PHE 23 A VAL 24 n 17 VAL 24 A VAL 25 n 18 VAL 25 A PHE 26 n 19 PHE 26 A LEU 27 n 20 LEU 27 A LEU 28 n 21 LEU 28 A VAL 29 n 22 VAL 29 A THR 30 n 23 THR 30 A LEU 31 n 24 LEU 31 A ALA 32 n 25 ALA 32 A ILE 33 n 26 ILE 33 A LEU 34 n 27 LEU 34 A THR 35 n 28 THR 35 A ALA 36 n 29 ALA 36 A LEU 37 n 30 LEU 37 A ARG 38 n 31 ARG 38 A GLU 8 n 1 GLU 8 B THR 9 n 2 THR 9 B GLY 10 n 3 GLY 10 B THR 11 n 4 THR 11 B LEU 12 n 5 LEU 12 B ILE 13 n 6 ILE 13 B VAL 14 n 7 VAL 14 B ASN 15 n 8 ASN 15 B SER 16 n 9 SER 16 B VAL 17 n 10 VAL 17 B LEU 18 n 11 LEU 18 B LEU 19 n 12 LEU 19 B PHE 20 n 13 PHE 20 B LEU 21 n 14 LEU 21 B ALA 22 n 15 ALA 22 B PHE 23 n 16 PHE 23 B VAL 24 n 17 VAL 24 B VAL 25 n 18 VAL 25 B PHE 26 n 19 PHE 26 B LEU 27 n 20 LEU 27 B LEU 28 n 21 LEU 28 B VAL 29 n 22 VAL 29 B THR 30 n 23 THR 30 B LEU 31 n 24 LEU 31 B ALA 32 n 25 ALA 32 B ILE 33 n 26 ILE 33 B LEU 34 n 27 LEU 34 B THR 35 n 28 THR 35 B ALA 36 n 29 ALA 36 B LEU 37 n 30 LEU 37 B ARG 38 n 31 ARG 38 B GLU 8 n 1 GLU 8 C THR 9 n 2 THR 9 C GLY 10 n 3 GLY 10 C THR 11 n 4 THR 11 C LEU 12 n 5 LEU 12 C ILE 13 n 6 ILE 13 C VAL 14 n 7 VAL 14 C ASN 15 n 8 ASN 15 C SER 16 n 9 SER 16 C VAL 17 n 10 VAL 17 C LEU 18 n 11 LEU 18 C LEU 19 n 12 LEU 19 C PHE 20 n 13 PHE 20 C LEU 21 n 14 LEU 21 C ALA 22 n 15 ALA 22 C PHE 23 n 16 PHE 23 C VAL 24 n 17 VAL 24 C VAL 25 n 18 VAL 25 C PHE 26 n 19 PHE 26 C LEU 27 n 20 LEU 27 C LEU 28 n 21 LEU 28 C VAL 29 n 22 VAL 29 C THR 30 n 23 THR 30 C LEU 31 n 24 LEU 31 C ALA 32 n 25 ALA 32 C ILE 33 n 26 ILE 33 C LEU 34 n 27 LEU 34 C THR 35 n 28 THR 35 C ALA 36 n 29 ALA 36 C LEU 37 n 30 LEU 37 C ARG 38 n 31 ARG 38 C GLU 8 n 1 GLU 8 D THR 9 n 2 THR 9 D GLY 10 n 3 GLY 10 D THR 11 n 4 THR 11 D LEU 12 n 5 LEU 12 D ILE 13 n 6 ILE 13 D VAL 14 n 7 VAL 14 D ASN 15 n 8 ASN 15 D SER 16 n 9 SER 16 D VAL 17 n 10 VAL 17 D LEU 18 n 11 LEU 18 D LEU 19 n 12 LEU 19 D PHE 20 n 13 PHE 20 D LEU 21 n 14 LEU 21 D ALA 22 n 15 ALA 22 D PHE 23 n 16 PHE 23 D VAL 24 n 17 VAL 24 D VAL 25 n 18 VAL 25 D PHE 26 n 19 PHE 26 D LEU 27 n 20 LEU 27 D LEU 28 n 21 LEU 28 D VAL 29 n 22 VAL 29 D THR 30 n 23 THR 30 D LEU 31 n 24 LEU 31 D ALA 32 n 25 ALA 32 D ILE 33 n 26 ILE 33 D LEU 34 n 27 LEU 34 D THR 35 n 28 THR 35 D ALA 36 n 29 ALA 36 D LEU 37 n 30 LEU 37 D ARG 38 n 31 ARG 38 D GLU 8 n 1 GLU 8 E THR 9 n 2 THR 9 E GLY 10 n 3 GLY 10 E THR 11 n 4 THR 11 E LEU 12 n 5 LEU 12 E ILE 13 n 6 ILE 13 E VAL 14 n 7 VAL 14 E ASN 15 n 8 ASN 15 E SER 16 n 9 SER 16 E VAL 17 n 10 VAL 17 E LEU 18 n 11 LEU 18 E LEU 19 n 12 LEU 19 E PHE 20 n 13 PHE 20 E LEU 21 n 14 LEU 21 E ALA 22 n 15 ALA 22 E PHE 23 n 16 PHE 23 E VAL 24 n 17 VAL 24 E VAL 25 n 18 VAL 25 E PHE 26 n 19 PHE 26 E LEU 27 n 20 LEU 27 E LEU 28 n 21 LEU 28 E VAL 29 n 22 VAL 29 E THR 30 n 23 THR 30 E LEU 31 n 24 LEU 31 E ALA 32 n 25 ALA 32 E ILE 33 n 26 ILE 33 E LEU 34 n 27 LEU 34 E THR 35 n 28 THR 35 E ALA 36 n 29 ALA 36 E LEU 37 n 30 LEU 37 E ARG 38 n 31 ARG 38 E author_defined_assembly 5 pentameric native gel electrophoresis NMR Distance Restraints 3920 -41 11950 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 identity operation 0.0000000000 0.0000000000 0.0000000000 1 A LEU 37 -21.61 86.61 1 B LEU 37 -24.86 85.81 1 C LEU 37 -27.85 85.23 1 D LEU 37 -33.39 90.70 1 E LEU 37 -48.24 102.55 2 A LEU 37 -48.27 102.50 2 B LEU 37 -21.98 86.85 2 C LEU 37 -23.94 85.16 2 D LEU 37 -25.83 83.56 2 E LEU 37 -31.72 88.62 3 A LEU 37 -18.89 86.02 3 B LEU 37 -22.78 85.02 3 C LEU 37 -26.52 84.21 3 D LEU 37 -32.57 89.80 3 E LEU 37 -48.57 104.46 4 A LEU 37 -42.00 86.94 4 B LEU 37 -42.81 84.23 4 C LEU 37 -45.07 81.16 4 D LEU 37 -53.66 65.40 4 E LEU 37 -50.64 96.63 5 A LEU 37 -31.43 89.21 5 B LEU 37 -32.56 86.16 5 C LEU 37 -35.10 83.09 5 D LEU 37 -44.37 70.56 5 E ALA 36 -56.70 -9.67 5 E LEU 37 -49.13 102.85 6 A LEU 37 -13.81 87.86 6 B LEU 37 -16.77 84.07 6 C LEU 37 -23.53 88.14 6 D LEU 37 -27.86 91.02 6 E LEU 37 -47.47 104.14 7 A LEU 37 -19.78 90.31 7 B LEU 37 -22.11 86.50 7 C LEU 37 -27.40 89.54 7 D LEU 37 -31.18 92.47 7 E LEU 37 -47.66 106.95 8 A LEU 37 -10.17 88.15 8 B LEU 37 -12.94 83.05 8 C LEU 37 -19.29 88.09 8 D LEU 37 23.92 -85.45 8 E LEU 37 -46.99 106.00 9 A LEU 37 -36.81 89.27 9 B LEU 37 -38.57 85.34 9 C LEU 37 -43.34 79.77 9 D LEU 37 -54.36 60.60 9 E LEU 37 -51.00 102.83 10 A LEU 37 -49.25 85.81 10 B LEU 37 -51.93 81.62 10 C LEU 37 -54.79 72.18 10 D LEU 37 -29.66 -32.11 10 E LEU 37 -52.58 97.38 N Open State of the SARS-CoV-2 Envelope Protein Transmembrane Domain, Determined by Solid-State NMR 1 N N 1 N N 1 N N 1 N N 1 N N A GLU 8 A GLU 1 HELX_P A ALA 36 A ALA 29 1 AA1 29 B THR 9 B THR 2 HELX_P B ALA 36 B ALA 29 1 AA2 28 C THR 9 C THR 2 HELX_P C ALA 36 C ALA 29 1 AA3 28 D THR 9 D THR 2 HELX_P D ALA 36 D ALA 29 1 AA4 28 E THR 9 E THR 2 HELX_P E ALA 36 E ALA 29 1 AA5 28 VIRAL PROTEIN Viroporin, SARS-CoV-2, Cation Channel, VIRAL PROTEIN VEMP_SARS2 UNP 1 8 P0DTC4 ETGTLIVNSVLLFLAFVVFLLVTLAILTALR 8 38 8SUZ 8 38 P0DTC4 A 1 1 31 8 38 8SUZ 8 38 P0DTC4 B 1 1 31 8 38 8SUZ 8 38 P0DTC4 C 1 1 31 8 38 8SUZ 8 38 P0DTC4 D 1 1 31 8 38 8SUZ 8 38 P0DTC4 E 1 1 31