1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Nishimura, K. Kim, S. Zhang, L. Cross, T.A. 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 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN 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 O 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 N N 58 N C N 59 N C N 60 N O N 61 N O N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N N N 68 S C N 69 N C N 70 N O N 71 N C Y 72 N C Y 73 N N Y 74 N C Y 75 N C Y 76 N N N 77 N O N 78 N H N 79 N H N 80 N H N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N N N 89 S C N 90 N C N 91 N O N 92 S C N 93 N C N 94 N C N 95 N C N 96 N O 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 H N 110 N N N 111 S C N 112 N C N 113 N O N 114 N C N 115 N C N 116 N C N 117 N C N 118 N O 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 H N 132 N N N 133 S C N 134 N C N 135 N O N 136 N C N 137 N C N 138 N C N 139 N O N 140 N H N 141 N H N 142 N H 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 N N 150 S C N 151 N C N 152 N O N 153 N C N 154 N O N 155 N O N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N N N 164 S C N 165 N C N 166 N O N 167 N C Y 168 N C Y 169 N C Y 170 N C Y 171 N N Y 172 N C Y 173 N C Y 174 N C Y 175 N C Y 176 N C N 177 N O 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 H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N N N 191 S C N 192 N C N 193 N O N 194 N C N 195 N C N 196 N C N 197 N O 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 204 N H N 205 N H N 206 N H N 207 N H N 208 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 doub N 61 N sing 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 Y 74 N sing Y 75 N doub Y 76 N doub N 77 N sing Y 78 N sing N 79 N sing Y 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 sing N 89 N sing N 90 N doub 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 sing N 110 N sing N 111 N doub 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 sing N 131 N sing N 132 N doub N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 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 doub N 150 N sing N 151 N sing N 152 N sing N 153 N sing 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 doub N 163 N sing N 164 N sing N 165 N sing N 166 N sing Y 167 N doub Y 168 N sing Y 169 N sing N 170 N sing Y 171 N doub Y 172 N sing Y 173 N sing N 174 N sing Y 175 N sing Y 176 N doub N 177 N sing Y 178 N doub N 179 N sing Y 180 N sing N 181 N sing N 182 N sing 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 doub N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing US Biochemistry BICHAW 0033 0006-2960 41 13170 13177 10.1021/bi0262799 12403618 The closed state of a H+ channel helical bundle combining precise orientational and distance restraints from solid state NMR 2002 US Protein Sci. PRCIEI 0795 0961-8368 10 2241 2250 10.1110/ps.17901 Structure of the transmembrane region of the M2 protein H+ channel 2001 10.2210/pdb1nyj/pdb pdb_00001nyj 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 2730.295 Matrix protein M2 Transmembrane peptide (residue 22-46) 4 syn polymer no no SSDPLVVAASIIGILHLILWILDRL SSDPLVVAASIIGILHLILWILDRL A,B,C,D 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 database_2 pdbx_struct_assembly pdbx_struct_oper_list chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Database references Derived calculations Data collection 1 0 2003-03-25 1 1 2008-04-29 1 2 2011-07-13 1 3 2022-02-23 1 4 2024-05-22 _database_2.pdbx_DOI _database_2.pdbx_database_accession RCSB Y RCSB 2003-02-12 REL THE PEPTIDE WAS SYNTHESIZED USING SOLID PHASE PEPTIDE SYNTHESIS. THIS SEQUENCE OCCURS NATURALLY IN THE INFLUENZA A VIRUS (UDORN/72). sample The heteronuclear distance was obtained by means of solid state NMR REDOR experiments. 13C-REDOR was performed on a DMX-300 with an XY8-pulse sequence for irradiation of 15N nuclei to compensate for errors in the flip angle, off resonance effect, and variation in the H1 field. The spinning speed was controlled at 4000 1 Hz and the experiments were performed at 38 C. REDOR and full echo spectra were recorded at various dipolar evolution times, Nctr, (where Nc and tr are the rotor cycle number and rotor period, respectively) from 2 to 16 ms to observe reasonable dipolar dephasing of the signals. The tetrameric oligomer conformation of M2-TMP was constructed using the monomer structure refined by solid-state NMR orientational data. The monomer structure was the lowest energy conformer from 30 simulated annealing attempts. 1 1 Solid state NMR PISEMA and REDOR none 7.0 ambient 303.00 K The symmetric, tetrameric bundle model of M2-TMP was constructed from the monomer structure (1MP6). The M2-TMP monomer coordinates were obtained by a geometrical search using a search algorithim to obtain a minimum of the global penalty function that incorporates all the orientational restraints and the CHARMM empirical function. The orientational restraints imposed on the structure during refinement are 15 15N chemical shifts and 15 15N-1H dipolar couplings from PISEMA experiments. The refinement was carried out in vacuo with the initial coordinates of an ideal a-helix structure (3.6 residues per turn) having a range of tilt and rotational orientations with respect to the bilayer spanning the values obtained from the PISA wheels. The resulting tetrameric bundle model was used to search the side chain orientations in accord with the experimentally measured distance between 15ND1 His37 and 13CG Trp41. Both chi 1 and chi 2 angles of the residues were searched extensively using 10 increments to discern whether the interaction was intramolecular or intermolecular and to find out which residues accounted for the observed spin interaction before characterizing the rotameric states of the sidechains. Note that while the His37 and Trp41 sidechain rotameric states are defined by the distance restraint, the rotameric states of other residues are taken from the backbone dependent sidechain rotamer library. simulated annealing To prepare an unoriented hydrated lipid bilayer sample, M2-TMP and dimyristoylphosphatidylcholine (DMPC) in a 1:16 molar ratio were co-solubilized in trifluoroethanol (TFE). After lyophilization, the white powder was hydrated by adding 50% (by total sample dry weight) pH 7.0, HPLC grade water followed by incubation for 2 days at 42 oC. The sample was then dispersed in 30 ml of 20 mM Citric/Na2HPO4 buffer at pH 7.0 and incubated at 45 oC for 2 hours before centrifuging at 20000 x g for 3 hours. After excess water was removed, the pellet was transferred to an eppendorf tube, tightly sealed to maintain the same hydration level, and then incubated at 45 oC for 2 days. Then, the sample was transferred to a glass insert for a Bruker 7 mm spinner and sealed with epoxy. To prepare an oriented bilayer sample, 20 mg of M2-TMP and 38.5 mg of DMPC (1:8 molar ratio) were co-dissolved in 1.5 ml of TFE. The sample was spread on 50 glass slides. After drying the organic solvent from the slides approximately 1.2 l of buffer (0.2 M phosphate and 0.1 M citric acid, pH 7.0) was added to each slide and then they were stacked into a glass tubing with a 6.0 x 6.0 mm internal dimension cross section. Ketchem, Roux, Cross refinement TORC V5.4 400 Home-built Chemagnetics 300 Bruker DMX-300 SER 1 n 1 SER 1 A SER 2 n 2 SER 2 A ASP 3 n 3 ASP 3 A PRO 4 n 4 PRO 4 A LEU 5 n 5 LEU 5 A VAL 6 n 6 VAL 6 A VAL 7 n 7 VAL 7 A ALA 8 n 8 ALA 8 A ALA 9 n 9 ALA 9 A SER 10 n 10 SER 10 A ILE 11 n 11 ILE 11 A ILE 12 n 12 ILE 12 A GLY 13 n 13 GLY 13 A ILE 14 n 14 ILE 14 A LEU 15 n 15 LEU 15 A HSE 16 n 16 HIS 16 A LEU 17 n 17 LEU 17 A ILE 18 n 18 ILE 18 A LEU 19 n 19 LEU 19 A TRP 20 n 20 TRP 20 A ILE 21 n 21 ILE 21 A LEU 22 n 22 LEU 22 A ASP 23 n 23 ASP 23 A ARG 24 n 24 ARG 24 A LEU 25 n 25 LEU 25 A SER 1 n 1 SER 1 B SER 2 n 2 SER 2 B ASP 3 n 3 ASP 3 B PRO 4 n 4 PRO 4 B LEU 5 n 5 LEU 5 B VAL 6 n 6 VAL 6 B VAL 7 n 7 VAL 7 B ALA 8 n 8 ALA 8 B ALA 9 n 9 ALA 9 B SER 10 n 10 SER 10 B ILE 11 n 11 ILE 11 B ILE 12 n 12 ILE 12 B GLY 13 n 13 GLY 13 B ILE 14 n 14 ILE 14 B LEU 15 n 15 LEU 15 B HSE 16 n 16 HIS 16 B LEU 17 n 17 LEU 17 B ILE 18 n 18 ILE 18 B LEU 19 n 19 LEU 19 B TRP 20 n 20 TRP 20 B ILE 21 n 21 ILE 21 B LEU 22 n 22 LEU 22 B ASP 23 n 23 ASP 23 B ARG 24 n 24 ARG 24 B LEU 25 n 25 LEU 25 B SER 1 n 1 SER 1 C SER 2 n 2 SER 2 C ASP 3 n 3 ASP 3 C PRO 4 n 4 PRO 4 C LEU 5 n 5 LEU 5 C VAL 6 n 6 VAL 6 C VAL 7 n 7 VAL 7 C ALA 8 n 8 ALA 8 C ALA 9 n 9 ALA 9 C SER 10 n 10 SER 10 C ILE 11 n 11 ILE 11 C ILE 12 n 12 ILE 12 C GLY 13 n 13 GLY 13 C ILE 14 n 14 ILE 14 C LEU 15 n 15 LEU 15 C HSE 16 n 16 HIS 16 C LEU 17 n 17 LEU 17 C ILE 18 n 18 ILE 18 C LEU 19 n 19 LEU 19 C TRP 20 n 20 TRP 20 C ILE 21 n 21 ILE 21 C LEU 22 n 22 LEU 22 C ASP 23 n 23 ASP 23 C ARG 24 n 24 ARG 24 C LEU 25 n 25 LEU 25 C SER 1 n 1 SER 1 D SER 2 n 2 SER 2 D ASP 3 n 3 ASP 3 D PRO 4 n 4 PRO 4 D LEU 5 n 5 LEU 5 D VAL 6 n 6 VAL 6 D VAL 7 n 7 VAL 7 D ALA 8 n 8 ALA 8 D ALA 9 n 9 ALA 9 D SER 10 n 10 SER 10 D ILE 11 n 11 ILE 11 D ILE 12 n 12 ILE 12 D GLY 13 n 13 GLY 13 D ILE 14 n 14 ILE 14 D LEU 15 n 15 LEU 15 D HSE 16 n 16 HIS 16 D LEU 17 n 17 LEU 17 D ILE 18 n 18 ILE 18 D LEU 19 n 19 LEU 19 D TRP 20 n 20 TRP 20 D ILE 21 n 21 ILE 21 D LEU 22 n 22 LEU 22 D ASP 23 n 23 ASP 23 D ARG 24 n 24 ARG 24 D LEU 25 n 25 LEU 25 D author_defined_assembly 4 tetrameric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 C D CD1 NE2 TRP HIS 20 16 1.58 1 B C CD1 NE2 TRP HIS 20 16 1.66 1 A B CD1 NE2 TRP HIS 20 16 1.67 1 A D NE2 CD1 HIS TRP 16 20 1.67 1 B C CD1 CB LEU HIS 17 16 1.73 1 C D CD1 CB LEU HIS 17 16 1.76 1 C D CD2 CA LEU GLY 17 13 1.77 1 A D CB CD1 HIS LEU 16 17 1.78 1 A B CD1 CB LEU HIS 17 16 1.80 1 B C CD1 O ILE ALA 14 9 1.84 1 B C CD2 CA LEU GLY 17 13 1.84 1 A D CA CD2 GLY LEU 13 17 1.86 1 A B CD2 CA LEU GLY 17 13 1.87 1 A D O CD1 ALA ILE 9 14 1.87 1 C D CD1 O ILE ALA 14 9 1.92 1 A B CD1 O ILE ALA 14 9 1.93 1 B C CD2 N LEU GLY 17 13 1.95 1 A D N CD2 GLY LEU 13 17 1.97 1 C D CD2 N LEU GLY 17 13 1.99 1 A B CD2 N LEU GLY 17 13 1.99 1 C D CD1 ND1 LEU HIS 17 16 2.04 1 B C CD1 C ILE ALA 14 9 2.06 1 A B CD1 ND1 LEU HIS 17 16 2.08 1 A D C CD1 ALA ILE 9 14 2.08 1 A D ND1 CD1 HIS LEU 16 17 2.09 1 B C CD1 ND1 LEU HIS 17 16 2.10 1 A B CD1 C ILE ALA 14 9 2.14 1 C D CD1 C ILE ALA 14 9 2.16 1 C D CD1 CG LEU HIS 17 16 2.19 1 6.70 0.90 118.30 125.00 A A A CB CG OD2 ASP ASP ASP 3 3 3 N 1 -6.59 0.90 118.30 111.71 A A A CB CG OD1 ASP ASP ASP 23 23 23 N 1 7.56 0.90 118.30 125.86 A A A CB CG OD2 ASP ASP ASP 23 23 23 N 1 -3.25 0.50 120.30 117.05 A A A NE CZ NH2 ARG ARG ARG 24 24 24 N 1 6.68 0.90 118.30 124.98 B B B CB CG OD2 ASP ASP ASP 3 3 3 N 1 -6.59 0.90 118.30 111.71 B B B CB CG OD1 ASP ASP ASP 23 23 23 N 1 7.57 0.90 118.30 125.87 B B B CB CG OD2 ASP ASP ASP 23 23 23 N 1 -3.25 0.50 120.30 117.05 B B B NE CZ NH2 ARG ARG ARG 24 24 24 N 1 6.64 0.90 118.30 124.94 C C C CB CG OD2 ASP ASP ASP 3 3 3 N 1 -6.61 0.90 118.30 111.69 C C C CB CG OD1 ASP ASP ASP 23 23 23 N 1 7.59 0.90 118.30 125.89 C C C CB CG OD2 ASP ASP ASP 23 23 23 N 1 -3.25 0.50 120.30 117.05 C C C NE CZ NH2 ARG ARG ARG 24 24 24 N 1 6.68 0.90 118.30 124.98 D D D CB CG OD2 ASP ASP ASP 3 3 3 N 1 -6.59 0.90 118.30 111.71 D D D CB CG OD1 ASP ASP ASP 23 23 23 N 1 7.57 0.90 118.30 125.87 D D D CB CG OD2 ASP ASP ASP 23 23 23 N 1 -3.25 0.50 120.30 117.05 D D D NE CZ NH2 ARG ARG ARG 24 24 24 N The closed state structure of M2 protein H+ channel by solid state NMR spectroscopy 1 N N 1 N N 1 N N 1 N N A SER 1 A SER 1 HELX_P A LEU 25 A LEU 25 1 1 25 B SER 1 B SER 1 HELX_P B LEU 25 B LEU 25 1 2 25 C SER 1 C SER 1 HELX_P C LEU 25 C LEU 25 1 3 25 D SER 1 D SER 1 HELX_P D LEU 25 D LEU 25 1 4 25 VIRAL PROTEIN influenza A virus, membrane protein structure, M2 proton channel, solid state NMR, Viral protein VMT2_IAUSS UNP 1 22 P35938 SSDPLVVAASIIGILHLILWILDRL 22 46 1NYJ 1 25 P35938 A 1 1 25 22 46 1NYJ 1 25 P35938 B 1 1 25 22 46 1NYJ 1 25 P35938 C 1 1 25 22 46 1NYJ 1 25 P35938 D 1 1 25