1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Barrientos, L.G. Louis, J.M. Botos, I. Mori, T. Han, Z. O'Keefe, B.R. Boyd, M.R. Wlodawer, A. Gronenborn, A.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 C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE 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 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 C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE 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 C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking UK Structure STRUE6 2005 0969-2126 10 673 686 10.1016/S0969-2126(02)00758-X 12015150 The domain-swapped dimer of cyanovirin-N is in a metastable folded state: reconciliation of X-ray and NMR structures. 2002 10.2210/pdb1l5e/pdb pdb_00001l5e 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 11022.090 Cyanovirin-N 2 man polymer CV-N no no LGKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQF VSTKINLDDHIANIDGTLKYE LGKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQF VSTKINLDDHIANIDGTLKYE A,B 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 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 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 n n n n n n n n Nostoc Escherichia Escherichia coli sample 45916 Nostoc ellipsosporum 511693 Escherichia coli BL21 BL21 plasmid pET database_2 pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Database references Derived calculations 1 0 2002-06-05 1 1 2008-04-28 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession SOLUTION NMR STRUCTURE OF CYANOVIRIN-N, RESTRAINED REGULARIZED MEAN COORDINATES X-RAY STRUCTURE OF CYANOVIRIN-N; DOMAIN-SWAPPED DIMER DOMAIN-SWAPPED CYANOVIRIN-N DIMER RCSB Y RCSB 2002-03-06 REL Residual dipolar couplings were measured in the presence of a colloidal phage solution of 11.5 mg/ml Pf1. 1 2D IPAP [15N-1H]-HSQC 6.0 1 atm 293 K The coordinates of the individual domains of the domain swapped dimer CV-N were taken directly from the X-Ray coordinates, 3EZM and 1L5B. The only protons added are the HNE1 of W(49/150) and all the backbone amide protons (HN), since domain-domain orientation was based only on HN/HNE1 residual dipolar couplings. The starting coordinates were those of two pseudo-monomer units (AB' and A'B) extracted from the refined trigonal 1.5 X-ray structure, in which proline 51 at the junction between A and B was removed, allowing for free rotation around this junction. We then treated AB' and A'B as two independent sub-domains. Assuming that the orientation of the two sub-domains is fixed in solution (at least to a first approximation), the principal axis systems, or alignment frames, of sub-domains AB' and A'B should be equivalent to the alignment system of the entire molecule and, vice versa, to each other. Using the residual dipolar couplings we calculated the order tensor principal axis systems for each domain. Rotation of pseudo sub-domain A'B around the hinge at amino acid position 51 until a superposition of the individual coordinate frames was obtained yielded the final model of the solution dimer. Determination of the domain orientation for the solution structure of the dimer was carried out using a procedure analogous to the one described for determining the relative domain orientation in a two-domain protein fragment of a lectin. 0.150 mM protein in 25 mM sodium phosphate buffer, pH 8.0 and 0.02 % NaN3 90% H2O/10% D2O F.Delaglio, S.Grzesiek, G.W.Vuister, G.Zhu, J.Pfeifer, A.Bax processing NMRPipe 2.1 M.Zweckstetter, A.Bax structure solution PALES M.Zweckstetter, A.Bax refinement PALES 600 Bruker DRX LEU 1 n 1 LEU 1 A GLY 2 n 2 GLY 2 A LYS 3 n 3 LYS 3 A PHE 4 n 4 PHE 4 A SER 5 n 5 SER 5 A GLN 6 n 6 GLN 6 A THR 7 n 7 THR 7 A CYS 8 n 8 CYS 8 A TYR 9 n 9 TYR 9 A ASN 10 n 10 ASN 10 A SER 11 n 11 SER 11 A ALA 12 n 12 ALA 12 A ILE 13 n 13 ILE 13 A GLN 14 n 14 GLN 14 A GLY 15 n 15 GLY 15 A SER 16 n 16 SER 16 A VAL 17 n 17 VAL 17 A LEU 18 n 18 LEU 18 A THR 19 n 19 THR 19 A SER 20 n 20 SER 20 A THR 21 n 21 THR 21 A CYS 22 n 22 CYS 22 A GLU 23 n 23 GLU 23 A ARG 24 n 24 ARG 24 A THR 25 n 25 THR 25 A ASN 26 n 26 ASN 26 A GLY 27 n 27 GLY 27 A GLY 28 n 28 GLY 28 A TYR 29 n 29 TYR 29 A ASN 30 n 30 ASN 30 A THR 31 n 31 THR 31 A SER 32 n 32 SER 32 A SER 33 n 33 SER 33 A ILE 34 n 34 ILE 34 A ASP 35 n 35 ASP 35 A LEU 36 n 36 LEU 36 A ASN 37 n 37 ASN 37 A SER 38 n 38 SER 38 A VAL 39 n 39 VAL 39 A ILE 40 n 40 ILE 40 A GLU 41 n 41 GLU 41 A ASN 42 n 42 ASN 42 A VAL 43 n 43 VAL 43 A ASP 44 n 44 ASP 44 A GLY 45 n 45 GLY 45 A SER 46 n 46 SER 46 A LEU 47 n 47 LEU 47 A LYS 48 n 48 LYS 48 A TRP 49 n 49 TRP 49 A GLN 50 n 50 GLN 50 A PRO 51 n 51 PRO 51 A SER 52 n 52 SER 52 A ASN 53 n 53 ASN 53 A PHE 54 n 54 PHE 54 A ILE 55 n 55 ILE 55 A GLU 56 n 56 GLU 56 A THR 57 n 57 THR 57 A CYS 58 n 58 CYS 58 A ARG 59 n 59 ARG 59 A ASN 60 n 60 ASN 60 A THR 61 n 61 THR 61 A GLN 62 n 62 GLN 62 A LEU 63 n 63 LEU 63 A ALA 64 n 64 ALA 64 A GLY 65 n 65 GLY 65 A SER 66 n 66 SER 66 A SER 67 n 67 SER 67 A GLU 68 n 68 GLU 68 A LEU 69 n 69 LEU 69 A ALA 70 n 70 ALA 70 A ALA 71 n 71 ALA 71 A GLU 72 n 72 GLU 72 A CYS 73 n 73 CYS 73 A LYS 74 n 74 LYS 74 A THR 75 n 75 THR 75 A ARG 76 n 76 ARG 76 A ALA 77 n 77 ALA 77 A GLN 78 n 78 GLN 78 A GLN 79 n 79 GLN 79 A PHE 80 n 80 PHE 80 A VAL 81 n 81 VAL 81 A SER 82 n 82 SER 82 A THR 83 n 83 THR 83 A LYS 84 n 84 LYS 84 A ILE 85 n 85 ILE 85 A ASN 86 n 86 ASN 86 A LEU 87 n 87 LEU 87 A ASP 88 n 88 ASP 88 A ASP 89 n 89 ASP 89 A HIS 90 n 90 HIS 90 A ILE 91 n 91 ILE 91 A ALA 92 n 92 ALA 92 A ASN 93 n 93 ASN 93 A ILE 94 n 94 ILE 94 A ASP 95 n 95 ASP 95 A GLY 96 n 96 GLY 96 A THR 97 n 97 THR 97 A LEU 98 n 98 LEU 98 A LYS 99 n 99 LYS 99 A TYR 100 n 100 TYR 100 A GLU 101 n 101 GLU 101 A LEU 102 n 1 LEU 102 B GLY 103 n 2 GLY 103 B LYS 104 n 3 LYS 104 B PHE 105 n 4 PHE 105 B SER 106 n 5 SER 106 B GLN 107 n 6 GLN 107 B THR 108 n 7 THR 108 B CYS 109 n 8 CYS 109 B TYR 110 n 9 TYR 110 B ASN 111 n 10 ASN 111 B SER 112 n 11 SER 112 B ALA 113 n 12 ALA 113 B ILE 114 n 13 ILE 114 B GLN 115 n 14 GLN 115 B GLY 116 n 15 GLY 116 B SER 117 n 16 SER 117 B VAL 118 n 17 VAL 118 B LEU 119 n 18 LEU 119 B THR 120 n 19 THR 120 B SER 121 n 20 SER 121 B THR 122 n 21 THR 122 B CYS 123 n 22 CYS 123 B GLU 124 n 23 GLU 124 B ARG 125 n 24 ARG 125 B THR 126 n 25 THR 126 B ASN 127 n 26 ASN 127 B GLY 128 n 27 GLY 128 B GLY 129 n 28 GLY 129 B TYR 130 n 29 TYR 130 B ASN 131 n 30 ASN 131 B THR 132 n 31 THR 132 B SER 133 n 32 SER 133 B SER 134 n 33 SER 134 B ILE 135 n 34 ILE 135 B ASP 136 n 35 ASP 136 B LEU 137 n 36 LEU 137 B ASN 138 n 37 ASN 138 B SER 139 n 38 SER 139 B VAL 140 n 39 VAL 140 B ILE 141 n 40 ILE 141 B GLU 142 n 41 GLU 142 B ASN 143 n 42 ASN 143 B VAL 144 n 43 VAL 144 B ASP 145 n 44 ASP 145 B GLY 146 n 45 GLY 146 B SER 147 n 46 SER 147 B LEU 148 n 47 LEU 148 B LYS 149 n 48 LYS 149 B TRP 150 n 49 TRP 150 B GLN 151 n 50 GLN 151 B PRO 152 n 51 PRO 152 B SER 153 n 52 SER 153 B ASN 154 n 53 ASN 154 B PHE 155 n 54 PHE 155 B ILE 156 n 55 ILE 156 B GLU 157 n 56 GLU 157 B THR 158 n 57 THR 158 B CYS 159 n 58 CYS 159 B ARG 160 n 59 ARG 160 B ASN 161 n 60 ASN 161 B THR 162 n 61 THR 162 B GLN 163 n 62 GLN 163 B LEU 164 n 63 LEU 164 B ALA 165 n 64 ALA 165 B GLY 166 n 65 GLY 166 B SER 167 n 66 SER 167 B SER 168 n 67 SER 168 B GLU 169 n 68 GLU 169 B LEU 170 n 69 LEU 170 B ALA 171 n 70 ALA 171 B ALA 172 n 71 ALA 172 B GLU 173 n 72 GLU 173 B CYS 174 n 73 CYS 174 B LYS 175 n 74 LYS 175 B THR 176 n 75 THR 176 B ARG 177 n 76 ARG 177 B ALA 178 n 77 ALA 178 B GLN 179 n 78 GLN 179 B GLN 180 n 79 GLN 180 B PHE 181 n 80 PHE 181 B VAL 182 n 81 VAL 182 B SER 183 n 82 SER 183 B THR 184 n 83 THR 184 B LYS 185 n 84 LYS 185 B ILE 186 n 85 ILE 186 B ASN 187 n 86 ASN 187 B LEU 188 n 87 LEU 188 B ASP 189 n 88 ASP 189 B ASP 190 n 89 ASP 190 B HIS 191 n 90 HIS 191 B ILE 192 n 91 ILE 192 B ALA 193 n 92 ALA 193 B ASN 194 n 93 ASN 194 B ILE 195 n 94 ILE 195 B ASP 196 n 95 ASP 196 B GLY 197 n 96 GLY 197 B THR 198 n 97 THR 198 B LEU 199 n 98 LEU 199 B LYS 200 n 99 LYS 200 B TYR 201 n 100 TYR 201 B GLU 202 n 101 GLU 202 B author_defined_assembly 2 dimeric 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 A N ALA 12 A N ALA 12 A O THR 19 A O THR 19 A N CYS 22 A N CYS 22 A O ASN 30 A O ASN 30 A N GLU 41 A N GLU 41 A O LYS 48 A O LYS 48 A N ALA 64 A N ALA 64 A O GLU 68 A O GLU 68 A N LEU 69 A N LEU 69 A O ILE 85 A O ILE 85 A N ALA 92 A N ALA 92 A O LYS 99 A O LYS 99 B N ALA 113 B N ALA 12 B O THR 120 B O THR 19 B N CYS 123 B N CYS 22 B O ASN 131 B O ASN 30 B N GLU 142 B N GLU 41 B O LYS 149 B O LYS 48 B N ALA 165 B N ALA 64 B O GLU 169 B O GLU 68 B N LEU 170 B N LEU 69 B O ILE 186 B O ILE 85 B N ALA 193 B N ALA 92 B O LYS 200 B O LYS 99 1 A VAL 39 14.44 1 B VAL 140 14.57 1 -11.70 1.90 111.40 99.70 A A A CB CA C VAL VAL VAL 39 39 39 N 1 -15.78 1.80 110.60 94.82 A A A N CA CB GLN GLN GLN 50 50 50 N 1 -11.94 1.90 111.40 99.46 B B B CB CA C VAL VAL VAL 140 140 140 N 1 -15.80 1.80 110.60 94.80 B B B N CA CB GLN GLN GLN 151 151 151 N 1 A GLN 50 -124.94 -155.93 1 A ASN 53 169.59 -174.73 1 A SER 67 -151.08 5.10 1 B GLN 151 -124.60 -155.28 1 B ASN 154 169.40 -174.65 1 B SER 168 -151.18 5.10 The domain-swapped dimer of CV-N in solution 1 N N 1 N N A LYS 3 A LYS 3 HELX_P A GLN 6 A GLN 6 5 1 4 B LYS 104 B LYS 3 HELX_P B GLN 107 B GLN 6 5 2 4 disulf 2.031 A CYS 8 A SG CYS 8 1_555 A CYS 22 A SG CYS 22 1_555 disulf 2.038 A CYS 58 A SG CYS 58 1_555 A CYS 73 A SG CYS 73 1_555 disulf 2.030 B CYS 109 B SG CYS 8 1_555 B CYS 123 B SG CYS 22 1_555 disulf 2.038 B CYS 159 B SG CYS 58 1_555 B CYS 174 B SG CYS 73 1_555 ANTIVIRAL PROTEIN 3D domain-swapping, cyanovirin-N, protein folding, ANTIVIRAL PROTEIN CVN_NOSEL UNP 1 1 P81180 LGKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQF VSTKINLDDHIANIDGTLKYE 1 101 1L5E 1 101 P81180 A 1 1 101 1 101 1L5E 102 202 P81180 B 1 1 101 3 2 3 2 3 2 3 2 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A CYS 8 A CYS 8 A GLN 14 A GLN 14 A VAL 17 A VAL 17 A GLU 23 A GLU 23 A TYR 29 A TYR 29 A ASP 35 A ASP 35 A ILE 40 A ILE 40 A VAL 43 A VAL 43 A SER 46 A SER 46 A TRP 49 A TRP 49 A CYS 58 A CYS 58 A ALA 64 A ALA 64 A GLU 68 A GLU 68 A LYS 74 A LYS 74 A PHE 80 A PHE 80 A ASN 86 A ASN 86 A ILE 91 A ILE 91 A ILE 94 A ILE 94 A THR 97 A THR 97 A TYR 100 A TYR 100 B CYS 109 B CYS 8 B GLN 115 B GLN 14 B VAL 118 B VAL 17 B GLU 124 B GLU 23 B TYR 130 B TYR 29 B ASP 136 B ASP 35 B ILE 141 B ILE 40 B VAL 144 B VAL 43 B SER 147 B SER 46 B TRP 150 B TRP 49 B CYS 159 B CYS 58 B ALA 165 B ALA 64 B GLU 169 B GLU 68 B LYS 175 B LYS 74 B PHE 181 B PHE 80 B ASN 187 B ASN 86 B ILE 192 B ILE 91 B ILE 195 B ILE 94 B THR 198 B THR 97 B TYR 201 B TYR 100