1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Massiah, M.A. Simmons, B.N. Short, K.M. Cox, T.C. 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 C5 H11 N O2 S 149.211 y METHIONINE 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 C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking Zn 2 65.409 ZINC ION non-polymer UK J.Mol.Biol. JMOBAK 0070 0022-2836 358 532 545 10.1016/j.jmb.2006.02.009 16529770 Solution Structure of the RBCC/TRIM B-box1 Domain of Human MID1: B-box with a RING. 2006 10.2210/pdb2ffw/pdb pdb_00002ffw 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 8630.673 Midline-1 6.3.2.- B-box 1 domain (RESIDUES: 87 - 164) 1 man polymer 65.409 ZINC ION 2 syn non-polymer Tripartite motif protein 18, Putative transcription factor XPRF, Midin, RING finger protein 59 no no QKASVSGPNSPSETRRERAFDANTMTSAEKVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKATHPNKKPFTGHRLIEP QKASVSGPNSPSETRRERAFDANTMTSAEKVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKATHPNKKPFTGHRLIEP A 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 human Homo Escherichia Escherichia coli sample MID1, FXY, RNF59, TRIM18, XPRF 9606 Homo sapiens 469008 Escherichia coli BL21(DE3) BL21(DE3) plasmid pGEX-4T2 database_2 pdbx_struct_assembly pdbx_struct_conn_angle pdbx_struct_oper_list struct_conn struct_site repository Initial release Version format compliance Version format compliance Database references Derived calculations 1 0 2006-05-09 1 1 2008-05-01 1 2 2011-07-13 1 3 2022-03-09 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2005-12-20 REL REL ZN ZINC ION Structure was determined using triple resonance data for backbone atom assignment and NOEs from 13C- and 15N-edited NOESY spectra target function 100 13 HNCA HNCACB CBCACONH 3D_15N-separated_ROESY 3D_13C-separated_NOESY HCCH-TOCSY 300 mM NaCl 7.5 1 atm 294 K torsion angle dynamics 1 lowest energy 0.75 mM U-15N,13C protein; 50 mM Tris-HCl, 300 mM NaCl, 50 mM beta-mercaptoethanol, 5 mM ZnCl2, 90% H2O, 10% D2O 50 mM Tris-HCl, 300 mM NaCl, 50 mM beta-mercaptoethanol, 5 mM ZnCl2, 90% H2O, 10% D2O P Guntert structure solution CYANA 2.1 Delagio, F processing NMRPipe Goddard collection Sparky sparky-mac10.2 P Guntert refinement CYANA 2.1 600 Varian INOVA CYS 119 2 ZN ZN 200 A CYS 134 2 ZN ZN 201 A GLN 87 n 1 GLN 87 A LYS 88 n 2 LYS 88 A ALA 89 n 3 ALA 89 A SER 90 n 4 SER 90 A VAL 91 n 5 VAL 91 A SER 92 n 6 SER 92 A GLY 93 n 7 GLY 93 A PRO 94 n 8 PRO 94 A ASN 95 n 9 ASN 95 A SER 96 n 10 SER 96 A PRO 97 n 11 PRO 97 A SER 98 n 12 SER 98 A GLU 99 n 13 GLU 99 A THR 100 n 14 THR 100 A ARG 101 n 15 ARG 101 A ARG 102 n 16 ARG 102 A GLU 103 n 17 GLU 103 A ARG 104 n 18 ARG 104 A ALA 105 n 19 ALA 105 A PHE 106 n 20 PHE 106 A ASP 107 n 21 ASP 107 A ALA 108 n 22 ALA 108 A ASN 109 n 23 ASN 109 A THR 110 n 24 THR 110 A MET 111 n 25 MET 111 A THR 112 n 26 THR 112 A SER 113 n 27 SER 113 A ALA 114 n 28 ALA 114 A GLU 115 n 29 GLU 115 A LYS 116 n 30 LYS 116 A VAL 117 n 31 VAL 117 A LEU 118 n 32 LEU 118 A CYS 119 n 33 CYS 119 A GLN 120 n 34 GLN 120 A PHE 121 n 35 PHE 121 A CYS 122 n 36 CYS 122 A ASP 123 n 37 ASP 123 A GLN 124 n 38 GLN 124 A ASP 125 n 39 ASP 125 A PRO 126 n 40 PRO 126 A ALA 127 n 41 ALA 127 A GLN 128 n 42 GLN 128 A ASP 129 n 43 ASP 129 A ALA 130 n 44 ALA 130 A VAL 131 n 45 VAL 131 A LYS 132 n 46 LYS 132 A THR 133 n 47 THR 133 A CYS 134 n 48 CYS 134 A VAL 135 n 49 VAL 135 A THR 136 n 50 THR 136 A CYS 137 n 51 CYS 137 A GLU 138 n 52 GLU 138 A VAL 139 n 53 VAL 139 A SER 140 n 54 SER 140 A TYR 141 n 55 TYR 141 A CYS 142 n 56 CYS 142 A ASP 143 n 57 ASP 143 A GLU 144 n 58 GLU 144 A CYS 145 n 59 CYS 145 A LEU 146 n 60 LEU 146 A LYS 147 n 61 LYS 147 A ALA 148 n 62 ALA 148 A THR 149 n 63 THR 149 A HIS 150 n 64 HIS 150 A PRO 151 n 65 PRO 151 A ASN 152 n 66 ASN 152 A LYS 153 n 67 LYS 153 A LYS 154 n 68 LYS 154 A PRO 155 n 69 PRO 155 A PHE 156 n 70 PHE 156 A THR 157 n 71 THR 157 A GLY 158 n 72 GLY 158 A HIS 159 n 73 HIS 159 A ARG 160 n 74 ARG 160 A LEU 161 n 75 LEU 161 A ILE 162 n 76 ILE 162 A GLU 163 n 77 GLU 163 A PRO 164 n 78 PRO 164 A author_defined_assembly 1 monomeric A CYS 119 A SG CYS 33 1_555 A ZN 200 B ZN ZN 1_555 A CYS 122 A SG CYS 36 1_555 110.6 A CYS 119 A SG CYS 33 1_555 A ZN 200 B ZN ZN 1_555 A CYS 142 A SG CYS 56 1_555 112.1 A CYS 122 A SG CYS 36 1_555 A ZN 200 B ZN ZN 1_555 A CYS 142 A SG CYS 56 1_555 108.7 A CYS 119 A SG CYS 33 1_555 A ZN 200 B ZN ZN 1_555 A CYS 145 A SG CYS 59 1_555 109.8 A CYS 122 A SG CYS 36 1_555 A ZN 200 B ZN ZN 1_555 A CYS 145 A SG CYS 59 1_555 107.6 A CYS 142 A SG CYS 56 1_555 A ZN 200 B ZN ZN 1_555 A CYS 145 A SG CYS 59 1_555 107.9 A CYS 134 A SG CYS 48 1_555 A ZN 201 C ZN ZN 1_555 A CYS 137 A SG CYS 51 1_555 107.6 A CYS 134 A SG CYS 48 1_555 A ZN 201 C ZN ZN 1_555 A HIS 150 A NE2 HIS 64 1_555 118.8 A CYS 137 A SG CYS 51 1_555 A ZN 201 C ZN ZN 1_555 A HIS 150 A NE2 HIS 64 1_555 113.4 A CYS 134 A SG CYS 48 1_555 A ZN 201 C ZN ZN 1_555 A HIS 159 A ND1 HIS 73 1_555 117.9 A CYS 137 A SG CYS 51 1_555 A ZN 201 C ZN ZN 1_555 A HIS 159 A ND1 HIS 73 1_555 112.8 A HIS 150 A NE2 HIS 64 1_555 A ZN 201 C ZN ZN 1_555 A HIS 159 A ND1 HIS 73 1_555 85.1 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 LYS 132 A N LYS 46 A O TYR 141 A O TYR 55 1 A SER 96 -157.62 69.99 1 A SER 98 -65.61 98.52 1 A GLU 103 -162.67 104.55 1 A PHE 106 -154.95 76.05 1 A ALA 108 -63.11 -178.43 1 A SER 113 -161.42 -66.34 1 A GLU 115 -130.25 -68.14 1 A LYS 116 63.08 -173.57 1 A ASP 123 -147.55 26.81 1 A ASP 125 60.43 85.53 1 A CYS 142 -101.57 -159.24 1 A HIS 150 -113.50 72.95 1 A PRO 151 -69.77 85.03 1 A LYS 154 62.68 161.32 1 A PHE 156 -162.01 43.37 1 A THR 157 -90.24 46.84 2 A LYS 88 60.75 -171.76 2 A SER 92 -163.88 91.43 2 A PRO 97 -69.82 87.84 2 A GLU 103 59.95 97.11 2 A ASP 107 -60.76 -174.02 2 A ALA 114 63.57 88.11 2 A GLU 115 -130.41 -67.79 2 A ASP 123 -148.53 27.22 2 A ASP 125 61.66 85.70 2 A CYS 142 -104.10 -160.45 2 A HIS 150 -113.71 72.56 2 A LYS 154 62.60 161.42 2 A PHE 156 -161.61 66.67 2 A THR 157 -96.06 40.60 3 A SER 98 -95.70 -70.70 3 A ARG 104 -174.86 147.08 3 A ALA 105 -142.97 -68.44 3 A ALA 108 62.88 162.98 3 A ASN 109 -174.80 62.69 3 A THR 110 64.13 158.47 3 A ALA 114 62.00 176.71 3 A GLU 115 -121.20 -68.10 3 A ASP 123 -151.05 26.52 3 A ASP 125 63.32 86.01 3 A CYS 142 -101.54 -159.26 3 A HIS 150 -113.57 72.74 3 A ASN 152 179.75 -174.47 3 A LYS 154 62.59 161.14 3 A HIS 159 -78.74 -169.13 4 A ASN 95 -69.03 -171.91 4 A ASN 109 -59.81 100.84 4 A SER 113 -60.45 -172.81 4 A GLU 115 -96.77 -68.20 4 A ASP 123 -140.12 26.26 4 A ASP 125 63.41 85.78 4 A CYS 142 -100.75 -159.70 4 A HIS 150 -113.08 74.08 4 A ASN 152 64.20 108.25 4 A LYS 154 -177.67 85.53 4 A PHE 156 -150.13 60.79 5 A PRO 94 -69.73 91.46 5 A SER 96 -159.34 70.26 5 A ARG 101 -163.78 91.18 5 A THR 110 56.74 -179.25 5 A SER 113 -101.37 78.60 5 A ASP 123 -145.20 25.89 5 A ASP 125 63.39 85.76 5 A THR 133 -161.56 105.47 5 A CYS 142 -101.38 -159.11 5 A HIS 150 -112.41 76.41 5 A ASN 152 63.49 -169.83 5 A LYS 154 65.07 112.75 5 A ARG 160 -109.95 -169.93 6 A GLU 99 -161.35 90.87 6 A PHE 106 -106.91 53.07 6 A ALA 114 -159.78 27.13 6 A ASP 123 -143.51 25.77 6 A ASP 125 63.51 85.94 6 A VAL 131 -145.75 17.22 6 A HIS 150 -113.19 73.63 6 A ASN 152 64.89 111.95 6 A LYS 153 -160.58 111.62 6 A LYS 154 -174.77 85.27 6 A PHE 156 -148.45 -70.01 6 A THR 157 37.47 43.12 6 A LEU 161 -169.88 -169.94 7 A THR 112 -155.40 -51.24 7 A SER 113 48.26 -94.49 7 A ALA 114 -149.07 25.70 7 A ASP 123 -141.73 26.40 7 A ASP 125 60.27 85.48 7 A CYS 142 -102.71 -159.75 7 A HIS 150 -113.07 74.26 7 A LYS 153 -121.84 -77.33 7 A PHE 156 -162.29 67.49 7 A THR 157 -90.63 46.37 7 A GLU 163 54.34 73.23 8 A LYS 88 57.23 -174.95 8 A SER 90 -105.67 73.52 8 A PRO 94 -69.75 98.67 8 A THR 100 -132.27 -44.07 8 A ARG 104 -108.59 -61.59 8 A PHE 106 -161.47 -71.99 8 A ASP 107 69.61 -75.43 8 A ALA 108 -174.61 -72.35 8 A SER 113 -63.97 99.39 8 A ASP 123 -142.97 25.24 8 A ASP 125 63.53 86.29 8 A CYS 142 -101.64 -158.13 8 A HIS 150 -113.26 72.98 8 A PRO 151 -69.75 90.72 8 A LYS 154 62.77 161.32 8 A PHE 156 -157.39 53.04 8 A THR 157 -94.48 37.98 9 A SER 92 -119.47 57.33 9 A ALA 114 63.68 169.79 9 A GLU 115 -100.74 -68.03 9 A ASP 123 -145.36 26.02 9 A ASP 125 62.53 85.72 9 A CYS 142 -100.11 -158.67 9 A HIS 150 -113.27 73.40 9 A LYS 154 61.61 163.35 9 A PHE 156 32.95 62.23 9 A GLU 163 52.31 73.19 10 A ALA 89 -177.96 144.80 10 A PRO 94 -69.76 -176.39 10 A ARG 104 62.36 173.53 10 A ALA 105 -166.55 -48.73 10 A PHE 106 63.22 162.23 10 A GLU 115 -131.68 -68.08 10 A ASP 123 -141.04 26.19 10 A ASP 125 63.35 85.71 10 A CYS 142 -101.52 -160.48 10 A HIS 150 -112.84 76.07 10 A PRO 151 -69.86 84.75 10 A ASN 152 -54.43 175.24 10 A LYS 153 -128.80 -79.39 10 A LYS 154 177.13 104.33 10 A PHE 156 -139.15 -55.95 10 A THR 157 37.32 43.36 11 A GLU 99 -112.72 77.54 11 A THR 100 -106.83 40.55 11 A ARG 101 -171.10 129.44 11 A ALA 108 56.67 92.59 11 A ALA 114 56.88 -178.30 11 A GLU 115 -129.48 -68.08 11 A LYS 116 62.14 171.92 11 A ASP 123 -143.11 26.39 11 A ASP 125 61.75 85.52 11 A VAL 131 -140.29 20.51 11 A HIS 150 -113.26 74.07 11 A PRO 151 -69.74 -170.01 11 A ASN 152 64.67 155.60 11 A LYS 154 66.41 137.62 11 A PHE 156 -135.93 -74.11 11 A THR 157 178.05 -31.90 11 A LEU 161 -165.31 -169.82 12 A SER 90 -178.54 83.43 12 A PRO 97 -69.76 93.92 12 A ASN 109 -151.75 40.56 12 A THR 112 51.46 -170.99 12 A ALA 114 -178.94 -33.83 12 A GLU 115 71.58 -69.54 12 A ASP 123 -148.21 26.28 12 A ASP 125 63.20 85.71 12 A THR 133 -161.01 104.33 12 A CYS 142 -101.61 -159.93 12 A HIS 150 -113.34 73.71 12 A ASN 152 66.74 137.90 12 A LYS 153 -179.52 115.62 12 A LYS 154 -175.42 85.44 12 A PHE 156 -150.44 60.99 12 A ARG 160 -110.00 -169.32 13 A SER 96 -118.44 71.37 13 A ALA 108 -161.63 108.26 13 A MET 111 -102.94 45.28 13 A THR 112 -172.54 72.19 13 A GLU 115 71.55 -69.45 13 A VAL 117 -68.37 97.18 13 A ASP 123 -147.49 26.58 13 A ASP 125 60.59 85.65 13 A CYS 142 -101.82 -158.94 13 A HIS 150 -112.62 74.27 13 A ASN 152 179.71 -174.09 13 A LYS 154 62.92 160.87 13 A PHE 156 -160.88 43.54 Solution structure of the RBCC/TRIM B-box1 domain of human MID1: B-box with a RING 1 N N 2 N N 2 N N A CYS 142 A CYS 56 HELX_P A HIS 150 A HIS 64 1 1 9 metalc 2.303 A CYS 119 A SG CYS 33 1_555 A ZN 200 B ZN ZN 1_555 metalc 2.379 A CYS 122 A SG CYS 36 1_555 A ZN 200 B ZN ZN 1_555 metalc 2.304 A CYS 134 A SG CYS 48 1_555 A ZN 201 C ZN ZN 1_555 metalc 2.436 A CYS 137 A SG CYS 51 1_555 A ZN 201 C ZN ZN 1_555 metalc 2.361 A CYS 142 A SG CYS 56 1_555 A ZN 200 B ZN ZN 1_555 metalc 2.392 A CYS 145 A SG CYS 59 1_555 A ZN 200 B ZN ZN 1_555 metalc 2.135 A HIS 150 A NE2 HIS 64 1_555 A ZN 201 C ZN ZN 1_555 metalc 2.144 A HIS 159 A ND1 HIS 73 1_555 A ZN 201 C ZN ZN 1_555 LIGASE B-box, MID1, RING FINGER, Zinc-finger, LIGASE A ASP 125 A ASP 39 1 A PRO 126 A PRO 40 0.03 A LYS 154 A LYS 68 1 A PRO 155 A PRO 69 -0.06 A ASP 125 A ASP 39 2 A PRO 126 A PRO 40 0.01 A LYS 154 A LYS 68 2 A PRO 155 A PRO 69 -0.09 A ASP 125 A ASP 39 3 A PRO 126 A PRO 40 0.14 A LYS 154 A LYS 68 3 A PRO 155 A PRO 69 -0.05 A ASP 125 A ASP 39 4 A PRO 126 A PRO 40 -0.03 A LYS 154 A LYS 68 4 A PRO 155 A PRO 69 -0.15 A ASP 125 A ASP 39 5 A PRO 126 A PRO 40 -0.07 A LYS 154 A LYS 68 5 A PRO 155 A PRO 69 0.10 A ASP 125 A ASP 39 6 A PRO 126 A PRO 40 -0.01 A LYS 154 A LYS 68 6 A PRO 155 A PRO 69 -0.16 A ASP 125 A ASP 39 7 A PRO 126 A PRO 40 0.13 A LYS 154 A LYS 68 7 A PRO 155 A PRO 69 0.00 A ASP 125 A ASP 39 8 A PRO 126 A PRO 40 0.07 A LYS 154 A LYS 68 8 A PRO 155 A PRO 69 -0.14 A ASP 125 A ASP 39 9 A PRO 126 A PRO 40 0.00 A LYS 154 A LYS 68 9 A PRO 155 A PRO 69 -0.12 A ASP 125 A ASP 39 10 A PRO 126 A PRO 40 0.04 A LYS 154 A LYS 68 10 A PRO 155 A PRO 69 -0.15 A ASP 125 A ASP 39 11 A PRO 126 A PRO 40 -0.02 A LYS 154 A LYS 68 11 A PRO 155 A PRO 69 -0.12 A ASP 125 A ASP 39 12 A PRO 126 A PRO 40 0.05 A LYS 154 A LYS 68 12 A PRO 155 A PRO 69 -0.14 A ASP 125 A ASP 39 13 A PRO 126 A PRO 40 -0.04 A LYS 154 A LYS 68 13 A PRO 155 A PRO 69 -0.10 TRI18_HUMAN UNP 1 87 O15344 87 164 2FFW 87 164 O15344 A 1 1 78 2 anti-parallel A LYS 132 A LYS 46 A CYS 134 A CYS 48 A VAL 139 A VAL 53 A TYR 141 A TYR 55 BINDING SITE FOR RESIDUE ZN A 200 A ZN 200 Software 4 BINDING SITE FOR RESIDUE ZN A 201 A ZN 201 Software 4 A CYS 119 A CYS 33 4 1_555 A CYS 122 A CYS 36 4 1_555 A CYS 142 A CYS 56 4 1_555 A CYS 145 A CYS 59 4 1_555 A CYS 134 A CYS 48 4 1_555 A CYS 137 A CYS 51 4 1_555 A HIS 150 A HIS 64 4 1_555 A HIS 159 A HIS 73 4 1_555