0.007321 0.000000 0.006151 0.000000 0.017124 0.000000 0.000000 0.000000 0.014228 0.000000 0.000000 0.000000 Otomo, C. Metlagel, Z. Takaesu, G. Otomo, T. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.000 130.040 90.000 136.601 58.399 91.802 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 Na 1 22.990 SODIUM ION non-polymer 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 US Nat.Struct.Mol.Biol. 1545-9993 20 59 66 10.1038/nsmb.2431 23202584 Structure of the human ATG12~ATG5 conjugate required for LC3 lipidation in autophagy. 2013 100 1 CCD 2009-11-06 ADSC QUANTUM 315 SINGLE WAVELENGTH M x-ray 1 1.0092 1.0 5.0.2 ALS 1.0092 SYNCHROTRON ALS BEAMLINE 5.0.2 10282.029 Ubiquitin-like protein ATG12 1 man polymer 32489.195 Autophagy protein 5 1 man polymer 4657.435 Autophagy-related protein 16-1 1 man polymer 22.990 SODIUM ION 1 syn non-polymer Autophagy-related protein 12, APG12-like APG5-like, Apoptosis-specific protein APG16-like 1 no no GSKKKIDILLKAVGDTPIMKTKKWAVERTRTIQGLIDFIKKFLKLVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKL VLHYCKSQAWG GSKKKIDILLKAVGDTPIMKTKKWAVERTRTIQGLIDFIKKFLKLVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKL VLHYCKSQAWG A polypeptide(L) no no MTDDKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVKKHFQKVMRQEDISEIWFEYEGTPLKWH YPIGLLFDLLASSSALPWNITVHFKSFPEKDLLHCPSKDAIEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQND RFDQFWAINRKLMEYPAEENGFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSAIDPEDGEKKNQVMI HGIEPMLETPLQWLSEHLSYPDNFLHISIIPQPTD MTDDKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVKKHFQKVMRQEDISEIWFEYEGTPLKWH YPIGLLFDLLASSSALPWNITVHFKSFPEKDLLHCPSKDAIEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQND RFDQFWAINRKLMEYPAEENGFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSAIDPEDGEKKNQVMI HGIEPMLETPLQWLSEHLSYPDNFLHISIIPQPTD B polypeptide(L) no no SHMPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLL SHMPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLL C 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 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 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 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 human sample APG12, APG12L, ATG12 9606 Homo sapiens 562 Escherichia coli BL21(DE3) plasmid pACYC Duet-1 human sample APG5L, ASP, ATG5 9606 Homo sapiens 562 Escherichia coli BL21(DE3) plasmid pACYC Duet-1 human sample APG16L, ATG16L1, UNQ9393/PRO34307 9606 Homo sapiens 562 Escherichia coli BL21(DE3) plasmid pET 1 2.96 58.38 VAPOR DIFFUSION, HANGING DROP 6.5 PROTEIN: 10 MG/ML in 0.01M HEPES pH 7.0, 0.3 M NaCl, 0.001 M DTT; RESERVOIR: 0.1M BICINE pH9.0, 0.2 M sodium phosphate dibasic, 18% PEG 3350, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP 293 software repository Initial release Database references Database references Refinement description 1 0 2012-12-05 1 1 2013-01-02 1 2 2013-01-16 1 3 2017-11-15 _software.classification _software.contact_author _software.contact_author_email _software.date _software.language _software.location _software.name _software.type _software.version The structure of the same complex in a different space group. RCSB Y RCSB 2012-07-31 REL REL NA SODIUM ION THERE IS AN ISOPEPTIDE LINKAGE BETWEEN RESIDUE GLY140 OF ATG12 AND LYS130 OF ATG5. THE ATG12~ATG5 CONJUGATE WAS GENERATED BY CO-EXPRESSING ATG12 AND ATG5 FROM PACYC DUET-1 AND ATG7 AND ATG10 FROM PCDF DUET-1 IN E. COLI NA 1 4 NA NA 301 B n 1 50 A n 2 51 A n 3 52 A LYS 53 n 4 LYS 53 A LYS 54 n 5 LYS 54 A ILE 55 n 6 ILE 55 A ASP 56 n 7 ASP 56 A ILE 57 n 8 ILE 57 A LEU 58 n 9 LEU 58 A LEU 59 n 10 LEU 59 A LYS 60 n 11 LYS 60 A ALA 61 n 12 ALA 61 A VAL 62 n 13 VAL 62 A GLY 63 n 14 GLY 63 A ASP 64 n 15 ASP 64 A THR 65 n 16 THR 65 A PRO 66 n 17 PRO 66 A ILE 67 n 18 ILE 67 A MET 68 n 19 MET 68 A LYS 69 n 20 LYS 69 A THR 70 n 21 THR 70 A LYS 71 n 22 LYS 71 A LYS 72 n 23 LYS 72 A TRP 73 n 24 TRP 73 A ALA 74 n 25 ALA 74 A VAL 75 n 26 VAL 75 A GLU 76 n 27 GLU 76 A ARG 77 n 28 ARG 77 A THR 78 n 29 THR 78 A ARG 79 n 30 ARG 79 A THR 80 n 31 THR 80 A ILE 81 n 32 ILE 81 A GLN 82 n 33 GLN 82 A GLY 83 n 34 GLY 83 A LEU 84 n 35 LEU 84 A ILE 85 n 36 ILE 85 A ASP 86 n 37 ASP 86 A PHE 87 n 38 PHE 87 A ILE 88 n 39 ILE 88 A LYS 89 n 40 LYS 89 A LYS 90 n 41 LYS 90 A PHE 91 n 42 PHE 91 A LEU 92 n 43 LEU 92 A LYS 93 n 44 LYS 93 A LEU 94 n 45 LEU 94 A VAL 95 n 46 VAL 95 A ALA 96 n 47 ALA 96 A SER 97 n 48 SER 97 A GLU 98 n 49 GLU 98 A GLN 99 n 50 GLN 99 A LEU 100 n 51 LEU 100 A PHE 101 n 52 PHE 101 A ILE 102 n 53 ILE 102 A TYR 103 n 54 TYR 103 A VAL 104 n 55 VAL 104 A ASN 105 n 56 ASN 105 A GLN 106 n 57 GLN 106 A SER 107 n 58 SER 107 A PHE 108 n 59 PHE 108 A ALA 109 n 60 ALA 109 A PRO 110 n 61 PRO 110 A SER 111 n 62 SER 111 A PRO 112 n 63 PRO 112 A ASP 113 n 64 ASP 113 A GLN 114 n 65 GLN 114 A GLU 115 n 66 GLU 115 A VAL 116 n 67 VAL 116 A GLY 117 n 68 GLY 117 A THR 118 n 69 THR 118 A LEU 119 n 70 LEU 119 A TYR 120 n 71 TYR 120 A GLU 121 n 72 GLU 121 A CYS 122 n 73 CYS 122 A PHE 123 n 74 PHE 123 A GLY 124 n 75 GLY 124 A SER 125 n 76 SER 125 A ASP 126 n 77 ASP 126 A GLY 127 n 78 GLY 127 A LYS 128 n 79 LYS 128 A LEU 129 n 80 LEU 129 A VAL 130 n 81 VAL 130 A LEU 131 n 82 LEU 131 A HIS 132 n 83 HIS 132 A TYR 133 n 84 TYR 133 A CYS 134 n 85 CYS 134 A LYS 135 n 86 LYS 135 A SER 136 n 87 SER 136 A GLN 137 n 88 GLN 137 A ALA 138 n 89 ALA 138 A TRP 139 n 90 TRP 139 A GLY 140 n 91 GLY 140 A n 1 1 B n 2 2 B ASP 3 n 3 ASP 3 B ASP 4 n 4 ASP 4 B LYS 5 n 5 LYS 5 B ASP 6 n 6 ASP 6 B VAL 7 n 7 VAL 7 B LEU 8 n 8 LEU 8 B ARG 9 n 9 ARG 9 B ASP 10 n 10 ASP 10 B VAL 11 n 11 VAL 11 B TRP 12 n 12 TRP 12 B PHE 13 n 13 PHE 13 B GLY 14 n 14 GLY 14 B ARG 15 n 15 ARG 15 B ILE 16 n 16 ILE 16 B PRO 17 n 17 PRO 17 B THR 18 n 18 THR 18 B CYS 19 n 19 CYS 19 B PHE 20 n 20 PHE 20 B THR 21 n 21 THR 21 B LEU 22 n 22 LEU 22 B TYR 23 n 23 TYR 23 B GLN 24 n 24 GLN 24 B ASP 25 n 25 ASP 25 B GLU 26 n 26 GLU 26 B ILE 27 n 27 ILE 27 B THR 28 n 28 THR 28 B GLU 29 n 29 GLU 29 B ARG 30 n 30 ARG 30 B GLU 31 n 31 GLU 31 B ALA 32 n 32 ALA 32 B GLU 33 n 33 GLU 33 B PRO 34 n 34 PRO 34 B TYR 35 n 35 TYR 35 B TYR 36 n 36 TYR 36 B LEU 37 n 37 LEU 37 B LEU 38 n 38 LEU 38 B LEU 39 n 39 LEU 39 B PRO 40 n 40 PRO 40 B ARG 41 n 41 ARG 41 B VAL 42 n 42 VAL 42 B SER 43 n 43 SER 43 B TYR 44 n 44 TYR 44 B LEU 45 n 45 LEU 45 B THR 46 n 46 THR 46 B LEU 47 n 47 LEU 47 B VAL 48 n 48 VAL 48 B THR 49 n 49 THR 49 B ASP 50 n 50 ASP 50 B LYS 51 n 51 LYS 51 B VAL 52 n 52 VAL 52 B LYS 53 n 53 LYS 53 B LYS 54 n 54 LYS 54 B HIS 55 n 55 HIS 55 B PHE 56 n 56 PHE 56 B GLN 57 n 57 GLN 57 B LYS 58 n 58 LYS 58 B VAL 59 n 59 VAL 59 B MET 60 n 60 MET 60 B ARG 61 n 61 ARG 61 B GLN 62 n 62 GLN 62 B GLU 63 n 63 GLU 63 B ASP 64 n 64 ASP 64 B ILE 65 n 65 ILE 65 B SER 66 n 66 SER 66 B GLU 67 n 67 GLU 67 B ILE 68 n 68 ILE 68 B TRP 69 n 69 TRP 69 B PHE 70 n 70 PHE 70 B GLU 71 n 71 GLU 71 B TYR 72 n 72 TYR 72 B GLU 73 n 73 GLU 73 B GLY 74 n 74 GLY 74 B THR 75 n 75 THR 75 B PRO 76 n 76 PRO 76 B LEU 77 n 77 LEU 77 B LYS 78 n 78 LYS 78 B TRP 79 n 79 TRP 79 B HIS 80 n 80 HIS 80 B TYR 81 n 81 TYR 81 B PRO 82 n 82 PRO 82 B ILE 83 n 83 ILE 83 B GLY 84 n 84 GLY 84 B LEU 85 n 85 LEU 85 B LEU 86 n 86 LEU 86 B PHE 87 n 87 PHE 87 B ASP 88 n 88 ASP 88 B LEU 89 n 89 LEU 89 B LEU 90 n 90 LEU 90 B ALA 91 n 91 ALA 91 B SER 92 n 92 SER 92 B SER 93 n 93 SER 93 B SER 94 n 94 SER 94 B ALA 95 n 95 ALA 95 B LEU 96 n 96 LEU 96 B PRO 97 n 97 PRO 97 B TRP 98 n 98 TRP 98 B ASN 99 n 99 ASN 99 B ILE 100 n 100 ILE 100 B THR 101 n 101 THR 101 B VAL 102 n 102 VAL 102 B HIS 103 n 103 HIS 103 B PHE 104 n 104 PHE 104 B LYS 105 n 105 LYS 105 B SER 106 n 106 SER 106 B PHE 107 n 107 PHE 107 B PRO 108 n 108 PRO 108 B GLU 109 n 109 GLU 109 B LYS 110 n 110 LYS 110 B ASP 111 n 111 ASP 111 B LEU 112 n 112 LEU 112 B LEU 113 n 113 LEU 113 B HIS 114 n 114 HIS 114 B CYS 115 n 115 CYS 115 B PRO 116 n 116 PRO 116 B SER 117 n 117 SER 117 B LYS 118 n 118 LYS 118 B ASP 119 n 119 ASP 119 B ALA 120 n 120 ALA 120 B ILE 121 n 121 ILE 121 B GLU 122 n 122 GLU 122 B ALA 123 n 123 ALA 123 B HIS 124 n 124 HIS 124 B PHE 125 n 125 PHE 125 B MET 126 n 126 MET 126 B SER 127 n 127 SER 127 B CYS 128 n 128 CYS 128 B MET 129 n 129 MET 129 B LYS 130 n 130 LYS 130 B GLU 131 n 131 GLU 131 B ALA 132 n 132 ALA 132 B ASP 133 n 133 ASP 133 B ALA 134 n 134 ALA 134 B LEU 135 n 135 LEU 135 B LYS 136 n 136 LYS 136 B HIS 137 n 137 HIS 137 B LYS 138 n 138 LYS 138 B SER 139 n 139 SER 139 B GLN 140 n 140 GLN 140 B VAL 141 n 141 VAL 141 B ILE 142 n 142 ILE 142 B ASN 143 n 143 ASN 143 B GLU 144 n 144 GLU 144 B MET 145 n 145 MET 145 B GLN 146 n 146 GLN 146 B LYS 147 n 147 LYS 147 B LYS 148 n 148 LYS 148 B ASP 149 n 149 ASP 149 B HIS 150 n 150 HIS 150 B LYS 151 n 151 LYS 151 B GLN 152 n 152 GLN 152 B LEU 153 n 153 LEU 153 B TRP 154 n 154 TRP 154 B MET 155 n 155 MET 155 B GLY 156 n 156 GLY 156 B LEU 157 n 157 LEU 157 B GLN 158 n 158 GLN 158 B ASN 159 n 159 ASN 159 B ASP 160 n 160 ASP 160 B ARG 161 n 161 ARG 161 B PHE 162 n 162 PHE 162 B ASP 163 n 163 ASP 163 B GLN 164 n 164 GLN 164 B PHE 165 n 165 PHE 165 B TRP 166 n 166 TRP 166 B ALA 167 n 167 ALA 167 B ILE 168 n 168 ILE 168 B ASN 169 n 169 ASN 169 B ARG 170 n 170 ARG 170 B LYS 171 n 171 LYS 171 B LEU 172 n 172 LEU 172 B MET 173 n 173 MET 173 B GLU 174 n 174 GLU 174 B TYR 175 n 175 TYR 175 B PRO 176 n 176 PRO 176 B ALA 177 n 177 ALA 177 B GLU 178 n 178 GLU 178 B GLU 179 n 179 GLU 179 B ASN 180 n 180 ASN 180 B GLY 181 n 181 GLY 181 B PHE 182 n 182 PHE 182 B ARG 183 n 183 ARG 183 B TYR 184 n 184 TYR 184 B ILE 185 n 185 ILE 185 B PRO 186 n 186 PRO 186 B PHE 187 n 187 PHE 187 B ARG 188 n 188 ARG 188 B ILE 189 n 189 ILE 189 B TYR 190 n 190 TYR 190 B GLN 191 n 191 GLN 191 B THR 192 n 192 THR 192 B THR 193 n 193 THR 193 B THR 194 n 194 THR 194 B GLU 195 n 195 GLU 195 B ARG 196 n 196 ARG 196 B PRO 197 n 197 PRO 197 B PHE 198 n 198 PHE 198 B ILE 199 n 199 ILE 199 B GLN 200 n 200 GLN 200 B LYS 201 n 201 LYS 201 B LEU 202 n 202 LEU 202 B PHE 203 n 203 PHE 203 B ARG 204 n 204 ARG 204 B PRO 205 n 205 PRO 205 B VAL 206 n 206 VAL 206 B ALA 207 n 207 ALA 207 B ALA 208 n 208 ALA 208 B ASP 209 n 209 ASP 209 B GLY 210 n 210 GLY 210 B GLN 211 n 211 GLN 211 B LEU 212 n 212 LEU 212 B HIS 213 n 213 HIS 213 B THR 214 n 214 THR 214 B LEU 215 n 215 LEU 215 B GLY 216 n 216 GLY 216 B ASP 217 n 217 ASP 217 B LEU 218 n 218 LEU 218 B LEU 219 n 219 LEU 219 B LYS 220 n 220 LYS 220 B GLU 221 n 221 GLU 221 B VAL 222 n 222 VAL 222 B CYS 223 n 223 CYS 223 B PRO 224 n 224 PRO 224 B SER 225 n 225 SER 225 B ALA 226 n 226 ALA 226 B ILE 227 n 227 ILE 227 B n 228 228 B n 229 229 B n 230 230 B n 231 231 B n 232 232 B n 233 233 B n 234 234 B LYS 235 n 235 LYS 235 B ASN 236 n 236 ASN 236 B GLN 237 n 237 GLN 237 B VAL 238 n 238 VAL 238 B MET 239 n 239 MET 239 B ILE 240 n 240 ILE 240 B HIS 241 n 241 HIS 241 B GLY 242 n 242 GLY 242 B ILE 243 n 243 ILE 243 B GLU 244 n 244 GLU 244 B PRO 245 n 245 PRO 245 B MET 246 n 246 MET 246 B LEU 247 n 247 LEU 247 B GLU 248 n 248 GLU 248 B THR 249 n 249 THR 249 B PRO 250 n 250 PRO 250 B LEU 251 n 251 LEU 251 B GLN 252 n 252 GLN 252 B TRP 253 n 253 TRP 253 B LEU 254 n 254 LEU 254 B SER 255 n 255 SER 255 B GLU 256 n 256 GLU 256 B HIS 257 n 257 HIS 257 B LEU 258 n 258 LEU 258 B SER 259 n 259 SER 259 B TYR 260 n 260 TYR 260 B PRO 261 n 261 PRO 261 B ASP 262 n 262 ASP 262 B ASN 263 n 263 ASN 263 B PHE 264 n 264 PHE 264 B LEU 265 n 265 LEU 265 B HIS 266 n 266 HIS 266 B ILE 267 n 267 ILE 267 B SER 268 n 268 SER 268 B ILE 269 n 269 ILE 269 B ILE 270 n 270 ILE 270 B PRO 271 n 271 PRO 271 B GLN 272 n 272 GLN 272 B PRO 273 n 273 PRO 273 B THR 274 n 274 THR 274 B n 275 275 B n 1 8 C n 2 9 C MET 10 n 3 MET 10 C PRO 11 n 4 PRO 11 C ARG 12 n 5 ARG 12 C TRP 13 n 6 TRP 13 C LYS 14 n 7 LYS 14 C ARG 15 n 8 ARG 15 C HIS 16 n 9 HIS 16 C ILE 17 n 10 ILE 17 C SER 18 n 11 SER 18 C GLU 19 n 12 GLU 19 C GLN 20 n 13 GLN 20 C LEU 21 n 14 LEU 21 C ARG 22 n 15 ARG 22 C ARG 23 n 16 ARG 23 C ARG 24 n 17 ARG 24 C ASP 25 n 18 ASP 25 C ARG 26 n 19 ARG 26 C LEU 27 n 20 LEU 27 C GLN 28 n 21 GLN 28 C ARG 29 n 22 ARG 29 C GLN 30 n 23 GLN 30 C ALA 31 n 24 ALA 31 C PHE 32 n 25 PHE 32 C GLU 33 n 26 GLU 33 C GLU 34 n 27 GLU 34 C ILE 35 n 28 ILE 35 C ILE 36 n 29 ILE 36 C LEU 37 n 30 LEU 37 C GLN 38 n 31 GLN 38 C TYR 39 n 32 TYR 39 C ASN 40 n 33 ASN 40 C LYS 41 n 34 LYS 41 C LEU 42 n 35 LEU 42 C LEU 43 n 36 LEU 43 C 3.6238 2.7977 0.6736 3.2452 0.8570 6.0662 -0.9306 1.6393 1.6291 -1.4487 0.1603 1.6733 -0.2069 -1.6583 0.8281 0.8731 0.5559 0.1543 1.5639 0.5159 1.5721 refined 131.9098 14.7466 14.7212 X-RAY DIFFRACTION 7.2938 -3.3147 -4.1637 3.7272 -0.7557 5.8908 0.3887 1.6713 -0.3986 -0.4764 -0.5727 0.9357 -0.0244 -2.8717 0.0498 0.6716 0.1147 -0.2917 1.8883 -0.1696 1.1547 refined 129.9928 6.0654 15.7652 X-RAY DIFFRACTION 6.5054 4.9979 -2.7965 3.8222 -1.8131 3.2700 -1.4633 0.6937 -2.0906 -1.9660 1.1251 -0.2622 1.6633 0.6728 0.3787 1.1311 -0.1251 0.0261 1.3008 -0.1878 1.5979 refined 133.6834 -2.2909 12.3846 X-RAY DIFFRACTION 9.7311 7.6172 -0.5108 8.8877 2.8401 3.3538 -0.3554 1.6975 0.9582 -1.0900 0.8627 0.3778 -1.1970 0.2940 -0.6039 0.9782 0.2414 -0.1224 1.6464 0.1838 1.2002 refined 140.0424 11.9384 13.0095 X-RAY DIFFRACTION 3.7752 5.6888 -0.1132 9.6962 1.3887 2.3201 0.0168 2.3705 0.7689 -1.8665 0.8880 0.5925 -0.1597 -1.8648 0.0609 1.5600 0.3194 -0.2346 2.3461 -0.1557 1.7240 refined 140.1161 -0.3734 4.6258 X-RAY DIFFRACTION 7.0139 -1.4957 1.3425 6.3927 -2.9860 7.1094 0.2765 0.2747 -1.2077 -0.3156 -0.0774 0.9176 0.7319 -0.3263 0.0475 0.6411 -0.0160 0.0173 0.9328 -0.2245 0.9535 refined 158.9248 -6.7631 28.9032 X-RAY DIFFRACTION 4.2388 -2.2128 0.0823 3.7026 -3.8407 6.3635 0.3081 3.5878 -0.2294 -0.8773 -0.0315 0.2101 0.2615 1.0743 -0.4028 1.1155 0.0125 -0.1655 2.5459 -0.2036 0.9501 refined 157.4494 3.1499 6.6807 X-RAY DIFFRACTION 6.8884 -0.0630 1.7123 4.0508 1.5365 2.8113 -0.4282 1.7108 2.1212 -0.3057 0.1234 0.0233 -0.6817 0.4777 0.2267 0.8807 -0.0844 -0.0671 0.9552 0.4015 1.0515 refined 158.9984 18.7852 20.0348 X-RAY DIFFRACTION 7.7345 -4.1351 4.4435 3.2343 -2.2397 4.4717 0.0006 0.9326 1.0446 -0.1225 -0.4194 -0.4746 -0.1523 0.8516 0.7474 0.7444 -0.0613 0.2367 1.4281 0.0818 0.7622 refined 175.8442 3.7178 25.6581 X-RAY DIFFRACTION A 53 A 61 X-RAY DIFFRACTION 1 chain 'A' and (resseq 53:61) A 62 A 91 X-RAY DIFFRACTION 2 chain 'A' and (resseq 62:91) A 92 A 104 X-RAY DIFFRACTION 3 chain 'A' and (resseq 92:104) A 105 A 134 X-RAY DIFFRACTION 4 chain 'A' and (resseq 105:134) A 135 A 140 X-RAY DIFFRACTION 5 chain 'A' and (resseq 135:140) B 3 B 117 X-RAY DIFFRACTION 6 chain 'B' and (resseq 3:117) B 118 B 173 X-RAY DIFFRACTION 7 chain 'B' and (resseq 118:173) B 174 B 274 X-RAY DIFFRACTION 8 chain 'B' and (resseq 174:274) C 10 C 43 X-RAY DIFFRACTION 9 chain 'C' and (resseq 10:43) author_defined_assembly 3 trimeric B ALA 95 B O ALA 95 1_555 B NA 301 D NA NA 1_555 B ASN 99 B OD1 ASN 99 1_555 152.4 B ALA 95 B O ALA 95 1_555 B NA 301 D NA NA 1_555 B PRO 97 B O PRO 97 1_555 82.7 B ASN 99 B OD1 ASN 99 1_555 B NA 301 D NA NA 1_555 B PRO 97 B O PRO 97 1_555 92.8 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 O TRP 73 A O TRP 24 A N ILE 57 A N ILE 8 A N LEU 58 A N LEU 9 A O LEU 131 A O LEU 82 A O CYS 134 A O CYS 85 A N PHE 101 A N PHE 52 B O TYR 35 B O TYR 35 B N PHE 20 B N PHE 20 B N PRO 17 B N PRO 17 B O TRP 98 B O TRP 98 B O THR 101 B O THR 101 B N GLU 71 B N GLU 71 B N TYR 72 B N TYR 72 B O THR 75 B O THR 75 B N TYR 190 B N TYR 190 B O ILE 267 B O ILE 267 B O ILE 270 B O ILE 270 B N GLN 237 B N GLN 237 1 A GLY 50 A GLY 1 1 Y 1 A SER 51 A SER 2 1 Y 1 A LYS 52 A LYS 3 1 Y 1 B MET 1 B MET 1 1 Y 1 B THR 2 B THR 2 1 Y 1 B ASP 228 B ASP 228 1 Y 1 B PRO 229 B PRO 229 1 Y 1 B GLU 230 B GLU 230 1 Y 1 B ASP 231 B ASP 231 1 Y 1 B GLY 232 B GLY 232 1 Y 1 B GLU 233 B GLU 233 1 Y 1 B LYS 234 B LYS 234 1 Y 1 B ASP 275 B ASP 275 1 Y 1 C SER 8 C SER 1 1 Y 1 C HIS 9 C HIS 2 1 Y 1 A SER 107 -133.91 -60.10 1 B SER 43 -107.38 -164.54 1 B SER 66 -146.50 -144.37 1 B PHE 104 -140.11 -38.90 1 B GLN 191 -166.06 118.20 1 B CYS 223 -156.28 65.91 1 B ALA 226 -159.42 17.75 1 B LEU 265 -101.67 75.59 1 B PRO 273 -61.62 -163.49 1 C GLN 28 -108.70 -67.83 283.770 138.7687 64.410 0.2540 0.2146 0.2186 2.8750 36.2240 1263 12465 10.1300 97.4100 1.000 1.000 0.7275 0.3200 RANDOM 1 1.340 MOLECULAR REPLACEMENT 32.8400 0.8000 1.0000 ML FLAT BULK SOLVENT MODEL 2.8750 36.2240 0 3227 1 0 3226 0.006 3316 0.510 4482 0.037 479 0.003 566 9.914 1256 0.4281 0.3301 2.9903 126 1081 1207 9 86.0000 0.3126 0.3040 3.1264 136 1222 1358 9 97.0000 0.2864 0.2506 3.2911 141 1257 1398 9 98.0000 0.2919 0.2514 3.4971 133 1253 1386 9 99.0000 0.3062 0.2354 3.7669 145 1258 1403 9 99.0000 0.2620 0.2207 4.1455 141 1269 1410 9 99.0000 0.2081 0.1802 4.7442 142 1267 1409 9 100.0000 0.2265 0.2030 5.9729 148 1287 1435 9 100.0000 0.2450 0.2006 36.2267 151 1308 1459 9 99.0000 2.8750 50.000 4GDL 12548 0.056 1.044 1 14.900 4.400 98.600 0.541 2.900 3.000 1174 1.042 1 3.700 92.400 0.467 3.000 3.120 1253 1.092 1 4.300 98.400 0.287 3.120 3.270 1232 1.139 1 4.500 99.000 0.208 3.270 3.440 1253 1.122 1 4.600 99.300 0.138 3.440 3.650 1256 1.092 1 4.600 99.600 0.092 3.650 3.940 1268 0.979 1 4.500 99.700 0.065 3.940 4.330 1244 0.929 1 4.500 99.500 0.055 4.330 4.960 1285 0.971 1 4.500 99.700 0.046 4.960 6.240 1281 0.955 1 4.300 99.800 0.031 6.240 50.000 1302 1.118 1 4.400 98.900 data reduction Zbyszek Otwinowski hkl@hkl-xray.com http://www.hkl-xray.com/ DENZO package data scaling Zbyszek Otwinowski hkl@hkl-xray.com http://www.hkl-xray.com/ SCALEPACK package refinement Paul D. Adams PDAdams@lbl.gov C++ http://www.phenix-online.org/ PHENIX package 1.8_1069 data extraction PDB deposit@deposit.rcsb.org April 22, 2011 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.11 Atg12, Atg5, Atg16L1 Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1 1 N N 2 N N 3 N N 4 N N A THR 80 A THR 31 HELX_P A LEU 92 A LEU 43 1 1 13 A GLU 115 A GLU 66 HELX_P A GLY 124 A GLY 75 1 2 10 B ASP 4 B ASP 4 HELX_P B PHE 13 B PHE 13 1 3 10 B TYR 44 B TYR 44 HELX_P B VAL 48 B VAL 48 5 4 5 B ASP 50 B ASP 50 HELX_P B LYS 58 B LYS 58 1 5 9 B PRO 82 B PRO 82 HELX_P B ALA 91 B ALA 91 1 6 10 B SER 117 B SER 117 HELX_P B LYS 138 B LYS 138 1 7 22 B GLN 146 B GLN 146 HELX_P B ASN 159 B ASN 159 1 8 14 B ARG 161 B ARG 161 HELX_P B ARG 170 B ARG 170 1 9 10 B LYS 171 B LYS 171 HELX_P B GLU 174 B GLU 174 5 10 4 B THR 214 B THR 214 HELX_P B CYS 223 B CYS 223 1 11 10 B PRO 250 B PRO 250 HELX_P B LEU 258 B LEU 258 1 12 9 C PRO 11 C PRO 4 HELX_P C GLN 28 C GLN 21 1 13 18 C GLN 28 C GLN 21 HELX_P C LEU 42 C LEU 35 1 14 15 metalc 2.245 B ALA 95 B O ALA 95 1_555 B NA 301 D NA NA 1_555 metalc 2.407 B ASN 99 B OD1 ASN 99 1_555 B NA 301 D NA NA 1_555 metalc 2.680 B PRO 97 B O PRO 97 1_555 B NA 301 D NA NA 1_555 covale 1.329 A GLY 140 A C GLY 91 1_555 B LYS 130 B NZ LYS 130 1_555 PROTEIN BINDING protein-protein conjugate, protein-protein complex, ubiquitin-like protein, autophagy, E3 ligase, ubiquitin-like fold, structural protein, isopeptide bond, Cytoplasm and autophagosomal membranes, protein binding A GLY 63 A GLY 14 1 A ASP 64 A ASP 15 2.84 B LEU 96 B LEU 96 1 B PRO 97 B PRO 97 -4.26 ATG12_HUMAN UNP 1 52 O94817 KKKIDILLKAVGDTPIMKTKKWAVERTRTIQGLIDFIKKFLKLVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKLVL HYCKSQAWG ATG5_HUMAN UNP 2 1 Q9H1Y0 MTDDKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVKKHFQKVMRQEDISEIWFEYEGTPLKWH YPIGLLFDLLASSSALPWNITVHFKSFPEKDLLHCPSKDAIEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQND RFDQFWAINRKLMEYPAEENGFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSAIDPEDGEKKNQVMI HGIEPMLETPLQWLSEHLSYPDNFLHISIIPQPTD A16L1_HUMAN UNP 3 11 Q676U5 PRWKRHISEQLRRRDRLQRQAFEEIILQYNKLL 52 140 4GDL 52 140 O94817 A 1 3 91 1 275 4GDL 1 275 Q9H1Y0 B 2 1 275 11 43 4GDL 11 43 Q676U5 C 3 4 36 1 EXPRESSION TAG GLY 50 4GDL A O94817 UNP 1 1 EXPRESSION TAG SER 51 4GDL A O94817 UNP 2 3 EXPRESSION TAG SER 8 4GDL C Q676U5 UNP 1 3 EXPRESSION TAG HIS 9 4GDL C Q676U5 UNP 2 3 EXPRESSION TAG MET 10 4GDL C Q676U5 UNP 3 4 5 3 anti-parallel parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel parallel anti-parallel A LYS 72 A LYS 23 A GLU 76 A GLU 27 A LYS 54 A LYS 5 A ALA 61 A ALA 12 A LYS 128 A LYS 79 A CYS 134 A CYS 85 A PHE 101 A PHE 52 A VAL 104 A VAL 55 B TYR 35 B TYR 35 B PRO 40 B PRO 40 B ARG 15 B ARG 15 B LEU 22 B LEU 22 B TRP 98 B TRP 98 B HIS 103 B HIS 103 B TRP 69 B TRP 69 B TYR 72 B TYR 72 B THR 75 B THR 75 B PRO 76 B PRO 76 B PHE 187 B PHE 187 B TYR 190 B TYR 190 B LEU 265 B LEU 265 B PRO 271 B PRO 271 B ASN 236 B ASN 236 B MET 239 B MET 239 BINDING SITE FOR RESIDUE NA B 301 Software 3 B ALA 95 B ALA 95 3 1_555 B PRO 97 B PRO 97 3 1_555 B ASN 99 B ASN 99 3 1_555 5 C 1 2 1