1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Yamasaki, K. Allen, M.D. Ohme-Takagi, M. Tateno, M. Suzuki, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA 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 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 EMBO J. EMJODG 0897 0261-4189 17 5484 5496 10.1093/emboj/17.18.5484 9736626 A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA. 1998 10.2210/pdb1gcc/pdb pdb_00001gcc 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3319.175 DNA (5'-D(*TP*AP*GP*CP*CP*GP*CP*CP*AP*GP*C)-3') 1 syn polymer 3390.209 DNA (5'-D(*GP*CP*TP*GP*GP*CP*GP*GP*CP*TP*A)-3') 1 syn polymer 7247.318 ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 1 GCC-BOX BINDING DOMAIN 1 man polymer no no (DT)(DA)(DG)(DC)(DC)(DG)(DC)(DC)(DA)(DG)(DC) TAGCCGCCAGC B polydeoxyribonucleotide no no (DG)(DC)(DT)(DG)(DG)(DC)(DG)(DG)(DC)(DT)(DA) GCTGGCGGCTA C polydeoxyribonucleotide no no KHYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPLRV KHYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPLRV 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 n n n n n n n thale cress Arabidopsis Escherichia Escherichia coli sample DNA-BINDING DOMAIN OF ATERF1; BL21 ATERF1 3702 Arabidopsis thaliana 469008 Escherichia coli BL21(DE3) BL21 (DE3) PAF104 0.405 1 20 B 3 C 24 -4.445 B_DT3:DA24_C 1 -7.228 0.063 -0.214 -0.200 -5.458 1 20 B 4 C 23 -4.874 B_DA4:DT23_C 2 -1.154 0.079 -0.343 -0.194 3.485 1 19 B 5 C 22 -2.008 B_DG5:DC22_C 3 -4.366 -0.777 0.105 -0.324 -3.044 1 19 B 6 C 21 -6.612 B_DC6:DG21_C 4 -7.903 0.192 0.533 -0.247 0.809 1 19 B 7 C 20 -3.302 B_DC7:DG20_C 5 -10.288 0.408 0.553 -0.314 5.644 1 19 B 8 C 19 -3.343 B_DG8:DC19_C 6 -2.602 -0.174 0.228 -0.152 -0.231 1 19 B 9 C 18 -3.747 B_DC9:DG18_C 7 -2.275 0.319 -0.087 -0.185 -6.658 1 19 B 10 C 17 -0.529 B_DC10:DG17_C 8 -6.688 0.349 0.314 -0.187 3.906 1 20 B 11 C 16 -6.134 B_DA11:DT16_C 9 -13.318 0.230 0.627 -0.230 7.256 1 19 B 12 C 15 -3.997 B_DG12:DC15_C 10 -6.167 -0.333 1.091 -0.405 2.333 1 19 B 13 C 14 -1.197 B_DC13:DG14_C 11 4.218 0.904 0.307 -0.413 3.372 40.875 B B 3 4 -0.817 C C 24 23 3.376 -0.571 -0.107 0.284 BB_DT3DA4:DT23DA24_CC 1 0.136 -0.195 40.871 0.471 0.168 2.981 28.127 B B 4 5 -8.901 C C 23 22 3.009 -4.303 0.108 -0.194 BB_DA4DG5:DC22DT23_CC 2 -2.605 5.389 27.682 0.532 -0.787 3.297 42.551 B B 5 6 -1.353 C C 22 21 3.278 -0.980 -0.334 -0.093 BB_DG5DC6:DG21DC22_CC 3 -4.657 6.430 42.296 -0.028 -0.014 3.092 35.326 B B 6 7 -3.513 C C 21 20 3.063 -2.127 -0.289 -0.351 BB_DC6DC7:DG20DG21_CC 4 -3.752 6.198 35.070 -0.282 -0.047 2.985 20.119 B B 7 8 3.082 C C 20 19 3.013 1.075 0.058 -0.295 BB_DC7DG8:DC19DG20_CC 5 1.895 -5.435 20.002 -1.300 0.637 3.326 38.883 B B 8 9 3.094 C C 19 18 3.338 2.056 0.344 -0.505 BB_DG8DC9:DG18DC19_CC 6 3.869 -5.824 38.644 -1.014 -0.037 3.404 34.356 B B 9 10 -3.102 C C 18 17 3.395 -1.831 -0.200 -0.156 BB_DC9DC10:DG17DG18_CC 7 -1.720 2.914 34.267 0.034 0.059 2.911 34.809 B B 10 11 -10.083 C C 17 16 2.946 -5.999 -0.388 0.081 BB_DC10DA11:DT16DG17_CC 8 -2.509 4.216 34.215 0.961 0.304 2.986 34.185 B B 11 12 -12.508 C C 16 15 3.029 -7.280 0.395 -0.462 BB_DA11DG12:DC15DT16_CC 9 -4.358 7.487 33.146 0.289 -1.315 3.570 43.031 B B 12 13 -4.476 C C 15 14 3.556 -3.276 0.137 -0.345 BB_DG12DC13:DG14DC15_CC 10 3.951 -5.398 42.738 -0.116 0.240 database_2 pdbx_database_status pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Other 1 0 1999-03-23 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_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_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id Y BNL 1998-03-13 REL REL SIGNALS DUE TO PROTEINS WERE OBTAINED BY NOESY, TOCSY, DQF-COSY FOR UNLABELED SAMPLE AND 1H-15N HSQC, 3D 1H-15N NOESY-HMQC AND 3D 1H-15N TOCSY-HMQC FOR THE SAMPLE WITH 15N-LABELED PROTEIN. SIGNALS DUE TO DNA WERE OBTAINED BY NOESY, TOCSY, AND DQF-COSY FOR UNLABELED SAMPLE AND 13C,15N-FILTERED NOESY FOR SAMPLE WITH 13C, 15N-LABELED PROTEIN. INTERMOLECULAR NOES WERE IDENTIFIED USING NOESY SPECTRA INCLUDING THOSE WITH AND WITHOUT 13C- OR 15N-DECOUPLING FOR SAMPLE WITH 13C,15N-LABELED PROTEIN. 1 1 NOESY TOCSY DQF-COSY 1H-15N HSQC 3D 1H-15N NOESY-HMQC 3D 1H-15N TOCSY-HMQC 13C 15N-FILTERED NOESY 90 mM 6.0 1 ATMOSPHERE 298 K SEE REMARK 210 OTHER PROGRAMS USED: AMBER 4.1 AUTHORS: PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM III, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN SIMULATED ANNEALING PROTOCOL IN X-PLOR 3.1 WAS CARRIED OUT TO OBTAIN 25 STRUCTURES. MINIMIZED MEAN STRUCTURE OF THEM WAS FURTHER REVISED BY A 300 PS RESTRAINED MOLECULAR DYNAMICAL CALCULATION IN THE PRESENCE OF APPROXIMATELY 5000 TIP3P WATER MOLSCULES, USING CORNELL FORCE FIELD IN AMBER 4.1. THE MEAN CO-ORDINATE OF 200 STRUCTURES OBTAINED AFTER THE EQUILIBRIUM (100 PS) WAS ENERGY-MINIMIZED. POTASIUM PHOSPHATE BRUNGER refinement X-PLOR 3.1 structure solution X-PLOR 3.1 structure solution Amber 4.1 750 Bruker DMX750 500 Bruker DMX500 T 3 n 1 DT 3 B A 4 n 2 DA 4 B G 5 n 3 DG 5 B C 6 n 4 DC 6 B C 7 n 5 DC 7 B G 8 n 6 DG 8 B C 9 n 7 DC 9 B C 10 n 8 DC 10 B A 11 n 9 DA 11 B G 12 n 10 DG 12 B C 13 n 11 DC 13 B G 14 n 1 DG 14 C C 15 n 2 DC 15 C T 16 n 3 DT 16 C G 17 n 4 DG 17 C G 18 n 5 DG 18 C C 19 n 6 DC 19 C G 20 n 7 DG 20 C G 21 n 8 DG 21 C C 22 n 9 DC 22 C T 23 n 10 DT 23 C A 24 n 11 DA 24 C LYS 144 n 1 LYS 144 A HIS 145 n 2 HIS 145 A TYR 146 n 3 TYR 146 A ARG 147 n 4 ARG 147 A GLY 148 n 5 GLY 148 A VAL 149 n 6 VAL 149 A ARG 150 n 7 ARG 150 A GLN 151 n 8 GLN 151 A ARG 152 n 9 ARG 152 A PRO 153 n 10 PRO 153 A TRP 154 n 11 TRP 154 A GLY 155 n 12 GLY 155 A LYS 156 n 13 LYS 156 A PHE 157 n 14 PHE 157 A ALA 158 n 15 ALA 158 A ALA 159 n 16 ALA 159 A GLU 160 n 17 GLU 160 A ILE 161 n 18 ILE 161 A ARG 162 n 19 ARG 162 A ASP 163 n 20 ASP 163 A PRO 164 n 21 PRO 164 A ALA 165 n 22 ALA 165 A LYS 166 n 23 LYS 166 A ASN 167 n 24 ASN 167 A GLY 168 n 25 GLY 168 A ALA 169 n 26 ALA 169 A ARG 170 n 27 ARG 170 A VAL 171 n 28 VAL 171 A TRP 172 n 29 TRP 172 A LEU 173 n 30 LEU 173 A GLY 174 n 31 GLY 174 A THR 175 n 32 THR 175 A PHE 176 n 33 PHE 176 A GLU 177 n 34 GLU 177 A THR 178 n 35 THR 178 A ALA 179 n 36 ALA 179 A GLU 180 n 37 GLU 180 A ASP 181 n 38 ASP 181 A ALA 182 n 39 ALA 182 A ALA 183 n 40 ALA 183 A LEU 184 n 41 LEU 184 A ALA 185 n 42 ALA 185 A TYR 186 n 43 TYR 186 A ASP 187 n 44 ASP 187 A ARG 188 n 45 ARG 188 A ALA 189 n 46 ALA 189 A ALA 190 n 47 ALA 190 A PHE 191 n 48 PHE 191 A ARG 192 n 49 ARG 192 A MET 193 n 50 MET 193 A ARG 194 n 51 ARG 194 A GLY 195 n 52 GLY 195 A SER 196 n 53 SER 196 A ARG 197 n 54 ARG 197 A ALA 198 n 55 ALA 198 A LEU 199 n 56 LEU 199 A LEU 200 n 57 LEU 200 A ASN 201 n 58 ASN 201 A PHE 202 n 59 PHE 202 A PRO 203 n 60 PRO 203 A LEU 204 n 61 LEU 204 A ARG 205 n 62 ARG 205 A VAL 206 n 63 VAL 206 A author_defined_assembly 3 trimeric 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 ARG 150 C O ARG 7 A N ALA 158 C N ALA 15 A O PHE 157 C O PHE 14 A N PHE 176 C N PHE 33 1 B DC 7 0.075 SIDE CHAIN 1 C DT 16 0.068 SIDE CHAIN 1 C DG 17 0.064 SIDE CHAIN 1 C DC 19 0.089 SIDE CHAIN 1 C DC 22 0.071 SIDE CHAIN 1 A ARG 147 0.137 SIDE CHAIN 1 A ARG 170 0.076 SIDE CHAIN 1 A TYR 186 0.096 SIDE CHAIN 1 3.73 0.60 106.00 109.73 B B B O4' C4' C3' DC DC DC 6 6 6 N 1 3.70 0.60 106.00 109.70 B B B O4' C4' C3' DC DC DC 10 10 10 N 1 1.99 0.30 108.30 110.29 C C C O4' C1' N1 DC DC DC 15 15 15 N 1 4.00 0.60 106.00 110.00 C C C O4' C4' C3' DT DT DT 16 16 16 N 1 2.05 0.30 108.30 110.35 C C C O4' C1' N9 DG DG DG 18 18 18 N 1 2.10 0.30 108.30 110.40 C C C O4' C1' N9 DG DG DG 20 20 20 N 1 3.71 0.60 106.00 109.71 C C C O4' C4' C3' DC DC DC 22 22 22 N 1 4.08 0.50 120.30 124.38 A A A NE CZ NH1 ARG ARG ARG 147 147 147 N 1 3.31 0.50 120.30 123.61 A A A NE CZ NH1 ARG ARG ARG 150 150 150 N 1 -3.36 0.50 120.30 116.94 A A A NE CZ NH2 ARG ARG ARG 150 150 150 N 1 A ARG 197 51.83 74.04 model building X-PLOR 3.1 refinement X-PLOR 3.1 phasing X-PLOR 3.1 SOLUTION NMR STRUCTURE OF THE COMPLEX OF GCC-BOX BINDING DOMAIN OF ATERF1 AND GCC-BOX DNA, MINIMIZED AVERAGE STRUCTURE 1 N N 2 N N 3 N N A ALA 179 C ALA 36 HELX_P A ARG 194 C ARG 51 1 1 16 covale 1.342 both A LYS 144 C C LYS 1 1_555 A HIS 145 C N HIS 2 1_555 covale 1.338 both A HIS 145 C C HIS 2 1_555 A TYR 146 C N TYR 3 1_555 hydrog WATSON-CRICK B DT 3 A N3 DT 1 1_555 C DA 24 B N1 DA 11 1_555 hydrog WATSON-CRICK B DT 3 A O4 DT 1 1_555 C DA 24 B N6 DA 11 1_555 hydrog WATSON-CRICK B DA 4 A N1 DA 2 1_555 C DT 23 B N3 DT 10 1_555 hydrog WATSON-CRICK B DA 4 A N6 DA 2 1_555 C DT 23 B O4 DT 10 1_555 hydrog WATSON-CRICK B DG 5 A N1 DG 3 1_555 C DC 22 B N3 DC 9 1_555 hydrog WATSON-CRICK B DG 5 A N2 DG 3 1_555 C DC 22 B O2 DC 9 1_555 hydrog WATSON-CRICK B DG 5 A O6 DG 3 1_555 C DC 22 B N4 DC 9 1_555 hydrog WATSON-CRICK B DC 6 A N3 DC 4 1_555 C DG 21 B N1 DG 8 1_555 hydrog WATSON-CRICK B DC 6 A N4 DC 4 1_555 C DG 21 B O6 DG 8 1_555 hydrog WATSON-CRICK B DC 6 A O2 DC 4 1_555 C DG 21 B N2 DG 8 1_555 hydrog WATSON-CRICK B DC 7 A N3 DC 5 1_555 C DG 20 B N1 DG 7 1_555 hydrog WATSON-CRICK B DC 7 A N4 DC 5 1_555 C DG 20 B O6 DG 7 1_555 hydrog WATSON-CRICK B DC 7 A O2 DC 5 1_555 C DG 20 B N2 DG 7 1_555 hydrog WATSON-CRICK B DG 8 A N1 DG 6 1_555 C DC 19 B N3 DC 6 1_555 hydrog WATSON-CRICK B DG 8 A N2 DG 6 1_555 C DC 19 B O2 DC 6 1_555 hydrog WATSON-CRICK B DG 8 A O6 DG 6 1_555 C DC 19 B N4 DC 6 1_555 hydrog WATSON-CRICK B DC 9 A N3 DC 7 1_555 C DG 18 B N1 DG 5 1_555 hydrog WATSON-CRICK B DC 9 A N4 DC 7 1_555 C DG 18 B O6 DG 5 1_555 hydrog WATSON-CRICK B DC 9 A O2 DC 7 1_555 C DG 18 B N2 DG 5 1_555 hydrog WATSON-CRICK B DC 10 A N3 DC 8 1_555 C DG 17 B N1 DG 4 1_555 hydrog WATSON-CRICK B DC 10 A N4 DC 8 1_555 C DG 17 B O6 DG 4 1_555 hydrog WATSON-CRICK B DC 10 A O2 DC 8 1_555 C DG 17 B N2 DG 4 1_555 hydrog WATSON-CRICK B DA 11 A N1 DA 9 1_555 C DT 16 B N3 DT 3 1_555 hydrog WATSON-CRICK B DA 11 A N6 DA 9 1_555 C DT 16 B O4 DT 3 1_555 hydrog WATSON-CRICK B DG 12 A N1 DG 10 1_555 C DC 15 B N3 DC 2 1_555 hydrog WATSON-CRICK B DG 12 A N2 DG 10 1_555 C DC 15 B O2 DC 2 1_555 hydrog WATSON-CRICK B DG 12 A O6 DG 10 1_555 C DC 15 B N4 DC 2 1_555 hydrog WATSON-CRICK B DC 13 A N3 DC 11 1_555 C DG 14 B N1 DG 1 1_555 hydrog WATSON-CRICK B DC 13 A N4 DC 11 1_555 C DG 14 B O6 DG 1 1_555 hydrog WATSON-CRICK B DC 13 A O2 DC 11 1_555 C DG 14 B N2 DG 1 1_555 TRANSCRIPTION/DNA TRANSCRIPTION FACTOR, PROTEIN-DNA COMPLEX, ETHYLENE INDUCIBLE, COMPLEX (TRANSCRIPTION FACTOR-DNA), TRANSCRIPTION-DNA COMPLEX ERF1A_ARATH UNP 3 O80337 1GCC PDB 1 1GCC 1GCC PDB 2 1GCC 144 206 1GCC 144 206 O80337 A 1 1 63 3 13 1GCC 3 13 1GCC B 2 1 11 14 24 1GCC 14 24 1GCC C 3 1 11 3 anti-parallel anti-parallel A VAL 149 C VAL 6 A ARG 152 C ARG 9 A LYS 156 C LYS 13 A ASP 163 C ASP 20 A ALA 169 C ALA 26 A PHE 176 C PHE 33 1 P 1