data_9AAM # _entry.id 9AAM # loop_ _atom_type.symbol C H MG N O P S ZN # loop_ _audit_author.name _audit_author.pdbx_ordinal "Wu, P." 1 "Allain, F.H.-T." 2 # loop_ _audit_conform.dict_location _audit_conform.dict_name _audit_conform.dict_version https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_ihm_ext.dic mmcif_ihm_ext.dic 1.28 http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic mmcif_pdbx.dic 5.403 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 9AAM _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2025-06-30 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2026-03-25 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 9AAM pdb_00009aam 10.2210/pdb9aam/pdb # loop_ _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.type "C3 H7 N O2" 89.094 ALA . ALANINE . "L-peptide linking" "C6 H15 N4 O2 1" 175.212 ARG . ARGININE . "L-peptide linking" "C4 H8 N2 O3" 132.119 ASN . ASPARAGINE . "L-peptide linking" "C4 H7 N O4" 133.103 ASP . "ASPARTIC ACID" . "L-peptide linking" "C10 H16 N5 O13 P3" 507.182 ATP . "ADENOSINE-5'-TRIPHOSPHATE" . non-polymer "C3 H7 N O2 S" 121.154 CYS . CYSTEINE . "L-peptide linking" "C10 H14 N5 O6 P" 331.225 DA . "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" . "DNA linking" "C9 H14 N3 O7 P" 307.199 DC . "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" . "DNA linking" "C10 H14 N5 O7 P" 347.224 DG . "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" . "DNA linking" "C10 H16 N5 O13 P3" 507.182 DGT . "2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE" . non-polymer "C10 H15 N2 O8 P" 322.21 DT . "THYMIDINE-5'-MONOPHOSPHATE" . "DNA linking" "C5 H10 N2 O3" 146.146 GLN . GLUTAMINE . "L-peptide linking" "C5 H9 N O4" 147.13 GLU . "GLUTAMIC ACID" . "L-peptide linking" "C2 H5 N O2" 75.067 GLY . GLYCINE . "peptide linking" "C6 H10 N3 O2 1" 156.165 HIS . HISTIDINE . "L-peptide linking" "C6 H13 N O2" 131.175 ILE . ISOLEUCINE . "L-peptide linking" "C6 H13 N O2" 131.175 LEU . LEUCINE . "L-peptide linking" "C6 H15 N2 O2 1" 147.198 LYS . LYSINE . "L-peptide linking" "C5 H11 N O2 S" 149.208 MET . METHIONINE . "L-peptide linking" "Mg 2" 24.305 MG . "MAGNESIUM ION" . non-polymer "C9 H11 N O2" 165.192 PHE . PHENYLALANINE . "L-peptide linking" "C5 H9 N O2" 115.132 PRO . PROLINE . "L-peptide linking" "C3 H7 N O3" 105.093 SER . SERINE . "L-peptide linking" "C4 H9 N O3" 119.12 THR . THREONINE . "L-peptide linking" "C11 H12 N2 O2" 204.229 TRP . TRYPTOPHAN . "L-peptide linking" "C9 H11 N O3" 181.191 TYR . TYROSINE . "L-peptide linking" "C5 H11 N O2" 117.148 VAL . VALINE . "L-peptide linking" "Zn 2" 65.38 ZN . "ZINC ION" . non-polymer # _citation.country . _citation.id 1 _citation.journal_abbrev "To Be Published" _citation.journal_id_ASTM . _citation.journal_id_CSD . _citation.journal_id_ISSN . _citation.journal_issue . _citation.journal_volume . _citation.page_first . _citation.page_last . _citation.pdbx_database_id_DOI . _citation.pdbx_database_id_PubMed . _citation.title "To be provided" _citation.year . # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal 1 "Wu, P." 1 1 "Allain, F.H.-T." 2 # loop_ _entity.details _entity.formula_weight _entity.id _entity.pdbx_description _entity.pdbx_number_of_molecules _entity.src_method _entity.type . 44477.87 1 "SF3 helicase domain-containing protein" 1 MAN POLYMER . 3245.125 2 "DNA (5'-D(*AP*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')" 1 MAN POLYMER . 507.182 3 "ADENOSINE-5'-TRIPHOSPHATE" 1 SYN NON-POLYMER . 507.182 4 "2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE" 1 SYN NON-POLYMER . 24.305 5 "MAGNESIUM ION" 3 SYN NON-POLYMER . 65.38 6 "ZINC ION" 1 SYN NON-POLYMER # loop_ _entity_name_com.entity_id _entity_name_com.name 1 "pRN1 primase, DNA primase" 2 "DNA template" # loop_ _entity_poly.entity_id _entity_poly.nstd_chirality _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_sequence_evidence_code _entity_poly.pdbx_strand_id _entity_poly.type 1 . NO NO SSERIRYAKWFLEHGFNIIPIDPESKKPVLKEWQKYSHEMPSDEEKQRFLKMIEEGYNYAIPGGQKGLVILDFESKEKLKAWIGESALEELCRKTLCTNTVHGGIHIYVLSNDIPPHKINPLFEENGKGIIDLQSYNSYVLGLGSCVNHLHCTTDKCPWKEQNYTTCYTLYNELKEISKVDLKSLLRFLAEKGKRLGITLSKTAKEWLEGKKEEEDTVVEFEELRKELVKRDSGKPVEKIKEEICTKSPPKLIKEIICENKTYADVNIDRSRGDWHVILYLMKHGVTDPDKILELLPRDSKAKENEKWNTQKYFVITLSKAWSVVKKYLEA SSERIRYAKWFLEHGFNIIPIDPESKKPVLKEWQKYSHEMPSDEEKQRFLKMIEEGYNYAIPGGQKGLVILDFESKEKLKAWIGESALEELCRKTLCTNTVHGGIHIYVLSNDIPPHKINPLFEENGKGIIDLQSYNSYVLGLGSCVNHLHCTTDKCPWKEQNYTTCYTLYNELKEISKVDLKSLLRFLAEKGKRLGITLSKTAKEWLEGKKEEEDTVVEFEELRKELVKRDSGKPVEKIKEEICTKSPPKLIKEIICENKTYADVNIDRSRGDWHVILYLMKHGVTDPDKILELLPRDSKAKENEKWNTQKYFVITLSKAWSVVKKYLEA . B polypeptide(L) 2 . NO NO (DA)(DC)(DT)(DG)(DT)(DG)(DC)(DT)(DC)(DA) ACTGTGCTCA . A polydeoxyribonucleotide # loop_ _entity_poly_seq.entity_id _entity_poly_seq.hetero _entity_poly_seq.mon_id _entity_poly_seq.num 1 . SER 1 1 . SER 2 1 . GLU 3 1 . ARG 4 1 . ILE 5 1 . ARG 6 1 . TYR 7 1 . ALA 8 1 . LYS 9 1 . TRP 10 1 . PHE 11 1 . LEU 12 1 . GLU 13 1 . HIS 14 1 . GLY 15 1 . PHE 16 1 . ASN 17 1 . ILE 18 1 . ILE 19 1 . PRO 20 1 . ILE 21 1 . ASP 22 1 . PRO 23 1 . GLU 24 1 . SER 25 1 . LYS 26 1 . LYS 27 1 . PRO 28 1 . VAL 29 1 . LEU 30 1 . LYS 31 1 . GLU 32 1 . TRP 33 1 . GLN 34 1 . LYS 35 1 . TYR 36 1 . SER 37 1 . HIS 38 1 . GLU 39 1 . MET 40 1 . PRO 41 1 . SER 42 1 . ASP 43 1 . GLU 44 1 . GLU 45 1 . LYS 46 1 . GLN 47 1 . ARG 48 1 . PHE 49 1 . LEU 50 1 . LYS 51 1 . MET 52 1 . ILE 53 1 . GLU 54 1 . GLU 55 1 . GLY 56 1 . TYR 57 1 . ASN 58 1 . TYR 59 1 . ALA 60 1 . ILE 61 1 . PRO 62 1 . GLY 63 1 . GLY 64 1 . GLN 65 1 . LYS 66 1 . GLY 67 1 . LEU 68 1 . VAL 69 1 . ILE 70 1 . LEU 71 1 . ASP 72 1 . PHE 73 1 . GLU 74 1 . SER 75 1 . LYS 76 1 . GLU 77 1 . LYS 78 1 . LEU 79 1 . LYS 80 1 . ALA 81 1 . TRP 82 1 . ILE 83 1 . GLY 84 1 . GLU 85 1 . SER 86 1 . ALA 87 1 . LEU 88 1 . GLU 89 1 . GLU 90 1 . LEU 91 1 . CYS 92 1 . ARG 93 1 . LYS 94 1 . THR 95 1 . LEU 96 1 . CYS 97 1 . THR 98 1 . ASN 99 1 . THR 100 1 . VAL 101 1 . HIS 102 1 . GLY 103 1 . GLY 104 1 . ILE 105 1 . HIS 106 1 . ILE 107 1 . TYR 108 1 . VAL 109 1 . LEU 110 1 . SER 111 1 . ASN 112 1 . ASP 113 1 . ILE 114 1 . PRO 115 1 . PRO 116 1 . HIS 117 1 . LYS 118 1 . ILE 119 1 . ASN 120 1 . PRO 121 1 . LEU 122 1 . PHE 123 1 . GLU 124 1 . GLU 125 1 . ASN 126 1 . GLY 127 1 . LYS 128 1 . GLY 129 1 . ILE 130 1 . ILE 131 1 . ASP 132 1 . LEU 133 1 . GLN 134 1 . SER 135 1 . TYR 136 1 . ASN 137 1 . SER 138 1 . TYR 139 1 . VAL 140 1 . LEU 141 1 . GLY 142 1 . LEU 143 1 . GLY 144 1 . SER 145 1 . CYS 146 1 . VAL 147 1 . ASN 148 1 . HIS 149 1 . LEU 150 1 . HIS 151 1 . CYS 152 1 . THR 153 1 . THR 154 1 . ASP 155 1 . LYS 156 1 . CYS 157 1 . PRO 158 1 . TRP 159 1 . LYS 160 1 . GLU 161 1 . GLN 162 1 . ASN 163 1 . TYR 164 1 . THR 165 1 . THR 166 1 . CYS 167 1 . TYR 168 1 . THR 169 1 . LEU 170 1 . TYR 171 1 . ASN 172 1 . GLU 173 1 . LEU 174 1 . LYS 175 1 . GLU 176 1 . ILE 177 1 . SER 178 1 . LYS 179 1 . VAL 180 1 . ASP 181 1 . LEU 182 1 . LYS 183 1 . SER 184 1 . LEU 185 1 . LEU 186 1 . ARG 187 1 . PHE 188 1 . LEU 189 1 . ALA 190 1 . GLU 191 1 . LYS 192 1 . GLY 193 1 . LYS 194 1 . ARG 195 1 . LEU 196 1 . GLY 197 1 . ILE 198 1 . THR 199 1 . LEU 200 1 . SER 201 1 . LYS 202 1 . THR 203 1 . ALA 204 1 . LYS 205 1 . GLU 206 1 . TRP 207 1 . LEU 208 1 . GLU 209 1 . GLY 210 1 . LYS 211 1 . LYS 212 1 . GLU 213 1 . GLU 214 1 . GLU 215 1 . ASP 216 1 . THR 217 1 . VAL 218 1 . VAL 219 1 . GLU 220 1 . PHE 221 1 . GLU 222 1 . GLU 223 1 . LEU 224 1 . ARG 225 1 . LYS 226 1 . GLU 227 1 . LEU 228 1 . VAL 229 1 . LYS 230 1 . ARG 231 1 . ASP 232 1 . SER 233 1 . GLY 234 1 . LYS 235 1 . PRO 236 1 . VAL 237 1 . GLU 238 1 . LYS 239 1 . ILE 240 1 . LYS 241 1 . GLU 242 1 . GLU 243 1 . ILE 244 1 . CYS 245 1 . THR 246 1 . LYS 247 1 . SER 248 1 . PRO 249 1 . PRO 250 1 . LYS 251 1 . LEU 252 1 . ILE 253 1 . LYS 254 1 . GLU 255 1 . ILE 256 1 . ILE 257 1 . CYS 258 1 . GLU 259 1 . ASN 260 1 . LYS 261 1 . THR 262 1 . TYR 263 1 . ALA 264 1 . ASP 265 1 . VAL 266 1 . ASN 267 1 . ILE 268 1 . ASP 269 1 . ARG 270 1 . SER 271 1 . ARG 272 1 . GLY 273 1 . ASP 274 1 . TRP 275 1 . HIS 276 1 . VAL 277 1 . ILE 278 1 . LEU 279 1 . TYR 280 1 . LEU 281 1 . MET 282 1 . LYS 283 1 . HIS 284 1 . GLY 285 1 . VAL 286 1 . THR 287 1 . ASP 288 1 . PRO 289 1 . ASP 290 1 . LYS 291 1 . ILE 292 1 . LEU 293 1 . GLU 294 1 . LEU 295 1 . LEU 296 1 . PRO 297 1 . ARG 298 1 . ASP 299 1 . SER 300 1 . LYS 301 1 . ALA 302 1 . LYS 303 1 . GLU 304 1 . ASN 305 1 . GLU 306 1 . LYS 307 1 . TRP 308 1 . ASN 309 1 . THR 310 1 . GLN 311 1 . LYS 312 1 . TYR 313 1 . PHE 314 1 . VAL 315 1 . ILE 316 1 . THR 317 1 . LEU 318 1 . SER 319 1 . LYS 320 1 . ALA 321 1 . TRP 322 1 . SER 323 1 . VAL 324 1 . VAL 325 1 . LYS 326 1 . LYS 327 1 . TYR 328 1 . LEU 329 1 . GLU 330 1 . ALA 331 2 . DA 1 2 . DC 2 2 . DT 3 2 . DG 4 2 . DT 5 2 . DG 6 2 . DC 7 2 . DT 8 2 . DC 9 2 . DA 10 # _entity_src_gen.entity_id 1 _entity_src_gen.gene_src_common_name . _entity_src_gen.gene_src_genus . _entity_src_gen.pdbx_alt_source_flag model _entity_src_gen.pdbx_gene_src_scientific_name "Sulfolobus islandicus" _entity_src_gen.pdbx_src_id 1 # _ihm_dataset_group.application modeling _ihm_dataset_group.details . _ihm_dataset_group.id 1 _ihm_dataset_group.name . # loop_ _ihm_dataset_group_link.dataset_list_id _ihm_dataset_group_link.group_id 1 1 2 1 3 1 4 1 5 1 # loop_ _ihm_dataset_list.data_type _ihm_dataset_list.database_hosted _ihm_dataset_list.details _ihm_dataset_list.id "NMR data" YES "Assigned chemical shifts" 1 "Experimental model" YES "3M1M provided primary distance restraints for the catalytic domain backbone and secondary structure elements and is the starting model for the DNA primase." 2 "Experimental model" YES "7QAZ supplied base-pair positioning in I-site (provided the distance restraints for the ribose and base moiety of dGTP, as well as for C1 of the DNA template)." 3 "Experimental model" YES "9RTJ provides distance restraints for HBD, residues T2 to C9 of DNA template, ATP, and dGTP triphosphate." 4 "NMR data" YES "Restraints used in the structure calculation performed using CYANA" 5 # loop_ _ihm_dataset_related_db_reference.accession_code _ihm_dataset_related_db_reference.dataset_list_id _ihm_dataset_related_db_reference.db_name _ihm_dataset_related_db_reference.details _ihm_dataset_related_db_reference.id _ihm_dataset_related_db_reference.version 53266 1 BMRB . 1 . 3M1M 2 PDB . 2 . 7QAZ 3 PDB . 3 . 9RTJ 4 PDB . 4 . Bmrbig143 5 BMRbig . 5 . # loop_ _ihm_entity_poly_segment.comp_id_begin _ihm_entity_poly_segment.comp_id_end _ihm_entity_poly_segment.entity_id _ihm_entity_poly_segment.id _ihm_entity_poly_segment.seq_id_begin _ihm_entity_poly_segment.seq_id_end SER ALA 1 1 1 331 DA DA 2 2 1 10 # _ihm_model_group.details . _ihm_model_group.id 1 _ihm_model_group.name . # loop_ _ihm_model_group_link.group_id _ihm_model_group_link.model_id 1 1 1 2 1 3 1 4 1 5 1 6 1 7 1 8 1 9 1 10 1 11 1 12 1 13 1 14 1 15 1 16 1 17 1 18 1 19 1 20 # loop_ _ihm_model_list.assembly_id _ihm_model_list.model_id _ihm_model_list.model_name _ihm_model_list.protocol_id _ihm_model_list.representation_id 1 1 . 1 1 1 2 . 1 1 1 3 . 1 1 1 4 . 1 1 1 5 . 1 1 1 6 . 1 1 1 7 . 1 1 1 8 . 1 1 1 9 . 1 1 1 10 . 1 1 1 11 . 1 1 1 12 . 1 1 1 13 . 1 1 1 14 . 1 1 1 15 . 1 1 1 16 . 1 1 1 17 . 1 1 1 18 . 1 1 1 19 . 1 1 1 20 . 1 1 # _ihm_model_representation.details . _ihm_model_representation.id 1 _ihm_model_representation.name . # loop_ _ihm_model_representation_details.description _ihm_model_representation_details.entity_asym_id _ihm_model_representation_details.entity_description _ihm_model_representation_details.entity_id _ihm_model_representation_details.entity_poly_segment_id _ihm_model_representation_details.id _ihm_model_representation_details.model_granularity _ihm_model_representation_details.model_mode _ihm_model_representation_details.model_object_count _ihm_model_representation_details.model_object_primitive _ihm_model_representation_details.representation_id _ihm_model_representation_details.starting_model_id . A "DNA primase" 1 1 1 by-atom flexible . atomistic 1 1 . B "DNA (5'-D(*AP*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')" 2 2 2 by-atom flexible . atomistic 1 2 . C "ADENOSINE-5'-TRIPHOSPHATE" 3 . 3 by-atom flexible . atomistic 1 . . D "2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE" 4 . 4 by-atom flexible . atomistic 1 . . E "MAGNESIUM ION" 5 . 5 by-atom flexible . atomistic 1 . . F "MAGNESIUM ION" 5 . 6 by-atom flexible . atomistic 1 . . G "MAGNESIUM ION" 5 . 7 by-atom flexible . atomistic 1 . . H "ZINC ION" 6 . 8 by-atom flexible . atomistic 1 . # _ihm_model_representative.id 1 _ihm_model_representative.model_group_id 1 _ihm_model_representative.model_id 1 _ihm_model_representative.selection_criteria . # _ihm_modeling_protocol.details . _ihm_modeling_protocol.id 1 _ihm_modeling_protocol.num_steps 3 _ihm_modeling_protocol.protocol_name modeling # loop_ _ihm_modeling_protocol_details.dataset_group_id _ihm_modeling_protocol_details.description _ihm_modeling_protocol_details.ensemble_flag _ihm_modeling_protocol_details.id _ihm_modeling_protocol_details.multi_scale_flag _ihm_modeling_protocol_details.multi_state_flag _ihm_modeling_protocol_details.num_models_begin _ihm_modeling_protocol_details.num_models_end _ihm_modeling_protocol_details.ordered_flag _ihm_modeling_protocol_details.protocol_id _ihm_modeling_protocol_details.script_file_id _ihm_modeling_protocol_details.software_id _ihm_modeling_protocol_details.step_id _ihm_modeling_protocol_details.step_method _ihm_modeling_protocol_details.step_name _ihm_modeling_protocol_details.struct_assembly_description _ihm_modeling_protocol_details.struct_assembly_id 1 . NO 1 NO NO 1 1 NO 1 . 1 1 "pseudo-distance restraints" "CYANA regularization" . 1 1 . YES 2 NO NO 1 50 NO 1 . 1 2 "torsion angle dynamics combined with simulated annealing" "CYANA calculation" . 1 1 . YES 3 NO NO 50 20 NO 1 . 2 3 "Energy minimization" "AMBER refinement" . 1 # _ihm_related_datasets.dataset_list_id_derived 5 _ihm_related_datasets.dataset_list_id_primary 1 _ihm_related_datasets.transformation_id . # loop_ _ihm_starting_model_details.asym_id _ihm_starting_model_details.dataset_list_id _ihm_starting_model_details.description _ihm_starting_model_details.entity_description _ihm_starting_model_details.entity_id _ihm_starting_model_details.entity_poly_segment_id _ihm_starting_model_details.starting_model_auth_asym_id _ihm_starting_model_details.starting_model_id _ihm_starting_model_details.starting_model_sequence_offset _ihm_starting_model_details.starting_model_source A 2 . . 1 1 A 1 -4 "experimental model" B 4 . . 2 2 A 2 1 "experimental model" # _ihm_struct_assembly.description "Integrative structure of primase-DNA-2bp modeled using the NMR structure of the HBD bound with single base-pair and the crystal structure of MsCAPP bound with two base pairs. The modeling workflow included CYANA regularization and calculation followed by AMBER refinement." _ihm_struct_assembly.id 1 _ihm_struct_assembly.name Primase-DNA-2bp # loop_ _ihm_struct_assembly_details.assembly_id _ihm_struct_assembly_details.asym_id _ihm_struct_assembly_details.entity_description _ihm_struct_assembly_details.entity_id _ihm_struct_assembly_details.entity_poly_segment_id _ihm_struct_assembly_details.id _ihm_struct_assembly_details.parent_assembly_id 1 A "SF3 helicase domain-containing protein" 1 1 1 1 1 B "DNA (5'-D(*AP*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')" 2 2 2 1 1 C "ADENOSINE-5'-TRIPHOSPHATE" 3 . 3 1 1 D "2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE" 4 . 4 1 1 E "MAGNESIUM ION" 5 . 5 1 1 F "MAGNESIUM ION" 5 . 6 1 1 G "MAGNESIUM ION" 5 . 7 1 1 H "ZINC ION" 6 . 8 1 # loop_ _pdbx_entity_nonpoly.comp_id _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name ATP 3 "ADENOSINE-5'-TRIPHOSPHATE" DGT 4 "2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE" MG 5 "MAGNESIUM ION" ZN 6 "ZINC ION" # loop_ _software.citation_id _software.classification _software.description _software.location _software.name _software.pdbx_ordinal _software.type _software.version . "model building" . https://www.las.jp/english/cyana.html CYANA 1 program 3.98 . refinement . https://ambermd.org/ AMBER 2 program 20 # _struct.entry_id 9AAM _struct.pdbx_CASP_flag N _struct.pdbx_descriptor . _struct.pdbx_details "Apo pRN1 Primase Structure (PDB: 3M1M): Provided primary distance restraints for the catalytic domain backbone and secondary structure elements, maintained by retaining upper distance restraints around the REG1 pseudo-residue. MsCAPP Complex Structure (PDB: 7QAZ): Supplied base-pair positioning in the I-site and E-site, with restraints retained around REG1 for the base pair binding in the active site. NMR Structure of HBD-DNA-ATP-dGTP Complex: Define the interactions among the HBD, DNA, and the ATP triphosphate group." _struct.pdbx_model_details . _struct.pdbx_model_type_details "Structure calculated using CYANA with NMR-based distance restraints and refined using AMBER molecular dynamics" _struct.pdbx_structure_determination_methodology integrative _struct.title "Integrated Structure of pRN1 DNA Primase in Complex with the First Two Base Pairs " # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_PDB_id _struct_asym.pdbx_alt_id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.pdbx_order _struct_asym.pdbx_type . 1 A . . . . . . . 2 B . . . . . . . 3 C . . . . . . . 4 D . . . . . . . 5 E . . . . . . . 5 F . . . . . . . 5 G . . . . . . . 6 H . . . . . . # loop_ _struct_ref.db_code _struct_ref.db_name _struct_ref.details _struct_ref.entity_id _struct_ref.id _struct_ref.pdbx_align_begin _struct_ref.pdbx_align_end _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code Q54324_SACIS UNP . 1 1 40 . Q54324 . SSERIRYAKWFLEHGFNIIPIDPESKKPVLKEWQKYSHEMPSDEEKQRFLKMIEEGYNYAIPGGQKGLVILDFESKEKLKAWIGESALEELCRKTLCTNTVHGGIHIYVLSNDIPPHKINPLFEENGKGIIDLQSYNSYVLGLGSCVNHLHCTTDKCPWKEQNYTTCYTLYNELKEISKVDLKSLLRFLAEKGKRLGITLSKTAKEWLEGKKEEEDTVVEFEELRKELVKRDSGKPVEKIKEEICTKSPPKLIKEIICENKTYADVNIDRSRRDWHVILYLMKHGVTDPDKILELLPRDSKAKENEKWNTQKYFVITLSKAWSVVKKYLEA 9AAM PDB . 2 2 1 10 9AAM . . # loop_ _struct_ref_seq.align_id _struct_ref_seq.db_align_beg _struct_ref_seq.db_align_end _struct_ref_seq.ref_id _struct_ref_seq.seq_align_beg _struct_ref_seq.seq_align_end 1 40 370 1 1 331 2 1 10 2 1 10 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code A 1 1 SER 40 40 SER SER B . A 1 2 SER 41 41 SER SER B . A 1 3 GLU 42 42 GLU GLU B . A 1 4 ARG 43 43 ARG ARG B . A 1 5 ILE 44 44 ILE ILE B . A 1 6 ARG 45 45 ARG ARG B . A 1 7 TYR 46 46 TYR TYR B . A 1 8 ALA 47 47 ALA ALA B . A 1 9 LYS 48 48 LYS LYS B . A 1 10 TRP 49 49 TRP TRP B . A 1 11 PHE 50 50 PHE PHE B . A 1 12 LEU 51 51 LEU LEU B . A 1 13 GLU 52 52 GLU GLU B . A 1 14 HIS 53 53 HIS HIS B . A 1 15 GLY 54 54 GLY GLY B . A 1 16 PHE 55 55 PHE PHE B . A 1 17 ASN 56 56 ASN ASN B . A 1 18 ILE 57 57 ILE ILE B . A 1 19 ILE 58 58 ILE ILE B . A 1 20 PRO 59 59 PRO PRO B . A 1 21 ILE 60 60 ILE ILE B . A 1 22 ASP 61 61 ASP ASP B . A 1 23 PRO 62 62 PRO PRO B . A 1 24 GLU 63 63 GLU GLU B . A 1 25 SER 64 64 SER SER B . A 1 26 LYS 65 65 LYS LYS B . A 1 27 LYS 66 66 LYS LYS B . A 1 28 PRO 67 67 PRO PRO B . A 1 29 VAL 68 68 VAL VAL B . A 1 30 LEU 69 69 LEU LEU B . A 1 31 LYS 70 70 LYS LYS B . A 1 32 GLU 71 71 GLU GLU B . A 1 33 TRP 72 72 TRP TRP B . A 1 34 GLN 73 73 GLN GLN B . A 1 35 LYS 74 74 LYS LYS B . A 1 36 TYR 75 75 TYR TYR B . A 1 37 SER 76 76 SER SER B . A 1 38 HIS 77 77 HIS HIS B . A 1 39 GLU 78 78 GLU GLU B . A 1 40 MET 79 79 MET MET B . A 1 41 PRO 80 80 PRO PRO B . A 1 42 SER 81 81 SER SER B . A 1 43 ASP 82 82 ASP ASP B . A 1 44 GLU 83 83 GLU GLU B . A 1 45 GLU 84 84 GLU GLU B . A 1 46 LYS 85 85 LYS LYS B . A 1 47 GLN 86 86 GLN GLN B . A 1 48 ARG 87 87 ARG ARG B . A 1 49 PHE 88 88 PHE PHE B . A 1 50 LEU 89 89 LEU LEU B . A 1 51 LYS 90 90 LYS LYS B . A 1 52 MET 91 91 MET MET B . A 1 53 ILE 92 92 ILE ILE B . A 1 54 GLU 93 93 GLU GLU B . A 1 55 GLU 94 94 GLU GLU B . A 1 56 GLY 95 95 GLY GLY B . A 1 57 TYR 96 96 TYR TYR B . A 1 58 ASN 97 97 ASN ASN B . A 1 59 TYR 98 98 TYR TYR B . A 1 60 ALA 99 99 ALA ALA B . A 1 61 ILE 100 100 ILE ILE B . A 1 62 PRO 101 101 PRO PRO B . A 1 63 GLY 102 102 GLY GLY B . A 1 64 GLY 103 103 GLY GLY B . A 1 65 GLN 104 104 GLN GLN B . A 1 66 LYS 105 105 LYS LYS B . A 1 67 GLY 106 106 GLY GLY B . A 1 68 LEU 107 107 LEU LEU B . A 1 69 VAL 108 108 VAL VAL B . A 1 70 ILE 109 109 ILE ILE B . A 1 71 LEU 110 110 LEU LEU B . A 1 72 ASP 111 111 ASP ASP B . A 1 73 PHE 112 112 PHE PHE B . A 1 74 GLU 113 113 GLU GLU B . A 1 75 SER 114 114 SER SER B . A 1 76 LYS 115 115 LYS LYS B . A 1 77 GLU 116 116 GLU GLU B . A 1 78 LYS 117 117 LYS LYS B . A 1 79 LEU 118 118 LEU LEU B . A 1 80 LYS 119 119 LYS LYS B . A 1 81 ALA 120 120 ALA ALA B . A 1 82 TRP 121 121 TRP TRP B . A 1 83 ILE 122 122 ILE ILE B . A 1 84 GLY 123 123 GLY GLY B . A 1 85 GLU 124 124 GLU GLU B . A 1 86 SER 125 125 SER SER B . A 1 87 ALA 126 126 ALA ALA B . A 1 88 LEU 127 127 LEU LEU B . A 1 89 GLU 128 128 GLU GLU B . A 1 90 GLU 129 129 GLU GLU B . A 1 91 LEU 130 130 LEU LEU B . A 1 92 CYS 131 131 CYS CYS B . A 1 93 ARG 132 132 ARG ARG B . A 1 94 LYS 133 133 LYS LYS B . A 1 95 THR 134 134 THR THR B . A 1 96 LEU 135 135 LEU LEU B . A 1 97 CYS 136 136 CYS CYS B . A 1 98 THR 137 137 THR THR B . A 1 99 ASN 138 138 ASN ASN B . A 1 100 THR 139 139 THR THR B . A 1 101 VAL 140 140 VAL VAL B . A 1 102 HIS 141 141 HIS HIS B . A 1 103 GLY 142 142 GLY GLY B . A 1 104 GLY 143 143 GLY GLY B . A 1 105 ILE 144 144 ILE ILE B . A 1 106 HIS 145 145 HIS HIS B . A 1 107 ILE 146 146 ILE ILE B . A 1 108 TYR 147 147 TYR TYR B . A 1 109 VAL 148 148 VAL VAL B . A 1 110 LEU 149 149 LEU LEU B . A 1 111 SER 150 150 SER SER B . A 1 112 ASN 151 151 ASN ASN B . A 1 113 ASP 152 152 ASP ASP B . A 1 114 ILE 153 153 ILE ILE B . A 1 115 PRO 154 154 PRO PRO B . A 1 116 PRO 155 155 PRO PRO B . A 1 117 HIS 156 156 HIS HIS B . A 1 118 LYS 157 157 LYS LYS B . A 1 119 ILE 158 158 ILE ILE B . A 1 120 ASN 159 159 ASN ASN B . A 1 121 PRO 160 160 PRO PRO B . A 1 122 LEU 161 161 LEU LEU B . A 1 123 PHE 162 162 PHE PHE B . A 1 124 GLU 163 163 GLU GLU B . A 1 125 GLU 164 164 GLU GLU B . A 1 126 ASN 165 165 ASN ASN B . A 1 127 GLY 166 166 GLY GLY B . A 1 128 LYS 167 167 LYS LYS B . A 1 129 GLY 168 168 GLY GLY B . A 1 130 ILE 169 169 ILE ILE B . A 1 131 ILE 170 170 ILE ILE B . A 1 132 ASP 171 171 ASP ASP B . A 1 133 LEU 172 172 LEU LEU B . A 1 134 GLN 173 173 GLN GLN B . A 1 135 SER 174 174 SER SER B . A 1 136 TYR 175 175 TYR TYR B . A 1 137 ASN 176 176 ASN ASN B . A 1 138 SER 177 177 SER SER B . A 1 139 TYR 178 178 TYR TYR B . A 1 140 VAL 179 179 VAL VAL B . A 1 141 LEU 180 180 LEU LEU B . A 1 142 GLY 181 181 GLY GLY B . A 1 143 LEU 182 182 LEU LEU B . A 1 144 GLY 183 183 GLY GLY B . A 1 145 SER 184 184 SER SER B . A 1 146 CYS 185 185 CYS CYS B . A 1 147 VAL 186 186 VAL VAL B . A 1 148 ASN 187 187 ASN ASN B . A 1 149 HIS 188 188 HIS HIS B . A 1 150 LEU 189 189 LEU LEU B . A 1 151 HIS 190 190 HIS HIS B . A 1 152 CYS 191 191 CYS CYS B . A 1 153 THR 192 192 THR THR B . A 1 154 THR 193 193 THR THR B . A 1 155 ASP 194 194 ASP ASP B . A 1 156 LYS 195 195 LYS LYS B . A 1 157 CYS 196 196 CYS CYS B . A 1 158 PRO 197 197 PRO PRO B . A 1 159 TRP 198 198 TRP TRP B . A 1 160 LYS 199 199 LYS LYS B . A 1 161 GLU 200 200 GLU GLU B . A 1 162 GLN 201 201 GLN GLN B . A 1 163 ASN 202 202 ASN ASN B . A 1 164 TYR 203 203 TYR TYR B . A 1 165 THR 204 204 THR THR B . A 1 166 THR 205 205 THR THR B . A 1 167 CYS 206 206 CYS CYS B . A 1 168 TYR 207 207 TYR TYR B . A 1 169 THR 208 208 THR THR B . A 1 170 LEU 209 209 LEU LEU B . A 1 171 TYR 210 210 TYR TYR B . A 1 172 ASN 211 211 ASN ASN B . A 1 173 GLU 212 212 GLU GLU B . A 1 174 LEU 213 213 LEU LEU B . A 1 175 LYS 214 214 LYS LYS B . A 1 176 GLU 215 215 GLU GLU B . A 1 177 ILE 216 216 ILE ILE B . A 1 178 SER 217 217 SER SER B . A 1 179 LYS 218 218 LYS LYS B . A 1 180 VAL 219 219 VAL VAL B . A 1 181 ASP 220 220 ASP ASP B . A 1 182 LEU 221 221 LEU LEU B . A 1 183 LYS 222 222 LYS LYS B . A 1 184 SER 223 223 SER SER B . A 1 185 LEU 224 224 LEU LEU B . A 1 186 LEU 225 225 LEU LEU B . A 1 187 ARG 226 226 ARG ARG B . A 1 188 PHE 227 227 PHE PHE B . A 1 189 LEU 228 228 LEU LEU B . A 1 190 ALA 229 229 ALA ALA B . A 1 191 GLU 230 230 GLU GLU B . A 1 192 LYS 231 231 LYS LYS B . A 1 193 GLY 232 232 GLY GLY B . A 1 194 LYS 233 233 LYS LYS B . A 1 195 ARG 234 234 ARG ARG B . A 1 196 LEU 235 235 LEU LEU B . A 1 197 GLY 236 236 GLY GLY B . A 1 198 ILE 237 237 ILE ILE B . A 1 199 THR 238 238 THR THR B . A 1 200 LEU 239 239 LEU LEU B . A 1 201 SER 240 240 SER SER B . A 1 202 LYS 241 241 LYS LYS B . A 1 203 THR 242 242 THR THR B . A 1 204 ALA 243 243 ALA ALA B . A 1 205 LYS 244 244 LYS LYS B . A 1 206 GLU 245 245 GLU GLU B . A 1 207 TRP 246 246 TRP TRP B . A 1 208 LEU 247 247 LEU LEU B . A 1 209 GLU 248 248 GLU GLU B . A 1 210 GLY 249 249 GLY GLY B . A 1 211 LYS 250 250 LYS LYS B . A 1 212 LYS 251 251 LYS LYS B . A 1 213 GLU 252 252 GLU GLU B . A 1 214 GLU 253 253 GLU GLU B . A 1 215 GLU 254 254 GLU GLU B . A 1 216 ASP 255 255 ASP ASP B . A 1 217 THR 256 256 THR THR B . A 1 218 VAL 257 257 VAL VAL B . A 1 219 VAL 258 258 VAL VAL B . A 1 220 GLU 259 259 GLU GLU B . A 1 221 PHE 260 260 PHE PHE B . A 1 222 GLU 261 261 GLU GLU B . A 1 223 GLU 262 262 GLU GLU B . A 1 224 LEU 263 263 LEU LEU B . A 1 225 ARG 264 264 ARG ARG B . A 1 226 LYS 265 265 LYS LYS B . A 1 227 GLU 266 266 GLU GLU B . A 1 228 LEU 267 267 LEU LEU B . A 1 229 VAL 268 268 VAL VAL B . A 1 230 LYS 269 269 LYS LYS B . A 1 231 ARG 270 270 ARG ARG B . A 1 232 ASP 271 271 ASP ASP B . A 1 233 SER 272 272 SER SER B . A 1 234 GLY 273 273 GLY GLY B . A 1 235 LYS 274 274 LYS LYS B . A 1 236 PRO 275 275 PRO PRO B . A 1 237 VAL 276 276 VAL VAL B . A 1 238 GLU 277 277 GLU GLU B . A 1 239 LYS 278 278 LYS LYS B . A 1 240 ILE 279 279 ILE ILE B . A 1 241 LYS 280 280 LYS LYS B . A 1 242 GLU 281 281 GLU GLU B . A 1 243 GLU 282 282 GLU GLU B . A 1 244 ILE 283 283 ILE ILE B . A 1 245 CYS 284 284 CYS CYS B . A 1 246 THR 285 285 THR THR B . A 1 247 LYS 286 286 LYS LYS B . A 1 248 SER 287 287 SER SER B . A 1 249 PRO 288 288 PRO PRO B . A 1 250 PRO 289 289 PRO PRO B . A 1 251 LYS 290 290 LYS LYS B . A 1 252 LEU 291 291 LEU LEU B . A 1 253 ILE 292 292 ILE ILE B . A 1 254 LYS 293 293 LYS LYS B . A 1 255 GLU 294 294 GLU GLU B . A 1 256 ILE 295 295 ILE ILE B . A 1 257 ILE 296 296 ILE ILE B . A 1 258 CYS 297 297 CYS CYS B . A 1 259 GLU 298 298 GLU GLU B . A 1 260 ASN 299 299 ASN ASN B . A 1 261 LYS 300 300 LYS LYS B . A 1 262 THR 301 301 THR THR B . A 1 263 TYR 302 302 TYR TYR B . A 1 264 ALA 303 303 ALA ALA B . A 1 265 ASP 304 304 ASP ASP B . A 1 266 VAL 305 305 VAL VAL B . A 1 267 ASN 306 306 ASN ASN B . A 1 268 ILE 307 307 ILE ILE B . A 1 269 ASP 308 308 ASP ASP B . A 1 270 ARG 309 309 ARG ARG B . A 1 271 SER 310 310 SER SER B . A 1 272 ARG 311 311 ARG ARG B . A 1 273 GLY 312 312 GLY GLY B . A 1 274 ASP 313 313 ASP ASP B . A 1 275 TRP 314 314 TRP TRP B . A 1 276 HIS 315 315 HIS HIS B . A 1 277 VAL 316 316 VAL VAL B . A 1 278 ILE 317 317 ILE ILE B . A 1 279 LEU 318 318 LEU LEU B . A 1 280 TYR 319 319 TYR TYR B . A 1 281 LEU 320 320 LEU LEU B . A 1 282 MET 321 321 MET MET B . A 1 283 LYS 322 322 LYS LYS B . A 1 284 HIS 323 323 HIS HIS B . A 1 285 GLY 324 324 GLY GLY B . A 1 286 VAL 325 325 VAL VAL B . A 1 287 THR 326 326 THR THR B . A 1 288 ASP 327 327 ASP ASP B . A 1 289 PRO 328 328 PRO PRO B . A 1 290 ASP 329 329 ASP ASP B . A 1 291 LYS 330 330 LYS LYS B . A 1 292 ILE 331 331 ILE ILE B . A 1 293 LEU 332 332 LEU LEU B . A 1 294 GLU 333 333 GLU GLU B . A 1 295 LEU 334 334 LEU LEU B . A 1 296 LEU 335 335 LEU LEU B . A 1 297 PRO 336 336 PRO PRO B . A 1 298 ARG 337 337 ARG ARG B . A 1 299 ASP 338 338 ASP ASP B . A 1 300 SER 339 339 SER SER B . A 1 301 LYS 340 340 LYS LYS B . A 1 302 ALA 341 341 ALA ALA B . A 1 303 LYS 342 342 LYS LYS B . A 1 304 GLU 343 343 GLU GLU B . A 1 305 ASN 344 344 ASN ASN B . A 1 306 GLU 345 345 GLU GLU B . A 1 307 LYS 346 346 LYS LYS B . A 1 308 TRP 347 347 TRP TRP B . A 1 309 ASN 348 348 ASN ASN B . A 1 310 THR 349 349 THR THR B . A 1 311 GLN 350 350 GLN GLN B . A 1 312 LYS 351 351 LYS LYS B . A 1 313 TYR 352 352 TYR TYR B . A 1 314 PHE 353 353 PHE PHE B . A 1 315 VAL 354 354 VAL VAL B . A 1 316 ILE 355 355 ILE ILE B . A 1 317 THR 356 356 THR THR B . A 1 318 LEU 357 357 LEU LEU B . A 1 319 SER 358 358 SER SER B . A 1 320 LYS 359 359 LYS LYS B . A 1 321 ALA 360 360 ALA ALA B . A 1 322 TRP 361 361 TRP TRP B . A 1 323 SER 362 362 SER SER B . A 1 324 VAL 363 363 VAL VAL B . A 1 325 VAL 364 364 VAL VAL B . A 1 326 LYS 365 365 LYS LYS B . A 1 327 LYS 366 366 LYS LYS B . A 1 328 TYR 367 367 TYR TYR B . A 1 329 LEU 368 368 LEU LEU B . A 1 330 GLU 369 369 GLU GLU B . A 1 331 ALA 370 370 ALA ALA B . B 2 1 DA -1 -1 DA DA A ? B 2 2 DC 1 1 DC DC A ? B 2 3 DT 2 2 DT DT A ? B 2 4 DG 3 3 DG DG A ? B 2 5 DT 4 4 DT DT A ? B 2 6 DG 5 5 DG DG A ? B 2 7 DC 6 6 DC DC A ? B 2 8 DT 7 7 DT DT A ? B 2 9 DC 8 8 DC DC A ? B 2 10 DA 9 9 DA DA A ? # # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 ATP 1 400 400 ATP C . D 4 DGT 1 410 410 DGT C . E 5 MG 1 420 420 MG C . F 5 MG 1 430 430 MG C . G 5 MG 1 440 440 MG C . H 6 ZN 1 450 450 ZN C . # # loop_ # #