Cryo-EM structure of Csm-crRNA-target RNA ternary complex in complex with cA4 in type III-A CRISPR-Cas system

2026-07-01 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DERIVED_CALCULATIONS chem_comp_atom chem_comp_bond database_2 struct_conn struct_conn_type _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_value_order _struct_conn.ptnr1_auth_asym_id _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_asym_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_conn_type.id STRUCTURE_SUMMARY atom_site chem_comp chem_comp_atom chem_comp_bond em_admin pdbx_entity_nonpoly pdbx_entry_details pdbx_nonpoly_scheme pdbx_unobs_or_zero_occ_atoms pdbx_validate_close_contact struct_conn struct_site _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.label_atom_id _atom_site.label_comp_id _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.type _em_admin.last_update _pdbx_entity_nonpoly.comp_id _pdbx_entry_details.has_protein_modification _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.dist _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.ptnr1_auth_asym_id _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_asym_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.details _struct_site.pdbx_auth_comp_id DATA_COLLECTION atom_site chem_comp_atom chem_comp_bond em_admin _atom_site.auth_atom_id _atom_site.label_atom_id _chem_comp_atom.atom_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _em_admin.last_update RCSB RCSB 2019-03-07 2019-05-15 2019-07-31 2026-07-01 Cryo-EM structure of Csm-crRNA-target RNA ternary complex in complex with cA4 in type III-A CRISPR-Cas system Jia N Patel DJ cryo-EM structure, Csm-crRNA-target RNA ternary complex in complex with CA4, Type III CRISPR-Cas systerm, IMMUNE SYSTEM, immune system-rna-dna complex, immune system-rna complex Jia N Jones R Sukenick G Patel DJ Second Messenger cA4Formation within the Composite Csm1 Palm Pocket of Type III-A CRISPR-Cas Csm Complex and Its Release Path. Mol.Cell US 75 933 943.e6 2019 31326272 doi:10.1016/j.molcel.2019.06.013 1097-2765 2168 MOCEFL 6o7h FULLOVERLAP EMDB EMD-0641 associated EM volume

Csm-crRNA-target RNA-AMPPNP complex Csm-crRNA-target RNA-AMPPNP complex 0 1 2 3 4 5 6 7 8 Thermococcus onnurineus CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) Thermococcus onnurineus (strain NA1) NA1 0.089750602 1 Escherichia coli LEVO MGSSHHHHHHSQDPMEIDELTALGGLLHDIGKPVQRAGLYSGDHSTQGARFLRDLAENTGRAEYELLSLFSEFHHKGHMK NDELMIRRIKELSPERFGLTMEDVLNALWIVYEADNLASGEREEGQPQASRPLYSVFNPGKAYPWAELDFEKELPVPGDV FSIRSQDYRELVKRLWEELSKAKLRSDRLLPVLEKYLTFVSSVTSEGNIISLYDHMRMTSAIALAMLRAGCTAEDVRSGR CRKEKRFLLIEGDFSGIQDFIYRVSGKGTLKYLRARSAYLELIGWDVVLEILSRLGLTRANVVFNAGGHFMIIAQNTPDA VKELEEIRAKAVEWLYREFESDLYLAIEWEPVSGREFGREGGKNLFAEARKRLKHKLTVRKLKRFGEIKGLFEHGHTERL AECPVCGRELPEGKLEPSASDPETKVCPTCNRLVSLGGNLPKLLGFGRTAKNDAGVLVEGPFSGFVPYLQGGRPVGEQIL VKNTLNPGEIPESAQFVPYFVADYFKKDPKGGVATFEELSMASTGTRRLGVMKGDVDRLGEFFSSMDSPSKLATASRFMD YFFKGYIGAIIEGKFGYIIGDVPSLRDWPEEPDIVVVYAGGDDFFIVGAWDQIFELAFRVRRAFNAYTGGKLTLSVGLGY FDERTPIYRMADVVSERLDTAKDEGRNRVFVVGRSRPLDGKHKLSYEWNHYEELWRTYAPRIYAGNGRLKGKLESKKGLL WKLLEIRELYVRDPNDVRWAYLTAYLLGRHGLSDLFPELVGIDTKAVERKEPQPVYWVDGVLKIVLMAVRR B6YWB8 3.1.-.- Csm2 Thermococcus onnurineus (strain NA1) NA1 0.021235279 1 Escherichia coli LEVO GSVAYHQKHGGYGRGGYGRQDRPQVDASRLFGESPDVVGIKKMLEGKGKQWEAIQPYFDNVVREAKNFLEWSPNKRLANA VTVAAYLTSQGLKTNQVRKILDMARTTELKVKRGEGDIKDDLVKMRYLLAYTVGKATGQSKYSLDAFHRILDPMLEVLMG SPKKENFEKFYDFLQAVVAYHKFFGGGD B6YWB9 Csm3 Thermococcus onnurineus (strain NA1) NA1 0.032822051 2 Escherichia coli LEVO GSMDRRFYGKIVIKGKIKAVTGLHIGSQRDISEIGGIANPVIKDPHTGLPYIPGSSLKGRLRSLFEILVNSRLGEWREKY PSLANYSPGSCRPDNQENCGKFFNRKINRGWIHVCPDYETALACPVCRLFGASGKESNFPSRIIVRDAFLTKEWEEKWRA GEAITEAKIEVGIDRVTSQANPRTNERVVAGAEFEFEIIYNVENTTHWRDDIKNLLTAMALLEDSYLGGSGSRGYGKVKF IFDSFEFRPLDYYRTGKDEDIVSIDAREKSVSDILSGFDSLFSEVEGKLEAG B6YWC0 Csm4 Thermococcus onnurineus (strain NA1) NA1 0.032345061 1 Escherichia coli LEVO MPKFIAVKLIPKGPFRDIPRADTLFGAIGNAISAIHGQSAVEELVDAFVGGARISSAFPYSGDTYYLPKPLSVEPALEGI LTGLDEEERYTTAKRLRKAKYLDLKNFELALRLRPFTIPEEIPYARVDVPRVVLDRVTQDSSIYFWEEIRFREKSGVYFL YSGPREVFDGYIAPAMRFLGDTGIGGKSTWGAGLFEVEFHEMKIDAPGSEYSVTLSNALPTKTPVLWRLLRKGGWSFGRR KPRMTFIAEGSIVKNDPGGMERLELGLSHEVYVYGLTFPLGVELPEGLE B6YWC1 RNA (38-MER) Thermococcus onnurineus (strain NA1) 0.012463438

crRNA

1 GUGGAAAGGCGGGCAGAGGCGGUUUGCGUAUUGGGCGC RNA (40-MER) Thermococcus onnurineus (strain NA1) 0.012750657999999998

taget RNA

1 CCCUGGCGCCCAAUACGCAAACCGCCUCUGCCCGCGGGCG Csm5 Thermococcus onnurineus (strain NA1) NA1 0.04058841 1 Escherichia coli LEVO MTERTLKVLSPLHIGTGNELTPVDIYPRENIIHVLDTER(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)RKSMQIKEFIKLNGRPYIPGSSLKGAIRTAVLYKA LKEC(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)IRYEPKRDPMKALIV RDSKPVGRKHLAVYHVEVIGNPQPIPIWVEAIEPGAATDVEIHVDTEALRLNADYFNGLLWECLKERGEPGEVFEDFLWE AVDEFYTAVMKYETIEVQKFGRYTSQVRSFYASLEDHSGHVLRLGWGSGWLAMTIGLLLVEKGYKWENVRKKLGLGKKPG GSGFSREFPKTRRLADGMPMGWVVLEHHHHHH Cyclic DNA cA4 synthetic construct 0.001271866 1 AAAA ZINC ION 6.5409e-05 3 ZN GUANOSINE-5'-MONOPHOSPHATE 0.000363221 1 5GP singleParticle particle 8.800000000000001 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) 1.35 1 PHASE FLIPPING AND AMPLITUDE CORRECTION C1 2.9 FSC 0.143 CUT-OFF 151715 RANDOM ASSIGNMENT MAXIMUM LIKELIHOOD emd_0641.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 278.784 278.784 278.784 90.0 90.0 90.0 X Y Z -0.16710114 0.3501203 0.00017349591 0.005167198 1.089 1.089 1.089 0.015 AUTHOR ::::EMDATABANK.org::::EMD-0641::::