{ "_id": "5f3a9264043d5cc5a75eb958", "admin": { "authors_list": { "author": [ { "instance_type": "author", "valueOf_": "Yin W" }, { "instance_type": "author", "valueOf_": "Mao C" } ] }, "current_status": { "code": { "valueOf_": "REL" }, "date": "2024-03-27T00:00:00", "processing_site": "PDBj" }, "key_dates": { "deposition": "2020-04-09T00:00:00", "header_release": "2020-04-22T00:00:00", "map_release": "2020-04-22T00:00:00", "update": "2024-03-27T00:00:00" }, "keywords": "SARS-CoV-2, RNA Polymerase, Remdesivir, VIRAL PROTEIN", "sites": { "deposition": "PDBj", "last_processing": "PDBj" }, "title": "The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of Remdesivir(RTP)" }, "crossreferences": { "citation_list": { "primary_citation": { "citation_type": { "author": [ { "instance_type": "author", "order": 1, "valueOf_": "Yin W" }, { "instance_type": "author", "order": 2, "valueOf_": "Mao C" }, { "instance_type": "author", "order": 3, "valueOf_": "Luan X" }, { "instance_type": "author", "order": 4, "valueOf_": "Shen DD" }, { "instance_type": "author", "order": 5, "valueOf_": "Shen Q" }, { "instance_type": "author", "order": 6, "valueOf_": "Su H" }, { "instance_type": "author", "order": 7, "valueOf_": "Wang X" }, { "instance_type": "author", "order": 8, "valueOf_": "Zhou F" }, { "instance_type": "author", "order": 9, "valueOf_": "Zhao W" }, { "instance_type": "author", "order": 10, "valueOf_": "Gao M" }, { "instance_type": "author", "order": 11, "valueOf_": "Chang S" }, { "instance_type": "author", "order": 12, "valueOf_": "Xie YC" }, { "instance_type": "author", "order": 13, "valueOf_": "Tian G" }, { "instance_type": "author", "order": 14, "valueOf_": "Jiang HW" }, { "instance_type": "author", "order": 15, "valueOf_": "Tao SC" }, { "instance_type": "author", "order": 16, "valueOf_": "Shen J" }, { "instance_type": "author", "order": 17, "valueOf_": "Jiang Y" }, { "instance_type": "author", "order": 18, "valueOf_": "Jiang H" }, { "instance_type": "author", "order": 19, "valueOf_": "Xu Y" }, { "instance_type": "author", "order": 20, "valueOf_": "Zhang S" }, { "instance_type": "author", "order": 21, "valueOf_": "Zhang Y" }, { "instance_type": "author", "order": 22, "valueOf_": "Xu HE" } ], "country": "US", "external_references": [ { "instance_type": "external_references", "type_": "PUBMED", "valueOf_": "32358203" }, { "instance_type": "external_references", "type_": "DOI", "valueOf_": "doi:10.1126/science.abc1560" }, { "instance_type": "external_references", "type_": "ISSN", "valueOf_": "1095-9203" }, { "instance_type": "external_references", "type_": "CSD", "valueOf_": "0038" }, { "instance_type": "external_references", "type_": "ASTM", "valueOf_": "SCIEAS" } ], "first_page": "1499", "journal": "Science", "journal_abbreviation": "Science", "last_page": "1504", "published": true, "title": "Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir.", "volume": "368", "year": "2020" } } }, "pdb_list": { "pdb_reference": [ { "instance_type": "pdb_reference", "pdb_id": "7bv2", "relationship": { "in_frame": "FULLOVERLAP" } } ] } }, "emdb_id": "EMD-30210", "map": { "axis_order": { "fast": "X", "medium": "Y", "slow": "Z" }, "cell": { "a": { "units": "\u212b", "valueOf_": "194.68802" }, "alpha": { "units": "deg", "valueOf_": "90.0" }, "b": { "units": "\u212b", "valueOf_": "194.68802" }, "beta": { "units": "deg", "valueOf_": "90.0" }, "c": { "units": "\u212b", "valueOf_": "194.68802" }, "gamma": { "units": "deg", "valueOf_": "90.0" } }, "contour_list": { "contour": [ { "instance_type": "contour", "level": 0.058, "primary": true, "source": "AUTHOR" } ] }, "data_type": "IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)", "dimensions": { "col": 192, "row": 192, "sec": 192 }, "file": "emd_30210.map.gz", "format": "CCP4", "label": "::::EMDATABANK.org::::EMD-30210::::", "origin": { "col": 0, "row": 0, "sec": 0 }, "pixel_spacing": { "x": { "units": "\u212b", "valueOf_": "1.014" }, "y": { "units": "\u212b", "valueOf_": "1.014" }, "z": { "units": "\u212b", "valueOf_": "1.014" } }, "size_kbytes": 28312, "spacing": { "x": 192, "y": 192, "z": 192 }, "statistics": { "average": -6.870601e-06, "maximum": 0.46138126, "minimum": -0.31185895, "std": 0.0135859335 }, "symmetry": { "space_group": 1 } }, "sample": { "macromolecule_list": { "macromolecule": [ { "ec_number": [ "2.7.7.48" ], "enantiomer": "LEVO", "instance_type": "protein_or_peptide", "macromolecule_id": 1, "molecular_weight": { "theoretical": { "units": "MDa", "valueOf_": "0.109070445" } }, "name": { "valueOf_": "RNA-directed RNA polymerase" }, "natural_source": { "database": "NCBI", "organism": { "ncbi": 2697049, "valueOf_": "Severe acute respiratory syndrome coronavirus 2" } }, "number_of_copies": "1", "recombinant_expression": { "database": "NCBI", "recombinant_organism": { "ncbi": 7108, "valueOf_": "Spodoptera frugiperda" } }, "sequence": { "external_references": [ { "instance_type": "external_references", "type_": "UNIPROTKB", "valueOf_": "P0DTD1" } ], "string": "MSADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSN YQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNK KDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYS LLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFST VFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVA ALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKY FDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAG VSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLA RKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKY VRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKC WTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYAD VFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQGGSENLYFQGHHHHHHHH" } }, { "enantiomer": "LEVO", "instance_type": "protein_or_peptide", "macromolecule_id": 2, "molecular_weight": { "theoretical": { "units": "MDa", "valueOf_": "0.023139418000000002" } }, "name": { "valueOf_": "Non-structural protein 8" }, "natural_source": { "database": "NCBI", "organism": { "ncbi": 2697049, "valueOf_": "Severe acute respiratory syndrome coronavirus 2" } }, "number_of_copies": "1", "recombinant_expression": { "database": "NCBI", "recombinant_organism": { "ncbi": 7108, "valueOf_": "Spodoptera frugiperda" } }, "sequence": { "external_references": [ { "instance_type": "external_references", "type_": "UNIPROTKB", "valueOf_": "P0DTD1" } ], "string": "MAIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDK RAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQV VDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQHHHHHHHH" } }, { "enantiomer": "LEVO", "instance_type": "protein_or_peptide", "macromolecule_id": 3, "molecular_weight": { "theoretical": { "units": "MDa", "valueOf_": "0.010485175999999999" } }, "name": { "valueOf_": "Non-structural protein 7" }, "natural_source": { "database": "NCBI", "organism": { "ncbi": 2697049, "valueOf_": "Severe acute respiratory syndrome coronavirus 2" } }, "number_of_copies": "1", "recombinant_expression": { "database": "NCBI", "recombinant_organism": { "ncbi": 7108, "valueOf_": "Spodoptera frugiperda" } }, "sequence": { "external_references": [ { "instance_type": "external_references", "type_": "UNIPROTKB", "valueOf_": "P0DTD1" } ], "string": "MSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNR ATLQHHHHHHHH" } }, { "instance_type": "rna", "macromolecule_id": 4, "molecular_weight": { "theoretical": { "units": "MDa", "valueOf_": "0.006410816" } }, "name": { "valueOf_": "Primer" }, "natural_source": { "database": "NCBI", "organism": { "ncbi": 2697049, "valueOf_": "Severe acute respiratory syndrome coronavirus 2" } }, "number_of_copies": "1", "sequence": { "string": "GCUAUGUGAGAUUAAGUUAU" } }, { "instance_type": "rna", "macromolecule_id": 5, "molecular_weight": { "theoretical": { "units": "MDa", "valueOf_": "0.009358456" } }, "name": { "valueOf_": "Templete" }, "natural_source": { "database": "NCBI", "organism": { "ncbi": 2697049, "valueOf_": "Severe acute respiratory syndrome coronavirus 2" } }, "number_of_copies": "1", "sequence": { "string": "UUUUUUUUUUAUAACUUAAUCUCACAUAGC" } }, { "formula": "ZN", "instance_type": "ligand", "macromolecule_id": 6, "molecular_weight": { "theoretical": { "units": "MDa", "valueOf_": "6.5409e-05" } }, "name": { "valueOf_": "ZINC ION" }, "number_of_copies": "2" }, { "formula": "POP", "instance_type": "ligand", "macromolecule_id": 7, "molecular_weight": { "theoretical": { "units": "MDa", "valueOf_": "0.000175959" } }, "name": { "valueOf_": "PYROPHOSPHATE 2-" }, "number_of_copies": "1" }, { "formula": "MG", "instance_type": "ligand", "macromolecule_id": 8, "molecular_weight": { "theoretical": { "units": "MDa", "valueOf_": "2.4305e-05" } }, "name": { "valueOf_": "MAGNESIUM ION" }, "number_of_copies": "2" }, { "formula": "F86", "instance_type": "ligand", "macromolecule_id": 9, "molecular_weight": { "theoretical": { "units": "MDa", "valueOf_": "0.000371243" } }, "name": { "valueOf_": "[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" }, "number_of_copies": "1" }, { "formula": "HOH", "instance_type": "ligand", "macromolecule_id": 10, "molecular_weight": { "theoretical": { "units": "MDa", "valueOf_": "1.8015e-05" } }, "name": { "valueOf_": "water" }, "number_of_copies": "5" } ] }, "name": { "valueOf_": "The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of Remdesivir(RTP)" }, "supramolecule_list": { "supramolecule": [ { "instance_type": "complex_supramolecule", "macromolecule_list": { "macromolecule": [ { "instance_type": "macromolecule", "macromolecule_id": 1 }, { "instance_type": "macromolecule", "macromolecule_id": 2 }, { "instance_type": "macromolecule", "macromolecule_id": 3 }, { "instance_type": "macromolecule", "macromolecule_id": 4 }, { "instance_type": "macromolecule", "macromolecule_id": 5 } ] }, "name": { "valueOf_": "The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of Remdesivir(RTP)" }, "natural_source": [ { "database": "NCBI", "instance_type": "natural_source", "organism": { "ncbi": 1431340, "valueOf_": "SARS bat coronavirus" } } ], "parent": 0, "supramolecule_id": 1 } ] } }, "structure_determination_list": { "structure_determination": [ { "aggregation_state": "particle", "image_processing": [ { "final_angle_assignment": { "type_": "MAXIMUM LIKELIHOOD" }, "final_reconstruction": { "number_images_used": 130386, "resolution": { "res_type": "BY AUTHOR", "units": "\u212b", "valueOf_": "2.5" }, "resolution_method": "FSC 0.143 CUT-OFF" }, "image_processing_id": 1, "image_recording_id": 1, "initial_angle_assignment": { "type_": "RANDOM ASSIGNMENT" }, "instance_type": "singleparticle_processing", "startup_model": [ { "emdb_id": "EMD-0520", "instance_type": "startup_model", "type_of_model": "EMDB MAP" } ] } ], "instance_type": "structure_determination", "method": "singleParticle", "microscopy_list": { "microscopy": [ { "acceleration_voltage": { "units": "kV", "valueOf_": "300" }, "electron_source": "FIELD EMISSION GUN", "illumination_mode": "FLOOD BEAM", "image_recording_list": { "image_recording": [ { "average_electron_dose_per_image": { "units": "e/\u212b^2", "valueOf_": "64.0" }, "detector_mode": "COUNTING", "film_or_detector_model": { "valueOf_": "GATAN K2 SUMMIT (4k x 4k)" }, "image_recording_id": 1, "instance_type": "image_recording" } ] }, "imaging_mode": "BRIGHT FIELD", "instance_type": "single_particle_microscopy", "microscope": "FEI TITAN KRIOS", "microscopy_id": 1 } ] }, "specimen_preparation_list": { "specimen_preparation": [ { "buffer": { "ph": 7.5 }, "grid": { "material": "GOLD", "model": "Quantifoil R1.2/1.3" }, "instance_type": "single_particle_preparation", "preparation_id": 1, "vitrification": { "cryogen_name": "ETHANE" } } ] }, "structure_determination_id": 1 } ] }, "version": "3.0.9.2" }