2023-11-22 REL RCSB RCSB RCSB 2023-05-04 2023-11-22 2023-11-22 2023-11-22 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States SARS-CoV-2 replication-transcription complex bound to nsp9 and UMPCPP, as a pre-catalytic NMPylation intermediate Small GI Darst SA Campbell EA RTC, nsp12, nsp9, NiRAN, SARS-CoV-2, NMPylation, UMPCPP, VIRAL PROTEIN Small GI Fedorova O Olinares PDB Chandanani J Banerjee A Choi YJ Molina H Chait BT Darst SA Campbell EA Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain. Mol.Cell US 83 3921 3930.e7 2023 37890482 doi:10.1016/j.molcel.2023.10.001 1097-2765 2168 MOCEFL 8sq9 FULLOVERLAP SARS-CoV-2 replication-transcription complex bound to nsp9 and UMPCPP, as a pre-catalytic NMPylation intermediate SARS-CoV-2 replication-transcription complex bound to nsp9 and UMPCPP, as a pre-catalytic NMPylation intermediate 0 1 2 3 4 5 6 Severe acute respiratory syndrome coronavirus 2 RNA-directed RNA polymerase Severe acute respiratory syndrome coronavirus 2 0.106780977 1 Escherichia coli BL21(DE3) LEVO SADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNY QHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKK DWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSL LMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTV FPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAA LTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYF DCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGV SICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLAR KHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYV RNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCW TETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADV FHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQ P0DTD1 2.7.7.48 Non-structural protein 8 Severe acute respiratory syndrome coronavirus 2 0.021903047 2 Escherichia coli BL21(DE3) LEVO AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVV DADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ P0DTD1 Non-structural protein 7 Severe acute respiratory syndrome coronavirus 2 0.009248804 1 Escherichia coli BL21(DE3) LEVO SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRA TLQ P0DTD1 Non-structural protein 9 Severe acute respiratory syndrome coronavirus 2 0.012391171 1 Escherichia coli BL21(DE3) LEVO NNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTP KGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ P0DTD1 Primer RNA Severe acute respiratory syndrome coronavirus 0.011155677 1 CGCGUAGCAUGCUACGUCAUUCUCCACGCGAAGCA Template RNA Severe acute respiratory syndrome coronavirus 0.017557342 1 CUAUCCCCAUUUUGUUGUCAUGCUUCGCGUGGAGAAUGACGUAGCAUGCUACGCG ZINC ION 6.5409e-05 2 ZN MAGNESIUM ION 2.4305e-05 4 MG 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine 0.000482168 2 WSB water 1.8015e-05 242 HOH singleParticle particle 8.0 ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.7000000000000001 2.5 GATAN K3 BIOQUANTUM (6k x 4k) 51.0 1 7CYQ 2.9 FSC 0.143 CUT-OFF 1190409 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_40699.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 273.664 273.664 273.664 90.0 90.0 90.0 Z Y X -28.509402999999999 54.754725999999998 -0.00017650679 0.9575291 1.069 1.069 1.069 2.48 AUTHOR Composite sharpened map. emd_40699_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 273.664 273.664 273.664 90.0 90.0 90.0 Z Y X -32.682026 54.515270000000001 -0.0023714919 1.0000578 1.069 1.069 1.069 AUTHOR Composite locally filtered map emd_40699_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 273.664 273.664 273.664 90.0 90.0 90.0 X Y Z -8.535316 24.854901999999999 -0.000002164157 0.99998134 1.069 1.069 1.069 AUTHOR Composite half map A emd_40699_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 273.664 273.664 273.664 90.0 90.0 90.0 X Y Z -9.053674000000001 24.042148999999998 -0.0000020833875 0.9999819 1.069 1.069 1.069 AUTHOR Composite half map B emd_40699_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 273.664 273.664 273.664 90.0 90.0 90.0 X Y Z -4.245137 7.2587733 0.0022622421 0.15613297 1.069 1.069 1.069 AUTHOR Focused refinement 2 used in composite emd_40699_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 273.664 273.664 273.664 90.0 90.0 90.0 X Y Z -3.813736 7.5676475 0.0020306914 0.13189533 1.069 1.069 1.069 AUTHOR Focused refinement 1 used in composite emd_40699_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 273.664 273.664 273.664 90.0 90.0 90.0 X Y Z -4.768603 6.9709716 0.0025741127 0.16078606 1.069 1.069 1.069 AUTHOR Consensus map used in composite