Journal: Nature / Year: 2020 Title: Structure of replicating SARS-CoV-2 polymerase. Authors: Hauke S Hillen / Goran Kokic / Lucas Farnung / Christian Dienemann / Dimitry Tegunov / Patrick Cramer / Abstract: The new coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses an RNA-dependent RNA polymerase (RdRp) for the replication of its genome and the transcription of its genes. ...The new coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses an RNA-dependent RNA polymerase (RdRp) for the replication of its genome and the transcription of its genes. Here we present a cryo-electron microscopy structure of the SARS-CoV-2 RdRp in an active form that mimics the replicating enzyme. The structure comprises the viral proteins non-structural protein 12 (nsp12), nsp8 and nsp7, and more than two turns of RNA template-product duplex. The active-site cleft of nsp12 binds to the first turn of RNA and mediates RdRp activity with conserved residues. Two copies of nsp8 bind to opposite sides of the cleft and position the second turn of RNA. Long helical extensions in nsp8 protrude along exiting RNA, forming positively charged 'sliding poles'. These sliding poles can account for the known processivity of RdRp that is required for replicating the long genome of coronaviruses. Our results enable a detailed analysis of the inhibitory mechanisms that underlie the antiviral activity of substances such as remdesivir, a drug for the treatment of coronavirus disease 2019 (COVID-19).
History
Deposition
May 6, 2020
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Header (metadata) release
May 13, 2020
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Map release
May 13, 2020
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Update
May 22, 2024
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Current status
May 22, 2024
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
EMPIAR-10409 (Title: Structure of replicating SARS-CoV-2 polymerase / Data size: 2.5 TB Data #1: Unaligned TIF movies of SARS-CoV2 RdRp in complex with nsp7, nsp8 and RNA (part 1) [micrographs - multiframe] Data #2: Unaligned TIF movies of SARS-CoV2 RdRp in complex with nsp7, nsp8 and RNA (part 2) [micrographs - multiframe] Data #3: Warp picked and extracted particles [picked particles - single frame - processed] Data #4: Reextraced particles at 1.3 A/px (for Map2 and Map3) [picked particles - single frame - processed] Data #5: Refined particles (Map 1) [picked particles - single frame - processed] Data #6: Refined particles (Map 2) [picked particles - single frame - processed] Data #7: Refined particles (Map 3) [picked particles - single frame - processed])
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
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Electron microscopy
Microscope
FEI TITAN KRIOS
Specialist optics
Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recording
Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8168 / Average exposure time: 2.2 sec. / Average electron dose: 60.0 e/Å2 Details: Images were collected at 30 degree stage tilt. Non-superres.
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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