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- PDB-7n0c: Cryo-EM structure of the monomeric form of SARS-CoV-2 nsp10-nsp14... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7n0c | ||||||
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Title | Cryo-EM structure of the monomeric form of SARS-CoV-2 nsp10-nsp14 (E191A)-RNA complex | ||||||
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Function / homology | ![]() Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / viral RNA-directed RNA polymerase complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, C. / Yang, Y. | ||||||
![]() | ![]() Title: Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme. Authors: Chang Liu / Wei Shi / Scott T Becker / David G Schatz / Bin Liu / Yang Yang / ![]() Abstract: Coronavirus 3′-to-5′ exoribonuclease (ExoN), residing in the nonstructural protein (nsp) 10–nsp14 complex, boosts replication fidelity by proofreading RNA synthesis and is critical for the ...Coronavirus 3′-to-5′ exoribonuclease (ExoN), residing in the nonstructural protein (nsp) 10–nsp14 complex, boosts replication fidelity by proofreading RNA synthesis and is critical for the virus life cycle. ExoN also recognizes and excises nucleotide analog inhibitors incorporated into the nascent RNA, undermining the effectiveness of nucleotide analog–based antivirals. Here we present cryo–electron microscopy structures of both wild-type and mutant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nsp10-nsp14 in complex with an RNA substrate bearing a 3′-end mismatch at resolutions ranging from 2.5 to 3.9 angstroms. The structures reveal the molecular determinants of ExoN substrate specificity and offer insight into the molecular mechanisms of mismatch correction during coronavirus RNA synthesis. Our findings provide guidance for rational design of improved anticoronavirus therapies. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 145 KB | Display | ![]() |
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PDB format | ![]() | 114.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 583.2 KB | Display | ![]() |
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Full document | ![]() | 589.3 KB | Display | |
Data in XML | ![]() | 23.4 KB | Display | |
Data in CIF | ![]() | 33.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 24103MC ![]() 7n0bC ![]() 7n0dC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 14802.930 Da / Num. of mol.: 1 / Fragment: UNP residues 4254-4392 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: rep, 1a-1b / Production host: ![]() ![]() ![]() |
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#2: Protein | Mass: 59829.441 Da / Num. of mol.: 1 / Fragment: UNP residues 5926-6452 / Mutation: E191A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: rep, 1a-1b / Production host: ![]() ![]() ![]() References: UniProt: P0DTD1, ![]() |
-RNA chain , 2 types, 2 molecules TD
#3: RNA chain | Mass: 11901.023 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() ![]() ![]() |
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#4: RNA chain | Mass: 10459.259 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() ![]() ![]() |
-Non-polymers , 3 types, 8 molecules 




#5: Chemical | ChemComp-ZN / #6: Chemical | #7: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Monomeric form of SARS-CoV-2 nsp10-nsp14 (E191A)-RNA complex Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 49.19 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 184500 / Symmetry type: POINT | ||||||||||||||||||||||||
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