Sequence : Nsp7

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Original Article
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Virus mutagenic capability depends upon several factors, including the fdelity of viral enzymes that replicate nucleic acids, as SARS-CoV-2 RNA dependent RNA polymerase (RdRp) According to the observations of the authors, after February 2020, when the first locally transmitted SARS-CoV-2 cases out of Asia were reported, viral genomes presented diferent point mutations, clearly distinguishable within different geographic areas. Over time, it was observed that they were able to identify three recurrent mutations in Europe (in positions 3036, 14408 and 23403) and 3 other different mutations in North America (in positions 17746, 17857 and 18060). So far, these mutations have not been detected in Asia. The number and the occurrence, as well as the median value of virus point mutations registered out of Asia, increase over time. In the preset study, they found that the RdRp mutation, located at position 14408, which is present in European viral genomes starting from February 20th, 2020, is associated with a higher number of point mutations compared to viral genomes from Asia.
32321524
(J Transl Med)
PMID
32321524
Date of Publishing: 2020 Apr 22
Title Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant
Author(s) namePachetti M, Marini B et al.
Journal J Transl Med
Impact factor
4.2
Citation count: 342
Date of Entry 2021 Jul 13



Structure : Nsp7

Total row(s): 7
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Original Article
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Structure of SARS-CoV-2 mini RTC assembly by viral RNA-dependent RNA polymerase (nsp12) with a template-primer RNA, nsp7 and nsp8, and two helicase molecules (nsp13-1 and nsp13-2). nsp13-1 stabilizes the mini RTC by contacting with nsp13-2, which anchors the 5'-extension of RNA template, and interacts with nsp7-nsp8-nsp12-RNA.
33208736
(Nat Commun)
PMID
33208736
Date of Publishing: 2020 Nov 18
Title Architecture of a SARS-CoV-2 mini replication and transcription complex
Author(s) nameYan L, Zhang Y et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 4


Structural characterisation of SARS-CoV-2 mini replication and transcription complex
33208736
(Nat Commun)
PMID
33208736
Date of Publishing: 2020 Nov 18
Title Architecture of a SARS-CoV-2 mini replication and transcription complex
Author(s) nameYan L, Zhang Y et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 4


The structure of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) complex in its active form comprises the 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. 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 help in the processivity of RdRp, required for replicating the long genome of coronaviruses. The active site of nsp12 consists of five conserved motif AE, of which the residues (D760 and D761) of motif C binds to the RNA 3 end and plays a crucial role in RNA synthesis. K58 is located in the nsp8 extension and plays an important role in interaction with RNA.
32438371
(Nature)
PMID
32438371
Date of Publishing: 2020 Aug
Title Structure of replicating SARS-CoV-2 polymerase
Author(s) nameHillen HS, Kokic G et al.
Journal Nature
Impact factor
24.36
Citation count: 207


Structural characterization of cryo-EM structure of the apo nsp12-nsp7-nsp8 complex Knowledge of viral replication mechanism as well as the structure of the protiens involved can prove to be fruitful for drug discovery against SARS-CoV-2 virus
32358203
(Science)
PMID
32358203
Date of Publishing: 2020 Jun 26
Title Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir
Author(s) nameYin W, Mao C et al.
Journal Science
Impact factor
20.57
Citation count: 367


Structural characteirzation of the nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of Remdesivir(RTP) The structure of the template-RTP RdRp complex provides a useful model to rationalize how these drugs inhibit the activity of SARS-CoV-2 RdRp.
32358203
(Science)
PMID
32358203
Date of Publishing: 2020 Jun 26
Title Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir
Author(s) nameYin W, Mao C et al.
Journal Science
Impact factor
20.57
Citation count: 367


Structure of SARS-Cov-2 RNA-dependent RNA polymerase nsp12, in complex with nsp7 and nsp8 reports a conserved polymerase core and a β hairpin domain (residues N215 to N218) at its N-terminus. This structure aids in the study of remdesivir and other drug candidates' antiviral activity. The structure of RdRp can be used as a source for discovering broad spectrum antivirals.
32277040
(Science)
PMID
32277040
Date of Publishing: 2020 May 15
Title Structure of the RNA-dependent RNA polymerase from COVID-19 virus
Author(s) nameGao Y, Yan L et al.
Journal Science
Impact factor
20.57
Citation count: 485
Date of Entry 2021 Jul 28


Structure of SARS-CoV-2 RNA-dependent RNA polymerase nsp12 in complex with cofactors nsp7 and nsp8 under reducing condition, forms a β hairpin domain (residues N215 to N218) at its N-terminus. This structure aids in antiviral viral study of remdesivir and other antiviral drugs. The structure of RdRp can be used as a source for discovering broad spectrum antivirals.
32277040
(Science)
PMID
32277040
Date of Publishing: 2020 May 15
Title Structure of the RNA-dependent RNA polymerase from COVID-19 virus
Author(s) nameGao Y, Yan L et al.
Journal Science
Impact factor
20.57
Citation count: 485
Date of Entry 2021 Jul 28



Molecular_interactions : Nsp7

Total row(s): 3
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Key Findings
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Original Article
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Nsp13-1 stabilizes SARS-CoV-2 replication and transcription (RTC) complex by contacting with nsp13-2, which anchors the 5'-extension of RNA template, and interacting with nsp7-nsp8-nsp12-RNA. Different orientations of nsp13-1 results in different interactions with the two forms of mini RTC. Mini RTC with an nsp12R365A mutation has greater helicase activity compared to individual apsnsp13. Nsp13-1T216A mutation has a decreased helicase activity.
33208736
(Nat Commun)
PMID
33208736
Date of Publishing: 2020 Nov 18
Title Architecture of a SARS-CoV-2 mini replication and transcription complex
Author(s) nameYan L, Zhang Y et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 4


Cryo-electron microscopy structure of the SARS-CoV-2 RdRp with non-structural protein 12 (nsp12), nsp8 and nsp7, and more than two turns of RNA template-product duplex, shows active-site cleft of nsp12 binds to the first turn of RNA and mediates RdRp activity and two copies of nsp8 bind to opposite sides of the cleft and position the second turn of RNA. Nsp8 along the exiting RNA, forms positively charged 'sliding poles' which affect the processivity of RdRp. The active site of nsp12 consists of five conserved motif AE, of which the residues (D760 and D761) of motif C binds to the RNA 3 end and plays a crucial role in RNA synthesis. K58 is located in the nsp8 extension and plays an important role in interaction with RNA.
32438371
(Nature)
PMID
32438371
Date of Publishing: 2020 Aug
Title Structure of replicating SARS-CoV-2 polymerase
Author(s) nameHillen HS, Kokic G et al.
Journal Nature
Impact factor
24.36
Citation count: 207


The complex cryo-electron microscopy structure of SARS-CoV-2 RdRp with a 50-base template-primer RNA and remdesivir, shows the partial double-stranded RNA template is present in the central channel of RdRp where remdesivir is covalently attached as the first replicated base pair and results in the termination of chain elongation. The conserved protein-RNA interactions and the catalytic active site residues, in the diverse RNA viruses, makes it possible to develop broad spectrum antiviral inhibitors.
32358203
(Science)
PMID
32358203
Date of Publishing: 2020 Jun 26
Title Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir
Author(s) nameYin W, Mao C et al.
Journal Science
Impact factor
20.57
Citation count: 367