Viral protein


Last updated: 2021 Sep 13
Total hit(s): 87
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The cryo-EM structure of the S protein of the Alpha variant in the apo form and receptor ACE-2 bound form were charecterised. The A570D mutation modulates the opening and closing of the receptor binding domain (RBD) by introducing a salt bridge. The N501Y mutation increases ACE-2 binding affinity by introducing pi-pi interaction.
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PMID
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Title Impacts on the structure-function relationship of SARS-CoV-2 spike by B.1.1.7 mutations
Date of Entry 2021 Sep 13


Structure of SARS-CoV-2 ORF8 accessory protein reveals a 60-residue core.It has is 16% sequence identity to SARS-CoV-2 ORF7a, a covalent disulfide linked dimer and a non-covalent dimer formed by 73YIDI76 sequence. ORF8 antibodies are major serological markers of SARS-CoV-2 infection.
33361333
(Proc Natl Acad Sci U S A)
PMID
33361333
Date of Publishing: 2021 Jan 12
Title Structure of SARS-CoV-2 ORF8, a rapidly evolving coronavirus protein implicated in immune evasion
Author(s) nameFlower TG, Buffalo CZ et al.
Journal Proc Natl Acad Sci U S A
Impact factor
9.35
Citation count: 4
Date of Entry 2021 Aug 22


Neuropilin-1 b1 domain binds with SARS-CoV-2 S1 C-end rule (CendR) peptide (7 residues -679-NSPRRAR-685) with an affinity of 20.3 µM at pH 7.5, and 13.0 µM at pH 5.5. In NRP1-depleted Caco-2 cells, viral uptake is halved compared to control cells. Blocking the interaction of NRP1-b1 with SARS-CoV-2 S1 CendR with inhibitors like EG00229 can lead to new anti COVID-19 therapeutics.
33082294
(Science)
PMID
33082294
Date of Publishing: 2020 Nov 13
Title Neuropilin-1 is a host factor for SARS-CoV-2 infection
Author(s) nameDaly JL, Simonetti B et al.
Journal Science
Impact factor
20.57
Citation count: 56
Date of Entry 2021 Aug 2


Structure of SARS-CoV-2 Nsp15 endoribonuclease with Uridine-2',3'-Vanadate (UV, a transition state analog), results in the formation of 2′,3′-cyclic phosphodiester. This is critical for further RNA maturations and functions. This structure proposes that Nsp15 should follow a two-step reaction mechanism with the final product being 3UMP.
33564093
(Commun Biol)
PMID
33564093
Date of Publishing: 2021 Feb 9
Title Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2
Author(s) nameKim Y, Wower J et al.
Journal Commun Biol
Impact factor
~
Citation count: 2
Date of Entry 2021 Aug 2


The structure of Tipiracil (a uracil derivative ) and SARS-CoV-2 Nsp15 endoribonuclease shows Tipiracil competitively inhibits the enzyme action by binding to its active site. Structure illustrates that uracil alone probably has similar inhibitory properties and provides basis for the uracil scaffold-based drug development.
33564093
(Commun Biol)
PMID
33564093
Date of Publishing: 2021 Feb 9
Title Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2
Author(s) nameKim Y, Wower J et al.
Journal Commun Biol
Impact factor
~
Citation count: 2
Date of Entry 2021 Aug 2


Structure of SARS-CoV-2 Nsp15 endoribonuclease in complex with dinucleoside monophosphate (GpU), which binds to the active site of the enzyme with uracil interacting with Tyr343 and Ser294. This results in the SARS-CoV-2 Nsp15 is inhibition. Complex structure demonstrates location and specificity determinants of the uridine with a 5-phosphoryl group. Nsp15 is shown to bind and hydrolyze 4, 7, and 20 nucleotide long RNA. Comparitive study of Nsp15 and RNase A active site displayed some conserved active site residues and indicated a common catalytic mechanism with a two-step reaction releasing 3UMP, despite distinct RNA binding site organization in both including both sequence and structure dissimilarity.
33564093
(Commun Biol)
PMID
33564093
Date of Publishing: 2021 Feb 9
Title Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2
Author(s) nameKim Y, Wower J et al.
Journal Commun Biol
Impact factor
~
Citation count: 2
Date of Entry 2021 Aug 2


Structure of SARS-CoV-2 Nsp15 endoribonuclease in complex with 3'-uridine monophosphate shows uracil demonstrates higher affinity for Trp333 site than in uracil-recognition site created by His235, His250, and Thr341. Structure emphasis that since the enzyme's substrate is a larger RNA molecule, the identity of the Trp333-interacting base is inappropriate.
33564093
(Commun Biol)
PMID
33564093
Date of Publishing: 2021 Feb 9
Title Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2
Author(s) nameKim Y, Wower J et al.
Journal Commun Biol
Impact factor
~
Citation count: 2
Date of Entry 2021 Aug 2


SARS-CoV-2 Nsp15 is inhibited by interactions with the uridine binding pocket in the enzyme's active site. Structure of SARS CoV-2 Nsp15 endoribonuclease in complex with Uridine-5'-Monophosphate shows Nsp15 discriminates between the uracil and purine bases by forming van der Waals contacts with Tyr343 and hydrogen bonds Ser294 (an active site residue ). Nsp15 enzyme is inhibited by the binding of 5'-UMP in the uracil binding pocket.
33564093
(Commun Biol)
PMID
33564093
Date of Publishing: 2021 Feb 9
Title Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2
Author(s) nameKim Y, Wower J et al.
Journal Commun Biol
Impact factor
~
Citation count: 2
Date of Entry 2021 Aug 2


Monovalent hACE2 decoy CTC-445.2 binds to all the three RBDs of a single spike protein with a low nanomolar affinity and high specificity. The divalent CTC-445.2d shows about ~10 fold increase in the binding. De novo protein design approach to generate decoys is independent to traditional therapeutics and has the potential to better overcome mutational viral evasion.
33154107
(Science)
PMID
33154107
Date of Publishing: 2020 Dec 4
Title De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2
Author(s) nameLinsky TW, Vergara R et al.
Journal Science
Impact factor
20.57
Citation count: 7
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: 198
Date of Entry 2021 Jul 28


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: 198
Date of Entry 2021 Jul 28


Binding of monoclonal antibody, B6-Fab to SARS-CoV/SARS-CoV-2 spike stem helix peptide, sterically interferes with the spike protein's fusion the membrane. B6 binds to the hydrophobic core of the stem helix bundle and disrupts its quaternary structure. It prevents S2 subunit refolding from the pre- to the post-fusion state and blocks viral entry. This study unveils an unexpected target for next-generation structure-guided design of a pan-beta-coronavirus vaccine.
33981021
(Nat Struct Mol Biol)
PMID
33981021
Date of Publishing: 2021 May 12
Title Structural basis for broad coronavirus neutralization
Author(s) nameSauer MM, Tortorici MA et al.
Journal Nat Struct Mol Biol
Impact factor
9.8
Citation count: 5
Date of Entry 2021 Jul 28


Structural characterization of SARS-CoV-2S 2P trimer complexed with C105 Fabs, state 2 (3RBD "up") shows mutations in the spike protein do not effect the RBD-binding of mAb C105. Anti-SARS-CoV-2 antibody class derived form VH3-53/VH3-66 have a structural basis for eliciting neutralizing antibodies. The RBD and S1A epitopes are not affected by the common mutations in various SARS_CoV-2 isolates, so the various vaccines and antibody therapeutics would be effective against the COVID-19.
32645326
(Cell)
PMID
32645326
Date of Publishing: 2020 Aug 20
Title Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies
Author(s) nameBarnes CO, West AP Jr et al.
Journal Cell
Impact factor
27.35
Citation count: 74
Date of Entry 2021 Jul 28


Polycolonal IgGs and Fabs from COVID-19 convalescent patients recognise different RBD epitopes of different coronaviruses. Structural characterization of SARS-CoV-2S 2P trimer complexed with C105 Fabs, state 1 (2RBD "up"), recognises both S1A and RBD epitopes on SARS-CoV-2 spike. It reveals an epitope that blocks ACE2 receptor binding. Mutations in the spike protein do not effect the RBD-binding mAb C105. The RBD and S1A epitopes are not affected by the common mutations in various SARS_CoV-2 isolates, so the various vaccines and antibody therapeutics would be effective against the COVID-19.
32645326
(Cell)
PMID
32645326
Date of Publishing: 2020 Aug 20
Title Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies
Author(s) nameBarnes CO, West AP Jr et al.
Journal Cell
Impact factor
27.35
Citation count: 74
Date of Entry 2021 Jul 28


Structure of SARS-CoV-2 spike receptor binding domain (RBD) using computational methods predicts antibody RBD recognition signatures which can be used to design vaccine against Covid-19. In this study the effects from RBD substitutions on ACE2 recognition were not considered.
Pre-print (bioRXiv)
Date of Publishing -
Title Structural and energetic profiling of SARS-CoV-2 antibody recognition and the impact of circulating variants
Author(s) name -
Date of Entry 2021 Jun 14


Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CV05-163 and CR3022 The CR3022 cryptic site and S309 site are promising targets to avoid interference by SARS-CoV-2 mutations observed to date.
Pre-print (bioRXiv)
Date of Publishing -
Title Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants
Author(s) name -
Date of Entry 2021 Jun 14


Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to VH ab8. Y501 inserts into a cavity at the binding interface near Y41 of ACE2 and this interaction causes the increased ACE2 affinity of the N501Y mutant and its increased infectivity. The cryo-EM structures show a small but significant effect of the N501Y mutation on Fab ab1 binding and neutralization, but with no measurable effects on VH ab8 binding or neutralization.
33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 2


Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to VH ab8 (focused refinement of RBD and VH ab8). Y501 shows increased ACE2 affinity and increased infectivity. Structural studies establish the molecular basis showing the increase in ACE2 binding efficiency conferred by the N501Y mutation. Despite the higher infectivity of SARS-CoV-2 viruses carrying the N501Y mutation, the availability of the extended epitope surface on the RBD enables effective neutralization by VH ab8 and Fab ab1.
33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 2


SARS-CoV-2 N501Y mutant spike protein ectodomain bound to human ACE2 ectodomain and Fab ab1 and VH ab8 Structural studies establish the molecular basis showing the increase in ACE2 binding efficiency conferred by the N501Y mutation. Despite the higher infectivity of SARS-CoV-2 viruses carrying the N501Y mutation, the availability of the extended epitope surface on the RBD enables effective neutralization by VH ab8 and Fab ab1.
33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 2


Structural characterization of the SARS-CoV-2 N501Y mutant spike protein ectodomain. Y501 inserts into a cavity at the binding interface near Y41 of ACE2 and this interaction causes the increased ACE2 affinity of the N501Y mutant and its increased infectivity. The cryo-EM methods to identify the footprints of antibodies produced byt the vaccinesis a critical tool to prevent and treact COVID-19.
33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 2


Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to human ACE2 ectodomain (focused refinement of RBD and ACE2). Y501 inserts into a cavity at the binding interface near Y41 of ACE2 and this interaction causes the increased ACE2 affinity of the N501Y mutant and its increased infectivity. The cryo-EM methods to identify the footprints of antibodies produced byt the vaccinesis a critical tool to prevent and treact COVID-19.
33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 2


Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to human ACE2 ectodomain. Y501 inserts into a cavity at the binding interface near Y41 of ACE2 and this interaction causes the increased ACE2 affinity of the N501Y mutant and its increased infectivity. The comparison of neutralization profiles shows that the IC50for neutralization of the N501Y mutant is lower, suggesting that full-length spikes bearing the N501Y mutation bind ACE2-mFc to a higher extent.
33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 2


Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to Fab ab1 . Y501 inserts into a cavity at the binding interface near Y41 of ACE2 and this interaction causes the increased ACE2 affinity of the N501Y mutant and its increased infectivity. The cryo-EM structures show a small but significant effect of the N501Y mutation on Fab ab1 binding and neutralization, but with no measurable effects on VH ab8 binding or neutralization.
33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 2


Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to Fab ab1 (class 2). Structural studies establish the molecular basis showing the increase in ACE2 binding efficiency conferred by the N501Y mutation. despite the higher infectivity of SARS-CoV-2 viruses carrying the N501Y mutation, the availability of the extended epitope surface on the RBD enables effective neutralization by VH ab8 and Fab ab1.
33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 2


Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to Fab ab1 (class 1). Structural studies establish the molecular basis showing the increase in ACE2 binding efficiency conferred by the N501Y mutation. Despite the higher infectivity of SARS-CoV-2 viruses carrying the N501Y mutation, the availability of the extended epitope surface on the RBD enables effective neutralization by VH ab8 and Fab ab1.
33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 2