Description

COVID-19, caused by SARS-CoV-2 virus has emerged as a major challenge to mankind and declared as a pandemic by the World Health Organization (WHO). The SARS-CoV-2 virus is zoonotic in its origin and capable of jumping from its natural host, bats, to other species, including humans. Phylogenetic analyses of viral genome sequences have indicated that it closely resembles SARS-like coronavirus strain Bat CovRaTG13. The novel coronavirus is made up of a Nucleocapsid Protein (N), Spike Proteins (S), Envelope Protein (E) and the Membrane Protein (M). The structures of only S-protein and N-protein have being solved experimentally. The S-protein is the most critical one as it binds to the host cell receptor thus enables the virus to enter the host cell. Specifically, both SARS-CoV and SARS-CoV-2 belong to β-coronaviruses, and are known to bind to angiotensin-converting Enzyme Receptor 2 (ACE2) in the host.

Genome and Proteins

Structure and Statistics

Protein Name Uniprot Accession RefSeq Accession Protein Length Description No. of Structures Method
ORF 1a Nsp1 P0DTD1 YP_009725297.1 180 Nsp1 is the first protein of the polyprotein 1ab and is therefore known as leader sequence. It acts as a potent inhibitor of host gene expression and is also known as host translation inhibitor. It binds to the 40S ribosome of the host cell and inhibits its translation. 34
X-RAY DIFFRACTION(19)

ELECTRON MICROSCOPY(14)

SOLUTION NMR(1)
ORF 1a Nsp2 P0DTD1 YP_009725298.1 638 Nsp2 is involved in binding to host proteins, prohibitin 1 and 2 (PHB1and PHB2), which are involved in maintaining mitochondria biogenesis. Thereby, binding of Nsp2 leads to disruption of the host cell environment. 4
ELECTRON MICROSCOPY(2)

X-RAY DIFFRACTION(2)
ORF 1a Nsp3 (Papain-like Proteinase) P0DTD1 YP_009725299.1 1945 Nsp3 is the largest protein in coronaviruses. It possesses several conserved domain including PLpro, a critical cysteine protease, which is required for processing viral polyproteins to generate a functional replicase complex and enable viral spread. It serves as an important target for antiviral activity. 665
ELECTRON MICROSCOPY(7)

X-RAY DIFFRACTION(656)

NEUTRON DIFFRACTION(3)

SOLUTION NMR(2)
ORF 1a Nsp4 P0DTD1 YP_009725300.1 500 It interacts with Nsp3 and plays a role in membrane rearrangement of the virus and also participates in viral replication. 4
ELECTRON MICROSCOPY(3)

X-RAY DIFFRACTION(1)
ORF 1a Nsp5 (Main Proteinase) P0DTD1 YP_009725301.1 306 Nsp5, also known as 3C-like protease or Mpro, is a cysteine protease which mediates the maturation cleavage of polyproteins during virus replication at 11 sites. 1467
X-RAY DIFFRACTION(1462)

ELECTRON MICROSCOPY(4)

NEUTRON DIFFRACTION(4)

ELECTRON CRYSTALLOGRAPHY(1)
ORF 1a Nsp6 P0DTD1 YP_009725302.1 290 Nsp6 was seen to lead to impaired lysosome acidification to inhibit autophagic flux, which prevented viral components from degradation leading to induced inflammatory cell death in lung epithelial cells. 2
X-RAY DIFFRACTION(2)
ORF 1a Nsp7 P0DTD1 YP_009725303.1 83 Nsp7 together with Nsp8 and Nsp12 forms a complex which plays a role in viral RNA synthesis. 70
ELECTRON MICROSCOPY(59)

X-RAY DIFFRACTION(10)

SOLUTION NMR(1)
ORF 1a Nsp8 P0DTD1 YP_009725304.1 198 Nsp8 participates in viral RNA synthesis by forming a hexadecamer with Nsp7 and Nsp12, thereby forming a RNA polymerase complex. Also, with Nsp9, it disrupts host immune defense by suppressing protein integration into the cell membrane. 69
ELECTRON MICROSCOPY(59)

X-RAY DIFFRACTION(9)

SOLUTION NMR(1)
ORF 1a Nsp9 P0DTD1 YP_009725305.1 113 Nsp9 is thought to be involved in viral replication and along with Nsp8, it disrupts host immune defense. Also, it has been reported to interact with ribosome signal recognition particle RNA (SRP). 24
ELECTRON MICROSCOPY(14)

X-RAY DIFFRACTION(10)
ORF 1a Nsp10 P0DTD1 YP_009725306.1 139 Nsp10 has been shown to interact with both Nsp14 (3'-5' exoribonuclease) and Nsp16 (2'-O-methyltransferase) and stimulate their activity. Therefore, it plays a critical role in viral transcription and mRNAs cap methylation. 92
X-RAY DIFFRACTION(82)

ELECTRON MICROSCOPY(10)
ORF 1a Nsp11 P0DTD1 YP_009725312.1 13 Nsp11 has been found to be an intrinsically disordered protein and its function is unknown. 0
ORF1b Nsp12 P0DTD1 YP_009725307.1 932 Nsp12 is RNA-dependent RNA polymerase (RdRp). It makes a complex with Nsp7 and Nsp8 and leads to replication and transcription of the viral RNA genome. 62
ELECTRON MICROSCOPY(62)
ORF1b Nsp13 P0DTD1 YP_009725308.1 601 Nsp13 is also known as helicase which unwinds RNA duplex and also possess 5-triphosphate activity required for 5-terminal capping. It also inhibits host TBK1 phosphorylation. 86
ELECTRON MICROSCOPY(28)

X-RAY DIFFRACTION(58)
ORF1b Nsp14 P0DTD1 YP_009725309.1 527 Nsp14 has both 3?-5? exoribonuclease activity and N7-methyltransferase activity. It acts as a proofreading exoribonuclease for RNA replication. 81
X-RAY DIFFRACTION(76)

ELECTRON MICROSCOPY(5)
ORF1b Nsp15 P0DTD1 YP_009725310.1 346 Nsp15 is also known as endoribonuclease that degrades the 5'-polyuridines generated during replication viral genomic and subgenomic RNAs, in a two-step reaction to form 3'-phosphate (3'-P). The degradation is carried out to prevent host recognition. 56
X-RAY DIFFRACTION(43)

ELECTRON MICROSCOPY(13)
ORF1b Nsp16 P0DTD1 YP_009725311.1 298 Nsp16 is also known as 2?-O-Ribose-Methyltransferase that carries out methylation of the N7-methylated guanine cap on viral mRNA. Methylation is an essential step to evade innate immunity mechanisms. 71
X-RAY DIFFRACTION(70)

ELECTRON MICROSCOPY(1)
ORF2 S protein P0DTC2 YP_009724390 1273 ORF2 or spike or S- protein is the protruding projection from the surface of the virus. It mediates viral attachment to the ACE2 protein on host cell membrane and facilitates virus entry. 1903
ELECTRON MICROSCOPY(1395)

X-RAY DIFFRACTION(502)

SOLUTION NMR(6)
ORF3a Orf3a protein P0DTC3 YP_009724391 275 ORF3a forms homotetrameric ion channels (viroporin) which blocks autolysosomal formation in host, thus, facilitating virus egress. 0
ORF4 E protein P0DTC4 YP_009724392 75 ORF4, also known as envelope or E-protein is a small integral membrane protein that oligomerizes to form viroporin and allow ion transport. It also plays multiple roles in viral replication: viral assembly, virion release and pathogenesis. It also assists S-protein localization at cis-Golgi. 9
X-RAY DIFFRACTION(5)

SOLID-STATE NMR(3)

ELECTRON MICROSCOPY(1)
ORF5 M protein P0DTC5 YP_009724393 222 ORF5, also known as membrane or M-protein is an integral membrane protein that plays a crucial role in viral assembly, induces apoptosis and also interacts with N- and S-protein and regulates their function. 6
ELECTRON MICROSCOPY(5)

X-RAY DIFFRACTION(1)
ORF6 Orf6 protein P0DTC6 YP_009724394 61 ORF6 is an accessory protein that interacts with Nsp8 to promote RNA polymerase activity. It also disrupts cell nuclear import complex formation and suppresses IFN-beta production. 0
ORF7a Orf7a protein P0DTC7 YP_009724395 121 ORF7a is an accessory type I transmembrane protein that binds to host ITGAL and plays a role in attachment or modulation of leukocytes. It also acts as antagonist of host tetherin (BST2), thereby, disrupting its antiviral effect. 0
ORF7b Orf7b protein P0DTD8 YP_009725318 43 ORF7b is an accessory transmembrane protein localized in the host Golgi complex and endosome membrane system. 0
ORF8 Orf8 protein P0DTC8 YP_009724396 121 ORF8 contributes in modulating host immune response by binding to IL17RA receptor, leading to its activation and an increased secretion of pro-inflammatory factors. It also leads to cytokine storm during COVID-19 infection. 0
ORF9a N protein P0DTC9 YP_009724397 419 ORF9a also called nucleocapsid or N-protein is a critical structural protein. It is an abundant RNA-binding protein which is expressed in the early stage of infection and is critical for genome packaging. It helps RNA to enter in the cell and to interact with cellular components 71
X-RAY DIFFRACTION(66)

SOLUTION NMR(4)

SOLID-STATE NMR(1)
ORF9b Orf9b protein P0DTD2 YP_009724397 97 ORF9b is generated by an alternative open reading frame within the N-protein. It supresses IFN-I which has plays a crtical role in immune response against viral infections. 0
ORF10 Orf10 protein A0A7D6CAT9 YP_009725255 38 ORF10 is a small transmembrane protein and its function is unknown as of now. 0