Overview of SARS-CoV-2 genome-encoded proteins

Abstract

Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) has spread rapidly throughout the world. SARS-CoV-2 is an enveloped, plus-stranded RNA virus with a single-stranded RNA genome of approximately 30,000 nucleotides. The SARS-CoV-2 genome encodes 29 proteins, including 16 nonstructural, 4 structural and 9 accessory proteins. To date, over 1,228 experimental structures of SARS-CoV-2 proteins have been deposited in the Protein Data Bank (PDB), including 16 protein structures, two functional domain structures of nucleocapsid (N) protein, and scores of complexes. Overall, they exhibit high similarity to SARS-CoV proteins. Here, we summarize the progress of structural and functional research on SARS-CoV-2 proteins. These studies provide structural and functional insights into proteins of SARS-CoV-2, and further elucidate the daedal relationship between different components at the atomic level in the viral life cycle, including attachment to the host cell, viral genome replication and transcription, genome packaging and assembly, and virus release. It is important to understand the structural and functional properties of SARS-CoV-2 proteins as it will facilitate the development of anti-CoV drugs and vaccines to prevent and control the current SARS-CoV-2 pandemic.

Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants

“…The SARS-CoV-2 virus belongs to the beta coronavirus family that contains single positive-strand RNA as a genetic material [9]. Its viral genome contains approximately 29,881 nucleotides (Gene ID-MN908947) which encode 9860 amino acids [10].…”

SARS-CoV-2 Membrane Protein: From Genomic Data to Structural New Insights

“…Since M protein is essential in the SARS-CoV-2, including for Virus-like particles (VLP) formation, a complete understanding of the structure–function relationship can help the development of more efficient therapeutics [ 9 , 19 , 21 ]. However, this task has been affected by the difficulty to stabilize and crystallize the M protein [ 22 , 23 , 24 ], and as such there is no experimentally resolved structure available by either Nuclear Magnetic Resonance (NMR), X-ray crystallography, or cryo-EM [ 25 ], thus far.…”

Translational Control of COVID-19 and Its Therapeutic Implication

“…Among the nonstructural proteins, the papain-like protease (PLpro) activity of NSP3, the chymotrypsin-like protease (3CLpro) activity of NSP5, and the RNA-dependent polymerase (RDRP) activity of NSP12 are the core of coronavirus replication ( 37 ). Pp1a is translated early and will be cleaved into NSP1 to NSP11 by NSP3 or by NSP5, while pp1ab synthesized through the -1 PRF is cleaved into NSP1-NSP10 and NSP12 to NSP16 ( 38 , 39 ) ( Figure 1A ). PLpro hydrolyzes the viral polyprotein precursors pp1a and pp1ab at three sites to produce the non-structural proteins NSP1, NSP2, and NSP3 ( 40 , 41 ).…”