Image credits: NIH/NIAID (by Kristen Browne).

SARS-CoV-2 Virion and Proteins

Curated by NIH/NIAID

The COVID-19 pandemic has led to the extremely rapid publication of experimental structures of the SARS-CoV-2 virus and its proteins. This collection consists of structures released by the Protein Data Bank, as well as additional “Featured” structures curated by NIAID, in 3D-printable formats. The latter are also based upon experimental data, but with custom depictions that highlight functional aspects of SARS-CoV-2 or related viruses. It also contains a model of the SARS-CoV-2 virion created at the NIAID Rocky Mountain Laboratories based on electron microscopy of the virus.

In addition to the “Featured” section, each type of viral protein has its own section within the collection. Many of these structures contain bound small molecule ligands, which could guide discovery of new drug candidates.

This collection will be updated as additional experimental structures become available.

Below are the most recent submissions for each SARS-CoV-2 protein. Search all models

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Featured SARS-CoV-2 Models

Featured models are custom representations of SARS-CoV-2 related structures designed by team members from NIH/NIAID. These 3D models are created from experimentally-derived data.

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Spike Receptor Protein

The Spike (S) is a homotrimeric transmembrane glycoprotein that protrudes from the viral surface giving coronavirus virions their crown-like appearance. The spike protein mediates the entry of coronavirus into host cells. It is a major target of immune response to the virus.

Two large polyproteins are synthesized from the SARS-CoV-2 genome. The main protease performs some of the cuts the polyprotein that process it into the individual mature proteins that the virus uses to replicate.

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Papain-Like Protease

One domain of non-structural protein 3 (NSP3), the papain-like protease makes 3 of the cuts in the polyprotein to make individual mature non-structural proteins, as well as proteins in the infected to cell to reduce the cellular defenses against the virus.

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RNA Dependent RNA Polymerase (NSP12)

The C-terminal part of non-structural protein 12 (NSP12) that contains the RNA dependent RNA polymerase, which synthesizes the RNA that is used to direct the construction of viral proteins, and also replicates the genome of the virus.

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Nucleocapsid Proteins

The nucleocapsid (N) protein binds to the viral RNA genome and packs it into a long, helical ribonucleoprotein complex, and arranges it within the viral membrane.

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Non-Structural Protein 3 (NSP3) ADP Ribose Phosphatase

Non-structural protein 3 (NSP3) is largest protein encoded by SARS-CoV-2 genome, with many functions related to replication and transcription of the genome. The ADP Ribose Phosphatase is one domain of NSP3; it is used in the maturation of the virus.

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Non-Structural Protein 7 (NSP7)

Non-structural protein 7 (NSP7) interacts with the RNA dependent RNA polymerase as part of a larger complex involved in RNA replication.

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Non-Structural Protein 8 (NSP8)

Non-structural protein 8 (NSP16) is an RNA binding protein that may catalyze the synthesis of RNA primers for use by the primer-dependent RNA dependent RNA polymerase.

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Non-Structural Protein 9 (NSP9) Replicase

Non-structural protein 9 (NSP9) is a single-stranded RNA-binding protein that is thought to stabilize and protect copied and template RNA strands during replication and/or transcription.

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Non-Structural Protein 10 (NSP10)

Non-structural protein 10 (NSP10) is a double-stranded RNA binding protein. It is thought to be involved in synthesis of the template RNA strand.

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Non-Structural Protein (NSP15) Endoribonuclease

Non-structural protein 15 (NSP15) is an endoribonuclease which is essential for efficient coronavirus RNA synthesis.

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Non-Structural Protein (NSP16)

Non-structural protein 16 (NSP16) provides 2′-O-ribose methyl transferase activity which is all used for efficient coronavirus RNA synthesis.

Open Reading Frame 3a (ORF3a) is implicated in viral release, inflammasome activation, and cell death.

Open Reading Frame 7a (ORF7a) is a transmembrane protein that interferes with the host’s immune system; it may enhance the release of newly-assembled virus from host cells.

Open Reading Frame 8 (ORF8) has been proposed to interfere with host immune responses, and is one of the most rapidly evolving accessory proteins among the betacoronaviruses.