Proteins and Virion

Viral/Host Proteins and the Virion itself

Virus (SARS-CoV-2 and SARS-CoV), and Host based proteins are referenced here as well as the whole virion particle.

Data classification:
  • Structures: Data defining structures determined by experimental methods and referenced via a unique identifier such as a PDB ID.
  • Models: Derived, integrated, or refined structures from multiple data sources prepared for different computational tasks.
  • Simulations: The datasets produced as a result of applying the models to different scientific techniques.
ZhangPLpro-nsp33CLpro-nsp5nsp7nsp9RdRPnsp1nsp2nsp4nsp6nsp8nsp10spikeHelicaseVirionVirionVirionNucleoproteinOpen Reading Frame 7a

Virion Particle

SARS-CoV-2 Virion

The complete virion particle consisting of all proteins and interactions in the Viral categories

Top Structural Data: [See All]

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Coarse Grained SARS-CoV-2 Virion

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Viral Proteins

Viral Spike Proteins

Viral Spike Fusion Core

Fusion core of the spike’s S2 stalk. Includes the Heptad Repeats, HR1 and HR2
Peptide
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[6lxt] Structure of Post Fusion Core of 2019-NCoV S2 Subunit
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SARS-CoV-2 Spike (S) glycoprotein

The external glyocoprotein of the virus envelope required for fusion and entry into human host cells.

Small Molecule Peptide Antiviral
Top Structural Data: [See All]
[6M1V] Crystal Structure of Post Fusion Core of 2019-NCoV S2 Subunit
[6m17] The 2019-NCoV RBD/ACE2-B0AT1 Complex
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Spike by Yang Zhang Lab

Ab 6D3 Bound to SARS-CoV-2 Spike in Down State

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Folding@home simulations of the SARS-CoV-2 spike RBD with P337L mutation bound to monoclonal antibody S309

SIRAH-CoV2 initiative - RBD triple glycosylated at Asn331, 343, and 481


Viral Protease, Polymerase, and Nonstructured Proteins

SARS-CoV-2 main protease (3CLpro or NSP5)

Cysteine protease essential for viral maturation

Small Molecule
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[6Y2G] Crystal Structure (Orthorhombic Form) of the Complex Resulting From the Reaction Between SARS-CoV-2 (2019-NCoV) Main Protease and Tert-Butyl (1-((S)-1-(((S)-4-(Benzylamino)-3,4-Dioxo-1-((S)-2-Oxopyrrolidin-3-Yl)butan-2-Yl)amino)-3-Cyclopropyl-1-Oxopropan-2-Yl)-2-Oxo-1,2-Dihydropyridin-3-Yl)carbamate (Alpha-Ketoamide 13b)
[5R8T] PanDDA Analysis Group Deposition of Ground-State Model of SARS-CoV-2 Main Protease Screened Against DSI Poised (Enamine), Fraglites and Peplites (Newcastle University), Mini Frags (Astex), York 3D (York University), Electrophile Cysteine Covalent (Weizman Institute) Fragment Libraries
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SWISS-MODEL 3CLpro

Docked Structures of the N-Terminal Natural Substrate to SARS-CoV and SARS-CoV-2 Mpro

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Folding@home SARS-CoV-2 main protease (apo, monomer) simulations

Riken BDR 10 Microsecond Trajectory System Snapshot every 10ns


SARS-CoV-2 Macrodomain (NSP3)

Macrodomain (NSP3, Macrodomain, or X) is a viral protein that is believed to be involved in repressing host immune response from its ability to remove ADP-ribose from ADP-ribosylated proteins and RNA.
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Folding@home simulations of nsp3 macrodomain

SIRAH-CoV2 initiative - Apo ADP-ribose phosphatase of NSP3


SARS-CoV-2 Papain-like protease (NSP3)

PLpro (NSP3, papain-like protease) is a viral cysteine protease responsible for maturation of the viral polyprotein, necessary for infection. Also involved in repressing host immune response.

Small Molecule
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[2FE8] SARS Coronavirus Papain-Like Protease: Structure of a Viral Deubiquitinating Enzyme
[4ow0] X-Ray Structural and Biological Evaluation of a Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-Like Proteases
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SARS-CoV-1 Ligand-Free (PDB 4OW0 Ligand Removed)

SARS-CoV-2 Ligand-Free (PDB 6W9C - Chain C)

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Apo SARS-CoV-2 PLPro (from PDB 6W9C C-chain)

Apo SARS-CoV PLpro


SARS-CoV-2 RNA Polymerase (NSP12)

RNA-dependent, RNA polymerase.
Antiviral Small Molecule
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[7BV1] Cryo-EM Structure of the Apo Nsp12-Nsp7-Nsp8 Complex
[7BV2] The Nsp12-Nsp7-Nsp8 Complex Bound to the Template-Primer RNA and Triphosphate Form of Remdesivir(RTP)
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SARS-CoV-2 RdRp Complex (Nsp12+2*nsp8+nsp7) + RNA Template-Primer + ATP Model for MD Simulations

SARS-CoV-2 RdRP (NSP12) in Complex With NSP7 and Two Copies of NSP8: ISOLDE Refined Model

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HADDOCK docking of approved Drugbank set against RdRp

DESRES-ANTON-10917618 10 µs simulation of SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex in aqueous solution


Helicase coronavirus nonstructural protein 13 (NSP13)

The NSP13 SARS sequence is conserved and helicase activity is necessary for COVID replication. Helicase inhibition has been used for virus (HSV-amenavir) and cancer treatment (eIF41, RocA rocaglamides) and has gained interested in a potential disrupting target.
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[6ZSL] Crystal Structure of the SARS-CoV-2 Helicase at 1.94 Angstrom Resolution
[6ZB5] SARS CoV-2 Spike Protein, Closed Conformation, C3 Symmetry
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Helicase (NSP13) by Yang Zhang Lab

SWISS-MODEL Helicase

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Folding@home simulations of nsp13

SIRAH-CoV2 initiative - Helicase


Coronavirus nonstructural protein 1

Suppressor of host genome expression
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Refinement of Nsp1 by FeigLab

Refinement of SWISS-MODEL Nsp1 by FeigLab

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Coronavirus nonstructural protein 10

Suppressor of host genome expression
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[6W4H] 1.80 Angstrom Resolution Crystal Structure of NSP16 - NSP10 Complex From SARS-CoV-2
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SWISS-MODEL NSP10 + NSP16

SWISS-MODEL NSP10

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Folding@home simulations of nsp10

SIRAH-CoV2 initiative - NSP16 - NSP10 Complex


Coronavirus nonstructural protein 11

Suppressor of host genome expression
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Coronavirus nonstructural protein 14

Suppressor of host genome expression
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SWISS-MODEL NSP10 + NSP14

NSP14 by Yang Zhang Lab

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Coronavirus nonstructural protein 15

Suppressor of host genome expression
Top Structural Data: [See All]
[6M03] The Crystal Structure of COVID-19 Main Protease in Apo Form
[6W01] The 1.9 a Crystal Structure of NSP15 Endoribonuclease From SARS CoV-2 in the Complex With a Citrate
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NSP15 by Yang Zhang Lab

SWISS-MODEL NSP15

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SIRAH-CoV2 initiative - NSP15 Endonuclease


Coronavirus nonstructural protein 16

Suppressor of host genome expression
Top Structural Data: [See All]
[6W4H] 1.80 Angstrom Resolution Crystal Structure of NSP16 - NSP10 Complex From SARS-CoV-2
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NSP16 by Yang Zhang Lab

SWISS-MODEL NSP10 + NSP16

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SIRAH-CoV2 initiative - NSP16 - NSP10 Complex


Coronavirus nonstructural protein 2

Suppressor of host genome expression
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NSP2 by Yang Zhang Lab

Refinement of Nsp2 by FeigLab

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Coronavirus nonstructural protein 4

Suppressor of host genome expression
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Refinement of NSP4 in Membrane Environment by FeigLab

Refinement of Nsp4 by FeigLab

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Coronavirus nonstructural protein 6

Suppressor of host genome expression
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NSP6 by Yang Zhang Lab

Refinement of Nsp6 by FeigLab

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Coronavirus nonstructural protein 7

Suppressor of host genome expression
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[6WIQ] Crystal Structure of the Co-Factor Complex of NSP7 and the C-Terminal Domain of NSP8 From SARS CoV-2
[6m71] SARS-Cov-2 RNA-Dependent RNA Polymerase in Complex With Cofactors
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SARS-CoV RdRP (NSP12) in Complex With Cofactors NSP7 and NSP8: ISOLDE Refined Model

SWISS-MODEL NSP7 + NSP8 + RdRP

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Gromacs 300 ns MD of SARS-CoV-2 apo-RdRp model, All Atom model

SIRAH-CoV2 initiative - NSP7-NSP8 complex


Coronavirus nonstructural protein 8

Suppressor of host genome expression
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[7BTF] SARS-CoV-2 RNA-Dependent RNA Polymerase in Complex With Cofactors in Reduced Condition
[6WIQ] Crystal Structure of the Co-Factor Complex of NSP7 and the C-Terminal Domain of NSP8 From SARS CoV-2
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SWISS-MODEL NSP7 + NSP8 + RdRP

NSP8 by Yang Zhang Lab

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DESRES-ANTON-10917618 10 µs simulation of SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex, no water or zinc

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + ATP model, All Atom model


Coronavirus nonstructural protein 9

Suppressor of host genome expression
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[6W4B] The Crystal Structure of Nsp9 RNA Binding Protein of SARS CoV-2
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NSP9 by Yang Zhang Lab

SWISS-MODEL NSP9

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SIRAH-CoV2 initiative - NSP9 RNA binding protein

Folding@home simulations of nsp9


Viral Open Reading Frame Proteins

Coronavirus Open Reading Frame 10

Behaviour of this protein is uncertain/unclear.
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Refinement of RaptorX ORF10 by FeigLab

Refinement of ORF10 by FeigLab

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Coronavirus Open Reading Frame 3a

Forms homotetrameric potassium sensitive ion channels and may modulate virus release.
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[6XDC] Cryo-EM Structure of SARS-CoV-2 ORF3a
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ORF3a by Yang Zhang Lab

Refinement of ORF3a by FeigLab

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SIRAH-CoV2 initiative - Membrane embedded ORF3a


Coronavirus Open Reading Frame 6

Possible determinant of virus virulence.
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ORF6 by Yang Zhang Lab

Refinement of RaptorX ORF6 by FeigLab

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Coronavirus Open Reading Frame 7a

Non-structural protein which is dispensable for virus replication in cell culture. May suppress small interfering RNA (siRNA). May bind to host ITGAL, thereby playing a role in attachment or modulation of leukocytes.
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[6W37] STRUCTURE of the SARS-CoV-2 ORF7A ENCODED ACCESSORY PROTEIN
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SWISS-MODEL Protein 7a

ORF7a by Yang Zhang Lab

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SIRAH-CoV2 initiative - ORF7A enconded accessory protein


Coronavirus Open Reading Frame 7b

Behaviour of this protein is uncertain/unclear.
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Refinement of ORF7b by FeigLab

Refinement of RaptorX ORF7b by FeigLab

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Coronavirus Open Reading Frame 8

Behaviour of this protein is uncertain/unclear.
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Refinement of RaptorX ORF8 by FeigLab

Refinement of SWISS-MODEL ORF8 by FeigLab

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Viral Membrane Proteins

Membrane Glycoprotein

Viral envelope component that plays a role in morphogenesis.
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M Protein by Yang Zhang Lab

Refinement of AplhaFold M_protein by FeigLab

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Viral Envelope Proteins

Envelope small membrane protein

Plays a central role in virus morphogenesis and assembly. Acts as a viroporin and self-assembles in host membranes forming pentameric protein-lipid pores that allow ion transport. Also plays a role in the induction of apoptosis.
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Refinement of E Protein in Membrane Environment by FeigLab

E Protein by Yang Zhang Lab

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All-atom molecular dynamics simulations of SARS-CoV-2 envelope protein E in the monomeric form

Coarse-grained molecular dynamics simulations of SARS-CoV-2 envelope protein E in the pentameric form


Viral Nucleocapsid Proteins

Nucleoprotein

Packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP) and plays a fundamental role during virion assembly through its interactions with the viral genome and membrane protein M. Plays an important role in enhancing the efficiency of subgenomic viral RNA transcription as well as viral replication.
Top Structural Data: [See All]
[6M3M] Crystal Structure of SARS-CoV-2 Nucleocapsid Protein N-Terminal RNA Binding Domain
[6VYO] Crystal Structure of RNA Binding Domain of Nucleocapsid Phosphoprotein From SARS Coronavirus 2
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SWISS-MODEL N Protein

N Protein by Yang Zhang Lab

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SIRAH-CoV2 initiative - RNA binding domain of nucleocapsid phosphoprotein

SIRAH-CoV2 initiative - Nucleocapsid protein N-terminal RNA binding domain



Host Proteins

Angiotensin-converting enzyme 2 (ACE2)

Extracellular carboxypeptidase expressed in lung tissue that is the host receptor for SARS-CoV-2 viral fusion.
Small Molecule Antiviral
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[1R42] Native Human Angiotensin Converting Enzyme-Related Carboxypeptidase (ACE2)
[2AJF] Structure of SARS Coronavirus Spike Receptor-Binding Domain Complexed With Its Receptor
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SARS-CoV-2 RBD/ACE2-B0AT1 Complex in Aqueous Solution

Coarse Grained ACE2 (PDB 1R42 Ligands Removed)

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DESRES-ANTON-10918441 2 µs simulations of 78 FDA approved or investigational drug molecules binding to the ectodomain of human ACE2

A 10 µs simulation of a SARS-CoV-1 and SARS-CoV-2 chimera-ACE2 complex, no water or ions


Sodium Dependent Neutral Amnio Acid Transporter (BoAT1)

Chaperoned by ACE2 during S1 binding
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[6m17] The 2019-NCoV RBD/ACE2-B0AT1 Complex
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SARS-CoV-2 RBD/ACE2-B0AT1 Complex in Aqueous Solution

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SIRAH-CoV2 initiative - Spike´s RBD/ACE2-B0AT1 complex

DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 complex in aqueous solution


Ab Receptor in Host Cells (FcR)

Polymeric immunoglobulin receptor
Antibody Antiviral Peptide Immunotherapy
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Furin / PACE

Furin or PACE protein
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Furin Bound to SARS-CoV-2 Spike in One RBD Up State

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Interleukin-6 (IL-6) receptor

Inflammatory cytokines and chemokines, including interleukin-6 (IL-6), have been observed to be significantly elevated in COVID-19 patients with severe disease. Blockade of IL-6 signaling has been proposed as a therapeutic mechanism to prevent cytokine storm, also known as cytokine release syndrome (CRS).
Antibody
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Programmed cell death factor 1

Immune checkpoint that guards against autoimmunity
Antibody
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p38 Mitogen-Activated Protein Kinase (MPAK)

p38 kinase which activates in response to infections
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Transmembrane Protease Serine 2

Transmembrane serine protease which has been shown to be involved in spike protein cleavage.
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TMPRSS2 Bound to SARS-CoV-2 Spike in One RBD Up State

TMPRSS2 Homology Model With Substrate Overlaid

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