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

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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
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[6m0j] Crystal Structure of SARS-CoV-2 Spike Receptor-Binding Domain Bound With ACE2
[6w41] Crystal Structure of SARS-CoV-2 Receptor Binding Domain in Complex With Human Antibody CR3022
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Spike_full-Length_closed_amarolab

Trimeric SARS-CoV-2 Spike Glycoprotein (Closed State) in Aqueous Solution

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DESRES-ANTON-10897136 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein in aqueous solution

DESRES-ANTON-11021566 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein, no water or ions


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)
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SARS-CoV-2 Dimeric Main Protease Without Ligand Based on PDB 6LU7

SWISS-MODEL 3CLpro

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DESRES 100 µs MD of 3CLpro, All Atom

Riken BDR 10 Microsecond Trajectory Protein Snapshot every 200ps


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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[6w9c] The Crystal Structure of Papain-Like Protease of SARS CoV-2
[6W02] Crystal Structure of ADP Ribose Phosphatase of NSP3 From SARS CoV-2 in the Complex With ADP Ribose
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Refinement of SWISS-MODEL PL-Pro Domain 4 by FeigLab

SWISS-MODEL PL-PRO

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SARS-CoV-2 RNA Polymerase (NSP12)

RNA-dependent, RNA polymerase.
Antiviral Small Molecule
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[6m71] SARS-Cov-2 RNA-Dependent RNA Polymerase in Complex With Cofactors
[7BV1] Cryo-EM Structure of the Apo Nsp12-Nsp7-Nsp8 Complex
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SARS-CoV-2 RdRP (NSP12) in Complex With Cofactors NSP7 and NSP8: ISOLDE Refined Model

SWISS-MODEL NSP7 + NSP8 + RdRP

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

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


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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SWISS-MODEL Helicase

Helicase (NSP13) by Yang Zhang Lab

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Coronavirus nonstructural protein 1

Suppressor of host genome expression
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Refinement of SWISS-MODEL Nsp1 by FeigLab

NSP1 by Yang Zhang Lab

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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

NSP10 by Yang Zhang Lab

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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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NSP14 by Yang Zhang Lab

SWISS-MODEL NSP10 + NSP14

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Coronavirus nonstructural protein 15

Suppressor of host genome expression
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[6W01] The 1.9 a Crystal Structure of NSP15 Endoribonuclease From SARS CoV-2 in the Complex With a Citrate
[6M03] The Crystal Structure of COVID-19 Main Protease in Apo Form
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SWISS-MODEL NSP15

NSP15 by Yang Zhang Lab

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Coronavirus nonstructural protein 16

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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NSP16 by Yang Zhang Lab

SWISS-MODEL NSP10 + NSP16

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Coronavirus nonstructural protein 2

Suppressor of host genome expression
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Refinement of AplhaFold Nsp2 by FeigLab

Refinement of Nsp2 by FeigLab

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Coronavirus nonstructural protein 4

Suppressor of host genome expression
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Refinement of SWISS-MODEL NSP4 Domain 3 by FeigLab

NSP4 by Yang Zhang Lab

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Coronavirus nonstructural protein 6

Suppressor of host genome expression
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Refinement of RaptorX Nsp6 by FeigLab

Refinement of NSP6 in Membrane Environment by FeigLab

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Coronavirus nonstructural protein 7

Suppressor of host genome expression
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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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SWISS-MODEL NSP7 + NSP8 + RdRP

SARS-CoV-2 Nsp7-Nsp8-Nsp12 RNA Polymerase Complex in Aqueous Solution

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

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + RTP (Remdesivir Tri-Phosphate) model, All Atom model


Coronavirus nonstructural protein 8

Suppressor of host genome expression
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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

SWISS-MODEL NSP7 + NSP8

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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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NSP9 by Yang Zhang Lab

SWISS-MODEL NSP9

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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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Refinement of RaptorX ORF3a by FeigLab

ORF3a by Yang Zhang Lab

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Coronavirus Open Reading Frame 6

Possible determinant of virus virulence.
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Refinement of RaptorX ORF6 by FeigLab

ORF6 by Yang Zhang Lab

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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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Refinement of ORF7a by FeigLab

SWISS-MODEL Protein 7a

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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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ORF8 by Yang Zhang Lab

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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Refinement of AplhaFold M_protein by FeigLab

Refinement of RaptorX 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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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.
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N Protein by Yang Zhang Lab

SWISS-MODEL N Protein

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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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[6m0j] Crystal Structure of SARS-CoV-2 Spike Receptor-Binding Domain Bound With ACE2
[6vw1] Structure of SARS-CoV-2 Chimeric Receptor-Binding Domain Complexed With Its Receptor Human ACE2
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Human ACE2 Ectodomain in Aqueous Solution (Inhibitor-Bound Closed State)

Chimeric RBD in Complex With Human ACE2

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DESRES-ANTON-10875754 10 µs simulation trajectory of the human ACE2 ectodomain, no water or ions

DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-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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DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 complex, no water or ions

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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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 Homology Model With Benzamidine Overlaid

TMPRSS2 Homology Model With Substrate Overlaid

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