Overview

Coronovirus3D viewer makes it possible to explore variability in the SARS-CoV-2 genome in the context of the 3D structures of SARS-CoV-2 proteins.

The initial view shows the entire genome with the information on proteins and their structures on separate tracks or layers. The top track shows the complete nucleotide sequence (MN908947.3) in the genome coordinates (the sequence is displayed at the appropriate zoom levels). The next track shows the SARS-CoV-2 proteins (with orf1ab polyprotein already cleaved into individual proteins). The following tracks show regions corresponding to the experimentally characterized 3D structures of SARS-CoV-2 proteins and models – regions with experimental 3D structures of proteins highly similar to SARS-CoV-2 proteins. The bottom track shows the amino-acid variability (downloaded from 2019 Novel Coronavirus Resource at CNCB). The Protael-based interface makes it possible to navigate and zoom to a specific part of the genome, the 3dmol-based viewer allows exploration of an experimental structure of a selected protein region including distribution of amino-acid variability in the structure and data tables provide access to the underlying data. The genome view, the 3D view and data tables are interactively connected.

Navigating genome viewer

The cursor (vertical green line) shows the current position in the viewer. The standard dragging action with a pointing device will select a part of the genome and then the viewer will automatically re-center and zoom to this part (this may take a couple of seconds). The scrollbar located at the bottom of the viewer makes it possible to scroll the genome view at its current zoom level.

The navigation bar located at the top of the genome viewer can be used to increase or decrease the zoom level by clicking zoom_out and zoom_in buttons, move back to currently selected region using Zoom to selection fullscreen_exit button or to return to full genome view by clicking Zoom to fit zoom_out_map button. The current selection start and end position is shown in the Selection field. Selection can also be cleared using Clear selection cached button. The Coloring drop-down field provides some coloring options for the nucleotide sequence.

Exploring protein structures

A protein structure can be selected by

The line representing selected structure is highlighted in bright magenta and the structure is then be displayed in the 3D viewer located at the bottom part of the window in the 3D view tab. The structure would be colored according to amino-acid variability in SARS-CoV-2 genomes. Hovering mouse over colored residues in this mode will display label with variability information.

The standard rainbow coloring according to residue numbering can be restored by clicking Default color button.

Any position in the structure can be labeled by either

A label would then be displayed by the corresponding residue in the 3D view and, at the same time, the corresponding position would be selected in the genome viewer and in the data table.

Data tables

Besides 3D viewer the bottom part of the window contains tables which provide access to data used by the viewer – lists of structures (Structures tab) and models (Models tab) and also current list of nucleotide variants (Nucleotide variants tab) with annotations from CNCB.

Clicking on blue column header will sort the table.

In addition to data imported from 2019nCoVR, each row of the nucleotide variability table contains  View  button which makes it possible to select the corresponding position in the genome viewer and label a corresponding residue in the 3D view. Genome position numbers in the table also serve as links to the list of specific genomes with amino-acid variants found at this position (available at 2019nCoVR resource). The subset of amino-acid variant found in the currently selected structure is displayed below the 3D view area.



 

Additional resources

Coronavirus3D focuses on providing structural context for mutations in SARS-CoV-2 genomes and currently only contains experimentally characterized structures of SARS-CoV-2 proteins (usually only one structure per protein region) and ‐ for protein regions without experimental structures ‐ structural models based on structures of very close homologs (almost solely from SARS-CoV).

There are , however, other resources focused on providing 3D models of SARS-CoV-2 proteins including models built using remote homology recognition and ab initio methods. Some of these resources also contain models of human proteins involved in SARS-CoV-2 infection and complexes of human and viral proteins. We recommend these resources, especially for proteins and protein regions which do not have models in the current release of Coronavirus3D:

Source Methods Link
Swiss Institute of Bioinformatics SwissModel models
Zhang Lab at University of Michigan I-TASSER models
DeepMind Alphafold models
Feig Lab at Michigan State University trRosetta, refinement by high-resolution molecular dynamics models