Groups 1D-3D Alignment

Access

Introduction

What is the Groups 1D-3D Alignment Viewer?

The 1D-3D Alignment tool displays multiple alignments of protein at 1D sequence and 3D structure levels. Multiple Sequence Alignments (MSAs) are computed for groups of PDB proteins based on grouping or sequence clustering for proteins sharing the same UniProt accession.

Why use Groups 1D-3D Alignment Viewer?

This tool allows users to quickly and easily view:

  • Alignment of multiple PDB structures (representing domains of structure) to a full length sequence of the UniProt entry and corresponding Computed Structure Model (where available).
  • Positional variations of specific amino acids of interest in different instances of polymer entities in PDB structures as identified in the sequence (1D panel). The variations may be related to presence of ligands and/or partner biomolecules or mutations.

Documentation

Access

The tool or app is available for UniProt Groups from Group Summary Pages Carousel (1D-3D Alignments link, Figure 1A) and Group Sequence Pages (View 1D-3D Alignments link, Figure 1B).

Figure 1. Ways to access the 1D-3D Alignments view from the Group Summary page marked with red outline boxes - A. in Group Summary tab, and B. in Group Sequence tab
Figure 1. Ways to access the 1D-3D Alignments view from the Group Summary page marked with red outline boxes - A. in Group Summary tab, and B. in Group Sequence tab

Interface

The 1D Protein Feature Viewer (PFV) displays the multiple sequence alignment on the left hand side of the web page, while 3D structures of protein entities listed in the MSA can be viewed in the panel on the right.

The 1D sequence alignment is displayed using specific color schemes.

  • The sequences of PDB experimental protein positions are represented as binary colors (blue/gray) indicating if residue’s 3D coordinates are available in the structure or not. Learn more about the color schemes.
  • Aligned positions of PDB proteins from Computed structure Models (CSMs) are colored based on their local pLDDT scores.

How to use the 1D-3D Alignment Viewer

  • New proteins can be added to the 3D view by clicking on the polymer entity listed in the MSA in the 1D panel (red box in Figure 2). The 3D structure of the selected entity is aligned with the currently visible displayed structures and the superposition is displayed.
  • Multiple proteins can be simultaneously superimposed and displayed by clicking on entity Id row title to load the entity/entry
Figure 2: The Groups 1D-3D alignment interface
Figure 2: The Groups 1D-3D alignment interface
  • Blue boxes next to the entity ID row titles allow users to show/hide different parts of the 3D structure (Figure 3)
    • The first box (on the left) can Hide/Display aligned instance
    • The second box (in the middle) can Hide/Display all polymer instances excluding the aligned one
    • The third box (on the right) can Hide/Display all non-polymer instance
Figure 3: Buttons to display the aligned polymer and other contents of the structure.
Figure 3: Buttons to display the aligned polymer and other contents of the structure.
  • Selection of residues on the 1D panel (by clicking on it or using Control+Click) will select the corresponding residues/region(s) in the 3D view being displayed. Similarly, selection in 3D structure will select the selected position in the 1D panel (see red outlined box regions in Figure 4)
  • Shift+Click on the entity Id allows you to navigate to the entity on the Structure Summary Page for the structure to learn more about that structure
Figure 4: Selecting residues in the 1D panel (red outlined box) selects the corresponding region in the 3D structure for all displayed entities.
Figure 4: Selecting residues in the 1D panel (red outlined box) selects the corresponding region in the 3D structure for all displayed entities.

Examples



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Last updated: 11/4/2022