Visualizing Molecules from the PDB Using Chimera

Visualizing Molecules from the PDB Using Chimera

Teaching Notes

Visual Comprehension: HIV-1 Reverse Transcriptase Inhibited by NRTI

Learning Goals:

  1. Visualize protein structures from the PDB using a visualization software (such as UCSF Chimera)
  2. Apply the knowledge and skills learned in this using to answer a challenge question.

Educational Standards

  1. Common Core
  2. Integration of Knowledge and Ideas
  3. RST.11-12.8
  4. RST.11-12.9
  5. Next Generation Science Standards
  6. Practices
  7. 2. Developing and using models
  8. 4. Analyzing and interpreting data
  9. 6. Constructing explanations
  10. Crosscutting Concepts
  11. 2. Cause and effects: Mechanisms and explanations
  12. 4. Systems and system models
  13. 6. Structure and function
  14. Disciplinary Core Ideas
  15. LS1.A: Structure and Functions
  16. Advanced Placement Biology - Essential Knowledge (EK), Learning Objectives (LO), Science Practices (SP)
  17. EK 4.A.1
  18. LO 4.2, SP 1.3
  19. LO 4.3, SP 6.1, 6.4
  20. EK 4.B.1
  21. LO 4.17, SP 5.1
  22. EK 4.C.1
  23. LO 4.22, SP 6.2

Teaching Notes and Key:

The notes here assume that you are not familiar with UCSF Chimera, so most of the steps are shown here.

Exercise 1:

  1. Upload 3v4i
  1. Try yourself
  2. Change all residues in the protein chains to a “ribbon”
  1. Tools… Depiction… Rainbow (by Residue) – multiple regions with rainbow colors (from blue to red), so not clear what is going on here

Rainbow by chain – 5 different colors representing 5 chains (hint: rotate molecule to see all chains)

  1. There are 8 different chains in the structure – 2 copies each of 4 different polymer chains. Of these 4 chains, 2 are proteins (HIV-RT P51 and P66), while the other 2 are DNA polymer chains (primer and template strands).

Confirm this by going to the structure summary page for the PDB entry 3v4i( Note names of the proteins represented by chains A, B, C, D, E here.

HIV-1 Reverse Transcriptase P66 subunit: Chains A and C

HIV-1 Reverse Transcriptase P51 subunit: Chains B and D

DNA: Chains E and T

DNA: Chains F and P

  1. The AZT is located in the active site of the polymerase – positioned where the next incoming nucleotide would be. Residues of the P66 chain of HIV-1 RT surround the inhibitor molecule (AZT).
  1. Figures showing the neighborhood of AZT in this structure (PDB entry 3v4i)

The HIV-RT P66 chain is shown in blue, the template DNA strand is shown in green, and the primer strand is shown in orange. The inhibitor AZT is shown in the figure above colored in yellow. Note that it is positioned where the next nucleotide would be added during polymerization. Of the 3 active-site Asp residues (Asp110, Asp185, and Asp186) the first 2 are shown and marked in the figure above. The last Asp (Asp 186) is positioned to interact with the last nucleotide in the primer strand (not shown here).

Challenge Question:

The AZT acts as an inhibitor because it lacks the chemical group needed to form the phosphodiester linkage on both ends (required for forming a long polymer). Instead it can form a phosphodiester linkage at one end and blocks growth of the chain. In the structure above the nucleotide just prior to AZT (called ATM, colored in CPK colors) is the last nucleotide in this chain since it cannot be extended any further. This forms the basis for blocking the HIV life cycle.

Developed as part of the RCSB Collaborative Curriculum Development Program 2015

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