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2015 RCSB PDB Video Challenge for High School Students

Detecting & Combating HIV in 3D

2015 Video Challenge

Winners | Entries | Judges | Overview | Learning Resources


Note: Videos are intended for communication and not rigorous scientific review.

In 2015, an additional Service to the Community Award was awarded by the AIDS Education Training Center (AETC) National Resource Center. AETC committed to include the winning video among the training materials for health care professionals, patients and their families.

Congratulations to the 2015 Winners:


Battling HIV: The Search for a Cure
By Calvin Qian, Matthew Brown, Charles Morse, and Justin Halim of Academy of Allied Health and Science, Neptune City, NJ (Team Advisor: Richard Tempsick)
  • Winner of the Judge's Award First Place
  • Winner of the Service to the Community Award


The Search for a Vaccine for HIV
By Alexa Skolnik and Maryann Zielinski of East Brunswick High School, East Brunswick, NJ (Team Advisor: Anne Sanelli)
  • Winner of the Judge's Award Second Place


HAART: A Stop Motion Story
By Justin May, Katarina Wang, Akshay Malavade, and Joy Song of East Brunswick High School, East Brunswick, NJ (Team Advisor: Louise Jasko)
  • Winner of the Judge's Award Third Place


The Search for a Vaccine
By Naszir Johnson, Henry Lucas, Matt Weiler, and Valeria Rodriguez of Engineering and Science University Magnet School, Hamden, CT (Team Advisor: Leon Tynes)
  • Winner of the Viewer's Choice Award

2015 Challenge Overview

For the second year in a row, the RCSB PDB invited high school students to create short videos that tell a story about HIV/AIDS. This time the entries were to focus on the molecular view combatting and containing the virus. The students could choose from one of the following topics:

  • HIV testing
  • Antiretroviral drugs and HAART
  • Drug resistance
  • The search for a vaccine
  • The search for a cure

Students were tasked to include a visualization/animation of at least one of the molecular structures from the 2015 Video Challenge Featured Structures List, and include a message about the importance of testing.

2015 Dates

The video submission opened on March 4, 2015 and concluded on May 31, 2015. Award winners were announced at rcsb.org on June 16, 2015.

2015 Video Challenge Featured Structures List

PDB ID

 Brief Molecular Description PDB Visualization Tips Selected RCSB PDB resources

Topic 1: HIV testing. HIV tests use antibodies against HIV proteins to detect the presence of HIV in the blood

1e6j

Part of the antibody (termed "Fab" for "antigen-binding fragment") bound to the viral capsid

Chains H and L contain the Fab; chain P is the viral capsid

1afv

Chains H and L are one Fab, chains K and M are a second Fab; chains A and B are the capsid protein

1igt, 1igy, 1hzh

Intact antibodies

 

Topic 2: Antiretroviral drugs and highly active antiretroviral therapy (HAART)

Protease

2aoi, 2aoj, 2aod

Protease with substrate analog of cleavage sites

Use the Ligand Chemical Component section of each Structure Summary page to learn about the chemical components attached to the protein

2aoi, 2aoj, 1hxb: use the only alternate position A of inhibitor

 

1hsg, 1hxb, 1hxw, 1ohr, 1hpv

Examples of HIV protease with clinically-used drugs

HIV Reverse Transcriptase

2hmi, 1hys

Reverse transcriptase in complex with nucleic acids

Chains C and D are a monoclonal antibody added to stabilize the protein for crystallization and should be omitted;
chain E in each is the template nucleic acid strand, and chain F is the strand being synthesized

1jlb

HIV reverse transcriptase with Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs)

NVP is the drug nevirapine

Integrase

1ex4

Catalytic core of the HIV-1 Integrase

Some domains are missing. Use a structure comparison tool e.g., Structure Comparison in Chimera to compare this structure to e.g. 3os1 to identify the DNA binding region

3os1

Prototype Foamy Virus (which is similar to HIV) integrase bound to DNA

Use the biological assembly file for visualization.

3os1: viral DNA is found in chains C and D, and target host DNA is in chain T

3oya: viral DNA is found in chains C and D, and the drug raltegravir is labeled RLT

3oya

PFV integrase bound to the drug raltegravir

CCR5

4mbs

C-C chemokine receptor type 5 (CCR5) with the drug maraviroc; first drug that targets a host protein instead of HIV

Use biological assembly file (only chain A); residues 1001-1054 represents rubredoxin, which was engineered into the protein to assist crystallization and should not be displayed

Topic 3: Drug resistance

2az8, 2az9, 2azb, 2azc

Structures of HIV protease that show the development of resistance against an experimental drug molecule

2az8 is the wild type, 2az9 has one mutation and is 4-fold resistant, 2azb has three mutations and is 11-fold resistant, and 2azc has six mutations and is 30-fold resistant; use the biological assembly file for 2az8, 2az9 and 2azb

Topic 4: The search for a vaccine

4nco

Broadly-neutralizing antibody bound to HIV envelope glycoprotein - these are the types of antibodies that need to be elicited by a vaccine

three antibody Fab are: C+D, G+H, K+L

Topic 5: The search for a cure

4mbs

CCR5 - Some experimental approaches attempt to remove C-C chemokine receptor type 5 from susceptible cells

Use biological assembly file (only chain A); residues 1001-1054 represents rubredoxin, which was engineered into the protein to assist crystallization and should not be displayed

4un3, 4oo8

Some experimental approaches attempt to introduce DNA-cutting molecules like Cas9/CRISPR into HIV-infected cells

4un3: chain A is the CRISPR guide RNA, and C+D is the targeted DNA;
4oo8: use only one biological assembly with chain A (Cas9), chain B (CRISPR guide RNA), and chain C (target DNA)