HIV-1 JR-FL gp120 core protein complex w/CD4 and the X5 antibody (PBD ID: 2B4C) from Human immunodeficiency virus 1
Created by: Abigail Smith
HIV-1 JR-FL gp120 core protein complex w/CD4 and the X5 antibody (PBD ID: 2B4C) is a viral protein found in the pathogenic Human immunodeficiency virus and Homo sapiens (H.sapiens). The gp120 core protein is immunodominant and necessary for coreceptor binding. The binding, conformation and antibody accessibility are rational for its role in HIV entry and neutralization.
Variational crystallization and various technologies from structural genomics were the techniques used to make crystals viable for x-ray structural analysis. Gp120 core with V3 from three clade B isolates were expressed in Drosophilia S2 cells. CD4 and a CD4-induced antibody unified with deglycosylated, purified proteins. When bound to CD4 and the antigen-binding fragment, gp120 core with V3 from JR-FL formed hexagonal crystals that diffracted to about 3.5 Angstrom resolution, with x-rays provided by an Advanced Photon Source undulator beam line. Molecular formation was used to solve the structure. The gp120 core with V3 entry mechanism was observed in unliganded states (5).
The gp120 core with V3 molecular weight is 106,675 Da, and the isoelectric point is 8.11 (9). The four subunits include an envelope glycoprotein, T-cell surface glycoprotein CD4, anti-HIV gp120 immunoglobulin X5 light chain, and anti-HIV gp120 immunoglobulin X5 heavy chain. Each subunit contains subunits of its own, leading to more in the structure. The total residue count is 975 (3). The structure of gp120 core with V3 is shown in Fig.1. Inner and outer domains make up gp120 core with V3. The outer domain is a stacked double barrel, which can be divided into three structural regions: a conserved base, a flexible stem, and a beta-hairpin tip. The protein achieved optimal crystallization (5).
The amino acid sequence follows an 11/25 rule, which states that if the 11th or 25th residue is positively charged, then it will use the coreceptor CXCR5. The gp120 core with V3’s sequences are primarily conserved for CCR5-using viruses. Residues 306 and 322 are within the variable stem, and the V3 stem has a moderate to high sequence variation. The gp120 core with V3 primarily consists of beta strands, while alpha helices, random coils and 3/10 helicesare present in smaller amounts. GP120 core with V3 contains 4 unique chains (3). The CD4 surface protein is the receptor, while the X5 antibody has a heavy and light chain attached to the core of HIV-1 gp120. The X5 heavy chain is involved in structural determination, and the antibody binds to the antigen (5).
Coreceptor binding and immunodominance are essential functions of gp120 core with V3. V3’s molecular hook action catches the coreceptor and inflects subunit associations within the viral spike. The molecular hook activity is allowed by V3’s high relative surface area, conformational flexibility, and overall extended nature. The extended conformation is suitable with the evocation of an immunodominant response. The coreceptor site is then revealed. The specific coreceptor, CCR5 or CXCR4, used for entry is determined by V3. Triggering of HIV evasion into the immune system and entry into cells occurs after binding of a coreceptor. GP120 core with V3 interacts with other elements in the viral spike to control the overall sensitivity of the virus to neutralization (5).
The side chains of Arg298 form hydrogen bonds with three carbonyl oxygens, including two on the outer domain. Pro299 initiates separation of incoming and outgoing V3 strands. Ile207-Ile209 form hydrogen bonds with the exposed backbone between the residues. This plays a role in the flexibility and position of the V3 tip. Coreceptor binding is influenced by residues 25 through 28. In the returning strand, residue 297and Cys331 form a disulfide bridge. Antiparallel beta sheets interact with gp120 core between the two residues, and the V3 tip varies in its conformation. From Ser306 to Gly312, a standard beta-conformation is acquired by the main chain, which terminates in a Gly-Pro-Gly-Arg beta-turn (5). A variety of specific residues play a vital role in the structure and function of the gp120 core with V3 protein.
The corresponding ligands of gp120 core with V3 include 2-acetamido-2-deoxy-bete-D-glucopyranose, Xylitol, and a sulfate ion (3). The sulfate ion binds to the CCR5 tyrosine-sulfated N-terminus. The N-terminus extends up and binds with the core and V3 tip base. The V3 tip of gp120 core with V3 reaches down to interact with the second extracellular loop of the coreceptor (8). Binding-induced conformational changes occur at H2 and H3 loops. Changes allow Leu105 and Glu55 to fit into their assigned pockets of gp120 core with V3. After CD4 binding, conformational changes occur to expose coreceptor binding sites and the epitopes for CD4i (5).
Psi-Blast is used to compare protein queries with protein databases and find the extent of similarity between the primary structures by creating a position-specific scoring matrix. The Psi-Blast is run twice in order to narrow down the results. The justification for the comparison protein is made by the E value. Having an E value below 0.05 indicates that there is significant similarity between the proteins. The Dali server compares tertiary structures of proteins. The query protein structural coordinates are compared to the Protein Data Bank. Similarities that may not be found during sequence comparison may arise when comparing 3D structures. The Dali server uses sum-of-pairs to determine the Z-score of proteins and shows the differences in intermolecular distances. Any Z score above two indicates similar folding between the proteins.
The comparison protein, Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b (PBD ID: 5VN3), has a residue count of 2814 with five unique protein chains (3). The E value of Cryo-EM model is 1E-175, and the Z score of the protein is 38 (1,4). The ligand of Cryo-EM model is 2-acetamido-2-deoxy-beta-D-glucopyranose. In structural comparison, the Cryo-EM model contains a larger proportion of alpha helices compared to beta sheets. Fig.2 shows the structure of Cryo-EM. This comparison protein has more subunits, and each subunit contains more chains than the assigned protein (3). Cryo-EM model is known for lowering neurovirulence of the human immunodeficiency virus (7).
A second comparison protein, crystal structure of broadly neutralizing antibody CH103 in complex with HIV-1 gp120 (PBD ID: 4JAN), has a residue count of 1164 with three unique protein chains (3). The E value of antibody CH103 is 2E-157, and the Z score of the protein is 19.3 (1,4). The ligands of antibody CH103 include 2-acetamido-2-deoxy-beta-D-glucopyranose, glycerol, and a sodium ion. Structurally, antibody CH103, is similar to gp120 core with V3, consisting of primarily beta sheets, with alpha helices, random coils, and 3/10 helices interwoven throughout (3). Antibody CH103’s structure is exhibited in Fig.3. Antibody CH1013 is an antibody that works against HIV-1 to neutralize it. The broad recognition and CD4-epitope specificity of antibody CH103 is created by the protein interacting with CD4 to provide a structural basis (6).
The pathogenic viral protein, HIV-1 JR-FL gp120 core protein complex w/CD4 and the X5 antibody, ultimately, plays an important role in coreceptor binding and immunodominance. The protein aids in HIV entry and neutralization. There is great potential in this area of study to determine more ways to neutralize HIV-1 with the use of similar proteins that contain the V3 region.