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Structure of Native HIV-1 Env trimer EMD 5021

Molecular architecture of native gp120 trimers

Liu J, Bartesaghi A, Borgnia MJ, Sapiro G, Subramaniam S

NATURE 455 109-113 (2008)

PMID: 18668044

Figure 1.   EMD-5021 (viral membrane), 5019 (spike), and PDB 3DNN (fitted coordinates).


The envelope glycoproteins (Env) of human and simian immunodeficiency viruses (HIV and SIV, respectively) mediate virus binding to the cell surface receptor CD4 on target cells to initiate infection. Env is a heterodimer of a transmembrane glycoprotein (gp41) and a surface glycoprotein (gp120), and forms trimers on the surface of the viral membrane. Using cryo-electron tomography combined with three-dimensional image classification and averaging, we report the three-dimensional structures of trimeric Env displayed on native HIV-1 in the unliganded state, in complex with the broadly neutralizing antibody b12 and in a ternary complex with CD4 and the 17b antibody. By fitting the known crystal structures of the monomeric gp120 core in the b12- and CD4/17b-bound conformations into the density maps derived by electron tomography, we derive molecular models for the native HIV-1 gp120 trimer in unliganded and CD4-bound states. We demonstrate that CD4 binding results in a major reorganization of the Env trimer, causing an outward rotation and displacement of each gp120 monomer. This appears to be coupled with a rearrangement of the gp41 region along the central axis of the trimer, leading to closer contact between the viral and target cell membranes. Our findings elucidate the structure and conformational changes of trimeric HIV-1 gp120 relevant to antibody neutralization and attachment to target cells.

Importing Cryo-electron microscopy (3DEM) data into  Sketchfab

EMD-5021 (viral membrane), EMD-5019 (spike), and PDB 3DNN (fitted coordinates) were downloaded from the EMDataBank and RCSB Protein Databank, respectively.   The model components were colored using Chimera’s interactive ribbon and volume gradient settings.

Once the model was imported into Sketchfab (SF), lighting and background color were adjusted. Annotation tag location and text were provided by Dr. Subramaniam (Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA).

The SF generated embed code was copied and pasted onto this page (see Fig. 1).  Click the “Play” button to start the interactivity. Use the arrows located on the bottom of the viewer ( arows) to navigate to the various positions!

General Information:

Cryo-electron microscopy (3DEM) is a field of structural biology that deals with the determination of 3D structures of macromolecular complexes and cells.   This emerging field helps to bridges the gap between cell biology and crystallography/NMR.

EMDataBank is the unified global portal for the deposition and retrieval of 3DEM density maps, atomic models and associated metadata.

In order to test if this type of data would import into Sketchfab (SF), various structures were downloaded from the above site.  After conversion into acceptable 3d formats, the models were uploaded to SF and embedded on the page above.

Model uploaded with color variations

Importing Protein Ribbons, Surfaces and EMD