3J70

Model of gp120, including variable regions, in complex with CD4 and 17b

Summary for 3J70

• Entry DOI: 10.2210/pdb3j70/pdb
• EMDB information: 5020
• Descriptor: monoclonal antibody 17b light chain, monoclonal antibody 17b heavy chain, T-cell surface glycoprotein CD4, ... (5 entities in total)
• Functional Keywords: gp120, v1v2, cd4, 17b, viral protein-immune system complex, viral protein/immune system
• Biological source: Homo sapiens (human); More
• Cellular location: Transmembrane protein gp41: Virion membrane; Single-pass type I membrane protein. Surface protein gp120: Virion membrane; Peripheral membrane protein: P01730; Cell membrane ; Single-pass type I membrane protein : P04578
• Total number of polymer chains: 15
• Total formula weight: 391383.66

Authors

Rasheed, M.,Bettadapura, R.,Bajaj, C. (deposition date: 2014-04-22, release date: 2015-08-26, Last modification date: 2024-10-16)

Primary citation

Rasheed, M.,Bettadapura, R.,Bajaj, C.
Computational Refinement and Validation Protocol for Proteins with Large Variable Regions Applied to Model HIV Env Spike in CD4 and 17b Bound State.
Structure, 23:1138-1149, 2015

PubMed Abstract: Envelope glycoprotein gp120 of HIV-1 possesses several variable regions; their precise structure has been difficult to establish. We report a new model of gp120, in complex with antibodies CD4 and 17b, complete with its variable regions. The model was produced by a computational protocol that uses cryo-electron microscopy (EM) maps, atomic-resolution structures of the core, and information on binding interactions. Our model has excellent fit with EMD: 5020, is stereochemically and energetically favorable, and has the expected binding interfaces. Comparison of the ternary arrangement of the loops in this model with those bound to PGT122 and PGV04 suggested a possible motion of the V1V2 away from the CCR5 binding site and toward CD4. Our study also revealed that the CD4-bound state of the V1V2 loop is not optimal for gp120 bound with several neutralizing antibodies.

PubMed: 26039348
DOI: 10.1016/j.str.2015.03.026

Experimental method

ELECTRON MICROSCOPY (20 Å)