T-cell receptor gene rearrangements were studied in Aotus monkeys developing high antibody titers and sterilizing immunity against the Plasmodium falciparum malaria parasite upon vaccination with the modified synthetic peptide 24112, which was identified in the Merozoite Surface Protein 2 (MSP-2) and is known to bind to HLA-DRb1*0403 molecules with high capacity. Spectratyping analysis showed a preferential usage of Vb12 and Vb6 TCR gene families in 67% of HLADRb1*0403-like genotyped monkeys. Docking of peptide 24112 into the HLA-DRb1*0401–HA peptide–HA1.7TCR complex containing the VDJ rearrangements identified in fully protected monkeys showed a different structural signature compared to nonprotected monkeys. These striking results show the exquisite specificity of the TCR/pMHCII complex formation needed for inducing sterilizing immunity and provide important hints for a logical and rational methodology to develop multiepitopic, minimal subunit-based synthetic vaccines against infectious diseases, among them malaria. Citation: Patarroyo MA, Bermudez A, Lopez C, Yepes G, Patarroyo ME (2010) 3D Analysis of the TCR/pMHCII Complex Formation in Monkeys Vaccinated with the First Peptide Inducing Sterilizing Immunity against Human Malaria. PLoS ONE 5(3): e9771. doi:10.1371/journal.pone.0009771 Editor: Aric Gregson, University of California Los Angeles, United States of America Received November 18, 2009; Accepted February 25, 2010; Published March 19, 2010 Copyright: 2010 Patarroyo et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This research has been supported by the Asociacion para la Investigacion Solidaria SADAR (Pamplona, Spain 2009) and the Agencia Espanola de Cooperacion Internacional para el Desarrollo AECID (Madrid, Spain 2009). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: mepatarr@mail.com . These authors contributed equally to this work.