Ignacia Echeverria Riesco, PhD
Assistant Professor
Bioengineering
School of Pharmacy

Education & Training

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• PhD Molecular Biophysics Johns Hopkins University

Websites

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• My website (echeverria.ucsf.edu)

Grants and Projects

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• Using in vivo genetic and physical interaction data for structure determination of protein assemblies, NIH, 2023-2028

Publications (39)

Top publication keywords:
vif Gene Products, Human Immunodeficiency VirusHistonesAPOBEC-3G DeaminaseDisaccharidesMolecular Dynamics SimulationCyclin TThermodynamicsMammalsOncogenesAmino AcidsNuclear Pore Complex ProteinsModels, MolecularSaccharomyces cerevisiaeNuclear PoreGalectin 1

• Molecular mechanism of substrate transport by human peroxisomal ABCD3.
  Proceedings of the National Academy of Sciences of the United States of America 2025 Gupta M, Khandelwal NK, Seka DJ, Balasubramani SG, Dickinson MS, Myasnikov A, Echeverria I, Stroud RM
• Publisher Correction: Multimodal cell maps as a foundation for structural and functional genomics.
  Nature 2025 Schaffer LV, Hu M, Qian G, Moon KM, Pal A, Soni N, Latham AP, Pontano Vaites L, Tsai D, Mattson NM, Licon K, Bachelder R, Cesnik A, Gaur I, Le T, Leineweber W, Palar A, Pulido E, Qin Y, Zhao X, Churas…
• Recognizing amino acid sidechains in a medium-resolution cryo-electron density map.
  Protein science : a publication of the Protein Society 2025 Mondal D, Kumar V, Satler T, Ramachandran R, Saltzberg D, Chemmama I, Pilla KB, Echeverria I, Webb BM, Gupta M, Verba K, Sali A
• Coronavirus protein interaction mapping in bat and human cells identifies molecular and genetic switches for immune evasion and replication.
  bioRxiv : the preprint server for biology 2025 Batra J, Rutkowska M, Zhou Y, Ye C, Adavikolanu R, Young JM, Anand D, Verma S, Gordon M, Malpotra S, Cupic A, Kehrer T, Moen JM, Winters DM, Rojc A, Mena I, Aslam S, Martinez-Romero C, Conde Viñas I, …
• Molecular mechanism of substrate transport by human peroxisomal ABCD3.
  bioRxiv : the preprint server for biology 2025 Gupta M, Khandelwal NK, Seka DJ, Balasubramani SG, Dickinson MS, Myasnikov A, Echeverria I, Stroud RM

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• Evolutionary Sequence and Structural Basis for the Epistatic Origins of Drug Resistance in HIV.
  bioRxiv : the preprint server for biology 2025 Biswas A, Choudhuri I, Huang K, Sun Q, Sali A, Echeverria I, Haldane A, Levy RM, Lyumkis D
• Multimodal cell maps as a foundation for structural and functional genomics.
  Nature 2025 Schaffer LV, Hu M, Qian G, Moon KM, Pal A, Soni N, Latham AP, Pontano Vaites L, Tsai D, Mattson NM, Licon K, Bachelder R, Cesnik A, Gaur I, Le T, Leineweber W, Palar A, Pulido E, Qin Y, Zhao X, Churas…
• Structural basis of disease mutation and substrate recognition by the human SLC2A9 transporter.
  Proceedings of the National Academy of Sciences of the United States of America 2025 Khandelwal NK, Gupta M, Kumar P, Balasubramani SG, Echeverria I, Stroud RM
• The molecular architecture of the nuclear basket.
  Cell 2024 Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, Rout MP, Sali A, Villa E
• Trioxane-based MS-cleavable Cross-linking Mass Spectrometry for Profiling Multimeric Interactions of Cellular Networks.
  bioRxiv : the preprint server for biology 2024 Yu C, Novitsky E, Wang X, Echeverria I, Rychnovsky S, Huang L
• The Molecular Architecture of the Nuclear Basket.
  bioRxiv : the preprint server for biology 2024 Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, Rout MP, Sali A, Villa E
• Implications of a multiscale structure of the yeast nuclear pore complex.
  Molecular cell 2023 Akey CW, Echeverria I, Ouch C, Nudelman I, Shi Y, Wang J, Chait BT, Sali A, Fernandez-Martinez J, Rout MP
• SARS-CoV-2 variants evolve convergent strategies to remodel the host response.
  Cell 2023 Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, …
• Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13.
  Nature structural & molecular biology 2023 Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM
• The structural basis for HIV-1 Vif antagonism of human APOBEC3G.
  Nature 2023 Li YL, Langley CA, Azumaya CM, Echeverria I, Chesarino NM, Emerman M, Cheng Y, Gross JD
• Integrative structure determination of histones H3 and H4 using genetic interactions.
  The FEBS journal 2022 Echeverria I, Braberg H, Krogan NJ, Sali A
• From systems to structure - using genetic data to model protein structures.
  Nature reviews. Genetics 2022 Braberg H, Echeverria I, Kaake RM, Sali A, Krogan NJ
• Comprehensive structure and functional adaptations of the yeast nuclear pore complex.
  Cell 2022 Akey CW, Singh D, Ouch C, Echeverria I, Nudelman I, Varberg JM, Yu Z, Fang F, Shi Y, Wang J, Salzberg D, Song K, Xu C, Gumbart JC, Suslov S, Unruh J, Jaspersen SL, Chait BT, Sali A, Fernandez-Martinez…
• Reversible phosphorylation of cyclin T1 promotes assembly and stability of P-TEFb.
  eLife 2021 Huang F, Nguyen TT, Echeverria I, Rakesh R, Cary DC, Paculova H, Sali A, Weiss A, Peterlin BM, Fujinaga K
• Characterization of an A3G-VifHIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes.
  Molecular & cellular proteomics : MCP 2021 Kaake RM, Echeverria I, Kim SJ, Von Dollen J, Chesarino NM, Feng Y, Yu C, Ta H, Chelico L, Huang L, Gross J, Sali A, Krogan NJ
• Genetic interaction mapping informs integrative structure determination of protein complexes.
  Science (New York, N.Y.) 2020 Braberg H, Echeverria I, Bohn S, Cimermancic P, Shiver A, Alexander R, Xu J, Shales M, Dronamraju R, Jiang S, Dwivedi G, Bogdanoff D, Chaung KK, Hüttenhain R, Wang S, Mavor D, Pellarin R, Schneidman D…
• Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure.
  Protein science : a publication of the Protein Society 2020 Saltzberg DJ, Viswanath S, Echeverria I, Chemmama IE, Webb B, Sali A
• Structural basis of CD4 downregulation by HIV-1 Nef.
  Nature structural & molecular biology 2020 Kwon Y, Kaake RM, Echeverria I, Suarez M, Karimian Shamsabadi M, Stoneham C, Ramirez PW, Kress J, Singh R, Sali A, Krogan N, Guatelli J, Jia X
• Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling.
  Proceedings of the National Academy of Sciences of the United States of America 2020 Gutierrez C, Chemmama IE, Mao H, Yu C, Echeverria I, Block SA, Rychnovsky SD, Zheng N, Sali A, Huang L
• Modeling Biological Complexes Using Integrative Modeling Platform.
  Methods in molecular biology (Clifton, N.J.) 2019 Saltzberg D, Greenberg CH, Viswanath S, Chemmama I, Webb B, Pellarin R, Echeverria I, Sali A
• Integrative structure and functional anatomy of a nuclear pore complex.
  Nature 2018 Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan JA, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, Wang J, Williams R, …
• Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones.
  Cell reports 2017 Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ
• Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex.
  eLife 2016 Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH
• Na+ coordination at the Na2 site of the Na+/I- symporter.
  Proceedings of the National Academy of Sciences of the United States of America 2016 Ferrandino G, Nicola JP, Sánchez YE, Echeverria I, Liu Y, Amzel LM, Carrasco N
• Oncogenic mutations weaken the interactions that stabilize the p110α-p85α heterodimer in phosphatidylinositol 3-kinase α.
  The FEBS journal 2015 Echeverria I, Liu Y, Gabelli SB, Amzel LM
• The Acetylation Landscape of the H4 Histone Tail: Disentangling the Interplay between the Specific and Cumulative Effects.
  Journal of the American Chemical Society 2015 Winogradoff D, Echeverria I, Potoyan DA, Papoian GA
• DNA exit ramps are revealed in the binding landscapes obtained from simulations in helical coordinates.
  PLoS computational biology 2015 Echeverria I, Papoian GA
• Concerted dihedral rotations give rise to internal friction in unfolded proteins.
  Journal of the American Chemical Society 2014 Echeverria I, Makarov DE, Papoian GA
• Activation of PI3Kα by physiological effectors and by oncogenic mutations: structural and dynamic effects.
  Biophysical reviews 2014 Gabelli SB, Echeverria I, Alexander M, Duong-Ly KC, Chaves-Moreira D, Brower ET, Vogelstein B, Amzel LM
• Estimation of free-energy differences from computed work distributions: an application of Jarzynski's equality.
  The journal of physical chemistry. B 2012 Echeverria I, Amzel LM
• Disaccharide binding to galectin-1: free energy calculations and molecular recognition mechanism.
  Biophysical journal 2011 Echeverria I, Amzel LM
• Structural insights into maize viviparous14, a key enzyme in the biosynthesis of the phytohormone abscisic acid.
  The Plant cell 2010 Messing SA, Gabelli SB, Echeverria I, Vogel JT, Guan JC, Tan BC, Klee HJ, McCarty DR, Amzel LM
• α-Helix peptides designed from EBV-gH protein display higher antigenicity and induction of monocyte apoptosis than the native peptide.
  Amino acids 2010 Urquiza M, Melo-Cardenas J, Guevara T, Echeverria I, Rodriguez IC, Vanegas M, Amzel M, Patarroyo ME
• Helix propensities calculations for amino acids in alanine based peptides using Jarzynski's equality.
  Proteins 2010 Echeverria I, Amzel LM