skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope

; ; ; ; ; ORCiD logo
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
OSTI Identifier:
Resource Type:
Journal Article
Journal Name:
Nature Structural & Molecular Biology
Additional Journal Information:
Journal Volume: 24; Journal Issue: 4; Journal ID: ISSN 1545-9993
Nature Publishing Group
Country of Publication:
United States

Citation Formats

Song, InYoung, Gil, Anna, Mishra, Rabinarayan, Ghersi, Dario, Selin, Liisa K., and Stern, Lawrence J. Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope. United States: N. p., 2017. Web. doi:10.1038/nsmb.3383.
Song, InYoung, Gil, Anna, Mishra, Rabinarayan, Ghersi, Dario, Selin, Liisa K., & Stern, Lawrence J. Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope. United States. doi:10.1038/nsmb.3383.
Song, InYoung, Gil, Anna, Mishra, Rabinarayan, Ghersi, Dario, Selin, Liisa K., and Stern, Lawrence J. Mon . "Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope". United States. doi:10.1038/nsmb.3383.
title = {Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope},
author = {Song, InYoung and Gil, Anna and Mishra, Rabinarayan and Ghersi, Dario and Selin, Liisa K. and Stern, Lawrence J.},
abstractNote = {},
doi = {10.1038/nsmb.3383},
journal = {Nature Structural & Molecular Biology},
issn = {1545-9993},
number = 4,
volume = 24,
place = {United States},
year = {2017},
month = {2}

Works referenced in this record:

Structural determinants of T-cell receptor bias in immunity
journal, November 2006

  • Turner, Stephen J.; Doherty, Peter C.; McCluskey, James
  • Nature Reviews Immunology, Vol. 6, Issue 12
  • DOI: 10.1038/nri1977

Molecular basis for universal HLA-A*0201–restricted CD8 + T-cell immunity against influenza viruses
journal, March 2016

  • Valkenburg, Sophie A.; Josephs, Tracy M.; Clemens, E. Bridie
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 16
  • DOI: 10.1073/pnas.1603106113

A structural voyage toward an understanding of the MHC-I-restricted immune response: lessons learned and much to be learned
journal, October 2012

Complex T-Cell Receptor Repertoire Dynamics Underlie the CD8 + T-Cell Response to HIV-1
journal, October 2014

  • Costa, Ana I.; Koning, Dan; Ladell, Kristin
  • Journal of Virology, Vol. 89, Issue 1
  • DOI: 10.1128/JVI.01765-14

Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

Naive T Cell Repertoire Skewing in HLA-A2 Individuals by a Specialized Rearrangement Mechanism Results in Public Memory Clonotypes
journal, January 2011

  • Yassai, Maryam; Bosenko, Dmitry; Unruh, Melissa
  • The Journal of Immunology, Vol. 186, Issue 5
  • DOI: 10.4049/jimmunol.1002764

Complex T Cell Memory Repertoires Participate in Recall Responses at Extremes of Antigenic Load
journal, July 2006

Molecular Basis of a Dominant T Cell Response to an HIV Reverse Transcriptase 8-mer Epitope Presented by the Protective Allele HLA-B*51:01
journal, March 2014

  • Motozono, Chihiro; Kuse, Nozomi; Sun, Xiaoming
  • The Journal of Immunology, Vol. 192, Issue 7
  • DOI: 10.4049/jimmunol.1302667

A Structural Basis for Varied αβ TCR Usage against an Immunodominant EBV Antigen Restricted to a HLA-B8 Molecule
journal, December 2011

  • Gras, Stephanie; Wilmann, Pascal G.; Chen, Zhenjun
  • The Journal of Immunology, Vol. 188, Issue 1
  • DOI: 10.4049/jimmunol.1102686

Collaboration gets the most out of software
journal, September 2013

Precursor Frequency and Competition Dictate the HLA-A2–Restricted CD8 + T Cell Responses to Influenza A Infection and Vaccination in HLA-A2.1 Transgenic Mice
journal, July 2011

  • Tan, Amabel C. L.; La Gruta, Nicole L.; Zeng, Weiguang
  • The Journal of Immunology, Vol. 187, Issue 4
  • DOI: 10.4049/jimmunol.1100664

T Cell-Mediated Protection against Lethal 2009 Pandemic H1N1 Influenza Virus Infection in a Mouse Model
journal, October 2010

  • Guo, H.; Santiago, F.; Lambert, K.
  • Journal of Virology, Vol. 85, Issue 1
  • DOI: 10.1128/JVI.01812-10

Structural and biophysical determinants of αβ T-cell antigen recognition: T-cell antigen recognition
journal, December 2011

Identification of viral molecules recognized by influenza-specific human cytotoxic T lymphocytes
journal, February 1987

Comprehensive assessment of T-cell receptor β-chain diversity in αβ T cells
journal, November 2009

Highly Divergent T-cell Receptor Binding Modes Underlie Specific Recognition of a Bulged Viral Peptide bound to a Human Leukocyte Antigen Class I Molecule
journal, April 2013

  • Liu, Yu Chih; Miles, John J.; Neller, Michelle A.
  • Journal of Biological Chemistry, Vol. 288, Issue 22
  • DOI: 10.1074/jbc.M112.447185

Sizing up the key determinants of the CD8+ T cell response
journal, October 2015

  • Tscharke, David C.; Croft, Nathan P.; Doherty, Peter C.
  • Nature Reviews Immunology, Vol. 15, Issue 11
  • DOI: 10.1038/nri3905

Regulatory T Cells Resist Virus Infection-Induced Apoptosis
journal, December 2014

  • Che, Jenny W.; Kraft, Anke R. M.; Selin, Liisa K.
  • Journal of Virology, Vol. 89, Issue 4
  • DOI: 10.1128/JVI.02245-14

Diversity index of mucosal resident T lymphocyte repertoire predicts clinical prognosis in gastric cancer
journal, January 2015

CD8 + TCR Repertoire Formation Is Guided Primarily by the Peptide Component of the Antigenic Complex
journal, December 2012

Deep Sequencing of Antiviral T-Cell Responses to HCMV and EBV in Humans Reveals a Stable Repertoire That Is Maintained for Many Years
journal, September 2012

Structural Basis for Clonal Diversity of the Public T Cell Response to a Dominant Human Cytomegalovirus Epitope
journal, October 2015

  • Yang, Xinbo; Gao, Mingming; Chen, Guobing
  • Journal of Biological Chemistry, Vol. 290, Issue 48
  • DOI: 10.1074/jbc.M115.691311

Naive CD8 + T-cell precursors display structured TCR repertoires and composite antigen-driven selection dynamics
journal, March 2015

  • Neller, Michelle A.; Ladell, Kristin; McLaren, James E.
  • Immunology and Cell Biology, Vol. 93, Issue 7
  • DOI: 10.1038/icb.2015.17

A small jab – a big effect: nonspecific immunomodulation by vaccines
journal, September 2013

  • Benn, Christine S.; Netea, Mihai G.; Selin, Liisa K.
  • Trends in Immunology, Vol. 34, Issue 9
  • DOI: 10.1016/

The molecular basis for public T-cell responses?
journal, March 2008

  • Venturi, Vanessa; Price, David A.; Douek, Daniel C.
  • Nature Reviews Immunology, Vol. 8, Issue 3
  • DOI: 10.1038/nri2260

Broad Cross-Reactive TCR Repertoires Recognizing Dissimilar Epstein-Barr and Influenza A Virus Epitopes
journal, November 2010

  • Clute, Shalyn C.; Naumov, Yuri N.; Watkin, Levi B.
  • The Journal of Immunology, Vol. 185, Issue 11
  • DOI: 10.4049/jimmunol.1000812

Scaling and assessment of data quality
journal, December 2005

  • Evans, Philip
  • Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 1, p. 72-82
  • DOI: 10.1107/S0907444905036693

Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding
journal, October 2015

  • Best, Katharine; Oakes, Theres; Heather, James M.
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep14629

Memory of mice and men: CD8+ T-cell cross-reactivity and heterologous immunity
journal, June 2006

A structural basis for immunodominant human T cell receptor recognition
journal, June 2003

  • Stewart-Jones, Guillaume B. E.; McMichael, Andrew J.; Bell, John I.
  • Nature Immunology, Vol. 4, Issue 7
  • DOI: 10.1038/ni942

T-cell Receptor Specificity Maintained by Altered Thermodynamics
journal, May 2013

  • Madura, Florian; Rizkallah, Pierre J.; Miles, Kim M.
  • Journal of Biological Chemistry, Vol. 288, Issue 26
  • DOI: 10.1074/jbc.M113.464560

Cytotoxic T lymphocytes recognize a fragment of influenza virus matrix protein in association with HLA-A2
journal, April 1987

  • Gotch, Frances; Rothbard, Jonathan; Howland, Kevin
  • Nature, Vol. 326, Issue 6116
  • DOI: 10.1038/326881a0

A Correlation between TCR Vα Docking on MHC and CD8 Dependence
journal, October 2003

iMOSFLM : a new graphical interface for diffraction-image processing with MOSFLM
journal, March 2011

  • Battye, T. Geoff G.; Kontogiannis, Luke; Johnson, Owen
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910048675

IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis
journal, May 2008

  • Brochet, X.; Lefranc, M. -P.; Giudicelli, V.
  • Nucleic Acids Research, Vol. 36, Issue Web Server
  • DOI: 10.1093/nar/gkn316

Sequence analysis of T-cell repertoires in health and disease
journal, January 2013

  • Woodsworth, Daniel J.; Castellarin, Mauro; Holt, Robert A.
  • Genome Medicine, Vol. 5, Issue 10
  • DOI: 10.1186/gm502

A Single TCRα-Chain with Dominant Peptide Recognition in the Allorestricted HER2/neu-Specific T Cell Repertoire
journal, December 2009

  • Liang, Xiaoling; Weigand, Luise U.; Schuster, Ingrid G.
  • The Journal of Immunology, Vol. 184, Issue 3
  • DOI: 10.4049/jimmunol.0902155

HLA-A2-peptide complexes: refolding and crystallization of molecules expressed in Escherichia coli and complexed with single antigenic peptides.
journal, April 1992

  • Garboczi, D. N.; Hung, D. T.; Wiley, D. C.
  • Proceedings of the National Academy of Sciences, Vol. 89, Issue 8
  • DOI: 10.1073/pnas.89.8.3429

T cell mediated immunity to influenza: mechanisms of viral control
journal, August 2014

Extensive conservation of alpha and beta chains of the human T-cell antigen receptor recognizing HLA-A2 and influenza A matrix peptide.
journal, October 1991

  • Moss, P. A.; Moots, R. J.; Rosenberg, W. M.
  • Proceedings of the National Academy of Sciences, Vol. 88, Issue 20
  • DOI: 10.1073/pnas.88.20.8987

Age-associated decline in T cell repertoire diversity leads to holes in the repertoire and impaired immunity to influenza virus
journal, March 2008

  • Yager, Eric J.; Ahmed, Mushtaq; Lanzer, Kathleen
  • The Journal of Experimental Medicine, Vol. 205, Issue 3
  • DOI: 10.1084/jem.20071140

The Role of Naive T Cell Precursor Frequency and Recruitment in Dictating Immune Response Magnitude
journal, April 2012

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

The Structural Dynamics and Energetics of an Immunodominant T Cell Receptor Are Programmed by Its Vβ Domain
journal, February 2008

Next generation sequencing for TCR repertoire profiling: Platform-specific features and correction algorithms: New technology
journal, September 2012

  • Bolotin, Dmitry A.; Mamedov, Ilgar Z.; Britanova, Olga V.
  • European Journal of Immunology, Vol. 42, Issue 11
  • DOI: 10.1002/eji.201242517

Crossreactive T Cells Spotlight the Germline Rules for αβ T Cell-Receptor Interactions with MHC Molecules
journal, March 2008

Multiple Glycines in TCR α-Chains Determine Clonally Diverse Nature of Human T Cell Memory to Influenza A Virus
journal, November 2008

Linking T-cell receptor sequence to functional phenotype at the single-cell level
journal, June 2014

  • Han, Arnold; Glanville, Jacob; Hansmann, Leo
  • Nature Biotechnology, Vol. 32, Issue 7
  • DOI: 10.1038/nbt.2938

Correction of multi-gene deficiency in vivo using a single 'self-cleaving' 2A peptide–based retroviral vector
journal, April 2004

  • Szymczak, Andrea L.; Workman, Creg J.; Wang, Yao
  • Nature Biotechnology, Vol. 22, Issue 5
  • DOI: 10.1038/nbt957

Production of soluble αβ T-cell receptor heterodimers suitable for biophysical analysis of ligand binding
journal, January 1999

  • Willcoj, Benjamin E.; Gao, George F.; Wyer, Jessica R.
  • Protein Science, Vol. 8, Issue 11
  • DOI: 10.1110/ps.8.11.2418

Heterologous immunity: Immunopathology, autoimmunity and protection during viral infections
journal, January 2011

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Narrowing of Human Influenza A Virus-Specific T Cell Receptor α and β Repertoires with Increasing Age
journal, January 2015

  • Gil, Anna; Yassai, Maryam B.; Naumov, Yuri N.
  • Journal of Virology, Vol. 89, Issue 8
  • DOI: 10.1128/JVI.03020-14

The problem of plain vanilla peptides
journal, July 2003

Stable, soluble T-cell receptor molecules for crystallization and therapeutics
journal, September 2003

  • Boulter, J. M.; Glick, M.; Todorov, P. T.
  • Protein Engineering Design and Selection, Vol. 16, Issue 9
  • DOI: 10.1093/protein/gzg087

IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs
journal, July 2004

Abundant cytomegalovirus (CMV) reactive clonotypes in the CD8 + T cell receptor alpha repertoire following allogeneic transplantation
journal, March 2016

  • Link, C. S.; Eugster, A.; Heidenreich, F.
  • Clinical & Experimental Immunology, Vol. 184, Issue 3
  • DOI: 10.1111/cei.12770

Physical detection of influenza A epitopes identifies a stealth subset on human lung epithelium evading natural CD8 immunity
journal, February 2015

  • Keskin, Derin B.; Reinhold, Bruce B.; Zhang, Guang Lan
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 7
  • DOI: 10.1073/pnas.1423482112

Superimposed Epitopes Restricted by the Same HLA Molecule Drive Distinct HIV-Specific CD8 + T Cell Repertoires
journal, June 2014

Immunomic Analysis of the Repertoire of T-Cell Specificities for Influenza A Virus in Humans
journal, October 2008

  • Assarsson, E.; Bui, H. -H.; Sidney, J.
  • Journal of Virology, Vol. 82, Issue 24
  • DOI: 10.1128/JVI.01563-08

T Cell Receptor Recognition Motifs Govern Immune Escape Patterns in Acute SIV Infection
journal, December 2004

The design and proof of concept for a CD8 + T cell-based vaccine inducing cross-subtype protection against influenza A virus
journal, November 2012

  • Tan, Amabel C. L.; Deliyannis, Georgia; Bharadwaj, Mandvi
  • Immunology and Cell Biology, Vol. 91, Issue 1
  • DOI: 10.1038/icb.2012.54

GagCM9-Specific CD8+ T Cells Expressing Limited Public TCR Clonotypes Do Not Suppress SIV Replication In Vivo
journal, August 2011

T cell receptor recognition of a 'super-bulged' major histocompatibility complex class I–bound peptide
journal, September 2005

  • Tynan, Fleur E.; Burrows, Scott R.; Buckle, Ashley M.
  • Nature Immunology, Vol. 6, Issue 11
  • DOI: 10.1038/ni1257

Direct Link Between mhc Polymorphism, T Cell Avidity, and Diversity in Immune Defense
journal, November 2002

Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

Lack of prominent peptide–major histocompatibility complex features limits repertoire diversity in virus-specific CD8+ T cell populations
journal, February 2005

  • Turner, Stephen J.; Kedzierska, Katherine; Komodromou, Helen
  • Nature Immunology, Vol. 6, Issue 4
  • DOI: 10.1038/ni1175

Using synthetic templates to design an unbiased multiplex PCR assay
journal, October 2013

  • Carlson, Christopher S.; Emerson, Ryan O.; Sherwood, Anna M.
  • Nature Communications, Vol. 4, Issue 1
  • DOI: 10.1038/ncomms3680

Impaired assembly and transport of HLA-A and -B antigens in a mutant TxB cell hybrid.
journal, May 1986