5NQ2

'Porcine (Sus scrofa) Major Histocompatibility Complex, class I, presenting IAYERMCNI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Induction of influenza-specific local CD8 T-cells in the respiratory tract after aerosol delivery of vaccine antigen or virus in the Babraham inbred pig.

Tungatt, K.Dolton, G.Morgan, S.B.Attaf, M.Fuller, A.Whalley, T.Hemmink, J.D.Porter, E.Szomolay, B.Montoya, M.Hammond, J.A.Miles, J.J.Cole, D.K.Townsend, A.Bailey, M.Rizkallah, P.J.Charleston, B.Tchilian, E.Sewell, A.K.

(2018) Plos Pathog. 14: e1007017-e1007017

  • DOI: 10.1371/journal.ppat.1007017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • There is increasing evidence that induction of local immune responses is a key component of effective vaccines. For respiratory pathogens, for example tuberculosis and influenza, aerosol delivery is being actively explored as a method to administer v ...

    There is increasing evidence that induction of local immune responses is a key component of effective vaccines. For respiratory pathogens, for example tuberculosis and influenza, aerosol delivery is being actively explored as a method to administer vaccine antigens. Current animal models used to study respiratory pathogens suffer from anatomical disparity with humans. The pig is a natural and important host of influenza viruses and is physiologically more comparable to humans than other animal models in terms of size, respiratory tract biology and volume. It may also be an important vector in the birds to human infection cycle. A major drawback of the current pig model is the inability to analyze antigen-specific CD8+ T-cell responses, which are critical to respiratory immunity. Here we address this knowledge gap using an established in-bred pig model with a high degree of genetic identity between individuals, including the MHC (Swine Leukocyte Antigen (SLA)) locus. We developed a toolset that included long-term in vitro pig T-cell culture and cloning and identification of novel immunodominant influenza-derived T-cell epitopes. We also generated structures of the two SLA class I molecules found in these animals presenting the immunodominant epitopes. These structures allowed definition of the primary anchor points for epitopes in the SLA binding groove and established SLA binding motifs that were used to successfully predict other influenza-derived peptide sequences capable of stimulating T-cells. Peptide-SLA tetramers were constructed and used to track influenza-specific T-cells ex vivo in blood, the lungs and draining lymph nodes. Aerosol immunization with attenuated single cycle influenza viruses (S-FLU) induced large numbers of CD8+ T-cells specific for conserved NP peptides in the respiratory tract. Collectively, these data substantially increase the utility of pigs as an effective model for studying protective local cellular immunity against respiratory pathogens.


    Organizational Affiliation

    California Institute for Quantitative Biosciences, University of California, Berkeley, United States.,Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.,p53 Laboratory , ASTAR (Agency for Science, Technology and Research) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648 . Email: cjbrown@p53lab.a-star.edu.sg ; Tel: +65 6478 8273.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: nathanael_gray@dfci.harvard.edu.,From the Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA.,Howard Hughes Medical Institute, University of California, Berkeley, United States.,Department of Biotechnology , The University of Tokyo , 1-1-1 Yayoi , Bunkyo-ku, Tokyo 113-8657 , Japan.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA. kyle.l.brown@vanderbilt.edu.,David Geffen School of Medicine, University of California Los Angeles and Greater West Los Angeles Health Care System, Los Angeles, CA 90095, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA. kyle.l.brown@vanderbilt.edu.,Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal.,Ipsen Bioscience , 650 East Kendall Street , Cambridge , MA 02142 , USA.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,the Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, Florida 32224.,School of Veterinary Sciences, University of Bristol, Bristol, United Kingdom.,Department of Agrifood Production and Environmental Sciences, University of Florence, Florence, Italy.,Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Porto, Portugal.,Department of Molecular and Cell Biology, University of California, Berkeley, United States.,NDBio Therapeutics Inc., Incheon 21984, Republic of Korea.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: peter_sorger@hms.harvard.edu.,Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232-2372, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Aspirnaut Summer research program, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Center for Structural Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Ipsen Innovation , 5, Avenue du Canada , Les Ulis , France 91940 . Email: sergeauvin@gmail.com ; Tel: +33 160 922481.,Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.,Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Life Sciences (BMLS) and Structural Genomics Consortium Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; German Cancer Network (DKTK), Frankfurt Site, 60438 Frankfurt am Main, Germany.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.,Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.,Veterans Affairs Hospital, Nashville, TN, 37232, USA.,the Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224, radisky.evette@mayo.edu.,School of Biological Sciences , Nanyang Technological University , 50 Nanyang Drive , Singapore 637551.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Leadership Alliance, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, United Kingdom.,RIKEN Program for Drug Discovery and Medical Technology Platforms , 2-1 Hirosawa , Wako , Saitama 351-0198 , Japan.,From the Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel, papo@bgu.ac.il.,Northeastern Collaborative Access Team, Argonne National Laboratory, Lemont, IL, 60439, USA.,the Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224.,Bioinformatics Institute , ASTAR (Agency for Science, Technology and Research) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 . Email: chandra@bii.a-star.edu.sg ; Tel: +65 6478 8273.,Center for Structural Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA. kyle.l.brown@vanderbilt.edu.,the National Institute for Biotechnology in the Negev (NIBN), Beer-Sheva 84105, Israel.,the Molecular Biophysics and Integrated Bioimaging Division, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and.,Systems Immunity Research Institute, Cardiff University, Cardiff, Wales, United Kingdom.,Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Life Sciences (BMLS) and Structural Genomics Consortium Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany.,James Cook University, Cairns, Australia.,California NanoSystems Institute, University California Los Angeles, Los Angeles, CA 90095, USA.,Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.,Division of Molecular Biotherapy, Cancer Chemotherapy Center , Japanese Foundation for Cancer Research , 3-8-31 Ariake , Koto-ku, Tokyo 135-8850 , Japan.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,The Pirbright Institute, Pirbright, Woking, United Kingdom.,Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MHC class I antigen
A
277Sus scrofaMutation(s): 0 
Gene Names: SLA-2
Find proteins for B1A9P6 (Sus scrofa)
Go to UniProtKB:  B1A9P6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
100Sus scrofaMutation(s): 0 
Gene Names: B2M
Find proteins for Q07717 (Sus scrofa)
Go to Gene View: B2M
Go to UniProtKB:  Q07717
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ILE-ALA-TYR-GLU-ARG-MET-CYS-ASN-ILE
C
9Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd)Mutation(s): 0 
Gene Names: NP
Find proteins for Q9Q0U8 (Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd))
Go to UniProtKB:  Q9Q0U8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 93.478α = 90.00
b = 80.843β = 119.66
c = 61.964γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
AutoPROCdata reduction
Aimlessdata scaling
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2019-05-08
    Type: Data collection, Database references