6BNK

Crystal structure of TCR-MHC-like molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dual Modifications of alpha-Galactosylceramide Synergize to Promote Activation of Human Invariant Natural Killer T Cells and Stimulate Anti-tumor Immunity.

Chennamadhavuni, D.Saavedra-Avila, N.A.Carreno, L.J.Guberman-Pfeffer, M.J.Arora, P.Yongqing, T.Koay, H.F.Godfrey, D.I.Keshipeddy, S.Richardson, S.K.Sundararaj, S.Lo, J.H.Wen, X.Gascon, J.A.Yuan, W.Rossjohn, J.Le Nours, J.Porcelli, S.A.Howell, A.R.

(2018) Cell Chem Biol 25: 571

  • DOI: 10.1016/j.chembiol.2018.02.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycosylceramides that activate CD1d-restricted invariant natural killer T (iNKT) cells have potential therapeutic applications for augmenting immune responses against cancer and infections. Previous studies using mouse models identified sphinganine ...

    Glycosylceramides that activate CD1d-restricted invariant natural killer T (iNKT) cells have potential therapeutic applications for augmenting immune responses against cancer and infections. Previous studies using mouse models identified sphinganine variants of α-galactosylceramide as promising iNKT cell activators that stimulate cytokine responses with a strongly proinflammatory bias. However, the activities of sphinganine variants in mice have generally not translated well to studies of human iNKT cell responses. Here, we show that strongly proinflammatory and anti-tumor iNKT cell responses were achieved in mice by a variant of α-galactosylceramide that combines a sphinganine base with a hydrocinnamoyl ester on C6″ of the sugar. Importantly, the activities observed with this variant were largely preserved for human iNKT cell responses. Structural and in silico modeling studies provided a mechanistic basis for these findings and suggested basic principles for capturing useful properties of sphinganine analogs of synthetic iNKT cell activators in the design of immunotherapeutic agents.


    Organizational Affiliation

    Department of Chemistry, The University of Connecticut, Storrs, CT 06269-3060, USA.,Graduate School of Science and Molecular Chirality Research Center, Chiba University, Inage, Chiba, Japan.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.,Department of Chemistry, The University of Connecticut, Storrs, CT 06269-3060, USA. Electronic address: amy.howell@uconn.edu.,Institute of Advanced Energy and Graduate School of Energy Science, Kyoto University, Uji, Kyoto, Japan.,Biochemistry Department, Indian Institute of Science, Bangalore 560012, India.,Department of Chemistry and Chemical Biology, Northeastern University, Boston, United States.,Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Food Technology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400085, India and snjam@barc.gov.in.,Japan Science and Technology Agency (JST) and Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. kobayashi.takuya.4r@kyoto-u.ac.jp.,Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biochemistry, McGill University, Montreal, QC, Canada.,Microbiology, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany.,Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea. yok5@snu.ac.kr.,Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 17, 38106, Braunschweig, Germany.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Millennium Institute on Immunology and Immunotherapy, Programa de Inmunologia, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Max-Planck-Institute for Biophysics Frankfurt, Max-von-Laue-Str. 3, 60438, Frankfurt, Germany.,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Korea.,Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia.,Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, USA. Electronic address: marzena.pazgier@usuhs.edu.,Computational Biochemistry, University of Bayreuth, Universitätsstrasse 30, NW I, 95447, Bayreuth, Germany.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA. Electronic address: steven.porcelli@einstein.yu.edu.,RIKEN, SPring-8 Center, Hyogo, Japan.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States.,From the High Pressure and Synchrotron Radiation Physics Division and.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.,School of Biochemistry, Devi Ahilya University, Indore 452001, India.,Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, 92093.,Department of Molecular Imaging and Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, USA.,Biochemistry, Faculty of Chemistry, University of Kaiserslautern, Erwin-Schrödinger-Straße 52, 67663, Kaiserslautern, Germany.,Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.,Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. kobayashi.takuya.4r@kyoto-u.ac.jp.,Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology (PRESTO), Kawaguchi, Saitama, Japan.,SPARC BioCentre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,National Institute for Research in Tuberculosis, Chennai 600031, India.,Max-Planck-Institute for Biophysics Frankfurt, Max-von-Laue-Str. 3, 60438, Frankfurt, Germany. ulrich.ermler@biophys.mpg.de.,Cancer Metabolism and Signaling Networks Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA.,Biophysics, Department of Physics, University of Kaiserslautern, Erwin-Schrödinger-Straße 46, 67663, Kaiserslautern, Germany.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States.,Center for Translational Medicine, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China. Electronic address: zhaole2@mail.xjtu.edu.cn.,Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, USA.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, USA. hjin@illinois.edu.,Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany.,Biolojic Design, Ltd., 12 Hamada Street, Rehovot 7670314, Israel.,Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany.,Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, United States.,Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, USA. hjin@illinois.edu.,Boston Biochem, a Bio-Techne Brand, 840 Memorial Drive, Cambridge, MA 02139, USA.,SPARC BioCentre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Korea.,Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia; Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, UK.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan.,Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia. Electronic address: jerome.lenours@monash.edu.,From the High Pressure and Synchrotron Radiation Physics Division and ravimakde@rrcat.gov.in.,The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, University of California, San Diego, La Jolla, California, 92093.,Antibody Discovery and Protein Engineering, MedImmune, Granta Park, Cambridge CB21 6GH, UK.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.,Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California, 92093.,Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. r.suno@mfour.med.kyoto-u.ac.jp.,Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 17, 38106, Braunschweig, Germany. U.Rau@tu-bs.de.,Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging at the University of Melbourne, Melbourne, Australia.,Microbiology, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany. matthias.boll@biologie.uni-freiburg.de.,Key Laboratory of Fermentation Engineering, Ministry of Education, College of Bioengineering, Hubei University of Technology, Wuhan, China; Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, USA.,Protech Inc., Yongeon 103 Daehangno, Jongno-gu, Seoul, 110-799, Republic of Korea. yok5@snu.ac.kr.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India. Electronic address: mrn@iisc.ac.in.,AstraZeneca R&D, Darwin Building Cambridge Science Park, Milton Road, Cambridge CB4 0WG, UK.,Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Korea.,Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria.,The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address: sachdev.sidhu@utoronto.ca.,Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.,Department of Biochemistry, McGill University, Montreal, QC, Canada; Corbin Therapeutics, Montreal, QC, Canada.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA. tatiana.kutateladze@ucdenver.edu.,Biolojic Design, Ltd., 12 Hamada Street, Rehovot 7670314, Israel; The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar Ilan University, Ramat Gan 52900, Israel. Electronic address: yanay@ofranlab.org.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antigen-presenting glycoprotein CD1d1
A, E
302Mus musculusMutation(s): 0 
Gene Names: Cd1d1 (Cd1.1)
Find proteins for P11609 (Mus musculus)
Go to UniProtKB:  P11609
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, F
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Human nkt tcr alpha chain
C, G
207N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Human nkt tcr beta chain
D, H
242N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGH
Query on AGH

Download SDF File 
Download CCD File 
A, E
N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE
C50 H99 N O9
VQFKFAKEUMHBLV-BYSUZVQFSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 79.970α = 90.00
b = 150.570β = 95.23
c = 101.200γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
BUSTERrefinement
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2018-04-11
    Type: Data collection, Database references
  • Version 1.2: 2018-05-30
    Type: Data collection, Database references