High resolution X-ray and NMR structural study of human T-cell immunoglobulin and mucin domain containing protein-3

  • Sci Rep. 2018 Nov 30;8(1):17512. doi: 10.1038/s41598-018-35754-0.
Amit K Gandhi  1 ,  Walter M Kim  1 ,  Zhen-Yu J Sun  2  3 ,  Yu-Hwa Huang  1 ,  Daniel A Bonsor  4 ,  Eric J Sundberg  4  5  6 ,  Yasuyuki Kondo  1  7 ,  Gerhard Wagner  2 ,  Vijay K Kuchroo  8 ,  Gregory Petsko  9 ,  Richard S Blumberg  10
Affiliations
  • 1. Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA.
  • 2. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
  • 3. Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
  • 4. Institute of Human Virology, School of Medicine, University of Maryland, 725 W Lombard St, Baltimore, MD, 21201, USA.
  • 5. Department of Medicine, School of Medicine, University of Maryland, Baltimore, MD, 21201, USA.
  • 6. Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, MD, 21201, USA.
  • 7. Division of Gastroenterology, Department of Internal Medicine, Graduate School of Medicine, Kobe University, Kobe, 650-0017, Japan.
  • 8. Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
  • 9. Department of Neurology and Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY, 10021, USA.
  • 10. Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA. [email protected].
PMID: 30504845 DOI: 10.1038/s41598-018-35754-0
Abstract

T-cell immunoglobulin and Mucin domain containing protein-3 (TIM-3) is an important immune regulator. Here, we describe a novel high resolution (1.7 Å) crystal structure of the human (h)TIM-3 N-terminal variable immunoglobulin (IgV) domain with bound calcium (CA++) that was confirmed by nuclear magnetic resonance (NMR) spectroscopy. Significant conformational differences were observed in the B-C, C'-C″ and C'-D loops of hTIM-3 compared to mouse (m)TIM-3, hTIM-1 and hTIM-4. Further, the conformation of the C-C' loop of hTIM-3 was notably different from hTIM-4. Consistent with the known metal ion-dependent binding of phosphatidylserine (PtdSer) to mTIM-3 and mTIM-4, the NMR spectral analysis and crystal structure of CA++-bound hTIM-3 revealed that residues in the hTIM-3 F-G loop coordinate binding to CA++. In addition, we established a novel biochemical assay to define hTIM-3 functionality as determined by binding to human carcinoembryonic antigen cell adhesion molecule 1 (CEACAM1). These studies provide new insights useful for understanding and targeting hTIM-3.

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