6CYW | pdb_00006cyw

Structure of sphingomyelin in complex with mouse CD1d

• PDB DOI: https://doi.org/10.2210/pdb6CYW/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2018-04-06 Released: 2019-04-10 
• Deposition Author(s): Zajonc, D.M., Wang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.256 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Control of CD1d-restricted antigen presentation and inflammation by sphingomyelin.

Melum, E., Jiang, X., Baker, K.D., Macedo, M.F., Fritsch, J., Dowds, C.M., Wang, J., Pharo, A., Kaser, A., Tan, C., Pereira, C.S., Kelly, S.L., Duan, J., Karlsen, T.H., Exley, M.A., Schutze, S., Zajonc, D.M., Merrill, A.H., Schuchman, E.H., Zeissig, S., Blumberg, R.S.

(2019) Nat Immunol 20: 1644-1655

• PubMed: 31636468 
• DOI: https://doi.org/10.1038/s41590-019-0504-0
• Primary Citation Related Structures: 
  6CYW


• PubMed Abstract: 
  

  Invariant natural killer T (iNKT) cells recognize activating self and microbial lipids presented by CD1d. CD1d can also bind non-activating lipids, such as sphingomyelin. We hypothesized that these serve as endogenous regulators and investigated humans and mice deficient in acid sphingomyelinase (ASM), an enzyme that degrades sphingomyelin. We show that ASM absence in mice leads to diminished CD1d-restricted antigen presentation and iNKT cell selection in the thymus, resulting in decreased iNKT cell levels and resistance to iNKT cell-mediated inflammatory conditions. Defective antigen presentation and decreased iNKT cells are also observed in ASM-deficient humans with Niemann-Pick disease, and ASM activity in healthy humans correlates with iNKT cell phenotype. Pharmacological ASM administration facilitates antigen presentation and restores the levels of iNKT cells in ASM-deficient mice. Together, these results demonstrate that control of non-agonistic CD1d-associated lipids is critical for iNKT cell development and function in vivo and represents a tight link between cellular sphingolipid metabolism and immunity.

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Organizational Affiliation: 
• Gastroenterology Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. [e-mail].
Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, and University of Oslo, Oslo, Norway. [e-mail].
Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, and University of Oslo, Oslo, Norway.
Gastroenterology Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Department of Oncology, Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.
i3S Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.
Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
Institute of Immunology, Christian-Albrechts University, Kiel, Germany.
Department of Infection Prevention and Infectious Diseases, University of Regensburg, Regensburg, Germany.
Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Christian-Albrechts University, Kiel, Germany.
Division of Immune Regulation, La Jolla Institute for Immunology, La Jolla, CA, USA.
Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
School of Biological Sciences and the Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA.
Human Aging Research Institute, School of Life Sciences, Nanchang University, Nanchang, China.
Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Department of Medicine I, University Medical Center Dresden, Technische Universität Dresden, Dresden, Germany.
Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany.
Gastroenterology Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 45.97 kDa 
• Atom Count: 3,419 
• Modeled Residue Count: 369 
• Deposited Residue Count: 384 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d1	A	285	Mus musculus	Mutation(s): 0  Gene Names: Cd1d1, mCG_3074
UniProt & NIH Common Fund Data Resources
Find proteins for P11609 (Mus musculus) Explore P11609  Go to UniProtKB:  P11609
IMPC:  MGI:107674
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P11609-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	Mus musculus	Mutation(s): 0  Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887
IMPC:  MGI:88127

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FO4	F [auth A]	sphingomyelin C47 H94 N2 O6 P NHYQHBPEJLFFSO-QYKFWSDSSA-O
NAG	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.256 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.134	α = 90
b = 105.256	β = 90
c = 106.388	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-10 
Deposition Author(s): Zajonc, D.M., Wang, J.

Revision History  

• Version 1.0: 2019-04-10
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-30
  Changes: Structure summary