6XNG | pdb_00006xng

MHC-like protein complex structure

• PDB DOI: https://doi.org/10.2210/pdb6XNG/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Mus musculus
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-02 Released: 2021-11-10 
• Deposition Author(s): Thirunavukkarasu, P., Le Nours, J., Rossjohn, J.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 
  0.277 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Host immunomodulatory lipids created by symbionts from dietary amino acids.

Oh, S.F., Praveena, T., Song, H., Yoo, J.S., Jung, D.J., Erturk-Hasdemir, D., Hwang, Y.S., Lee, C.C., Le Nours, J., Kim, H., Lee, J., Blumberg, R.S., Rossjohn, J., Park, S.B., Kasper, D.L.

(2021) Nature 600: 302-307

• PubMed: 34759313 
• DOI: https://doi.org/10.1038/s41586-021-04083-0
• Primary Citation Related Structures: 
  6XNG, 7M72


• PubMed Abstract: 
  

  Small molecules derived from symbiotic microbiota critically contribute to intestinal immune maturation and regulation ¹ . However, little is known about the molecular mechanisms that control immune development in the host-microbiota environment. Here, using a targeted lipidomic analysis and synthetic approach, we carried out a multifaceted investigation of immunomodulatory α-galactosylceramides from the human symbiont Bacteroides fragilis (BfaGCs). The characteristic terminal branching of BfaGCs is the result of incorporation of branched-chain amino acids taken up in the host gut by B. fragilis. A B. fragilis knockout strain that cannot metabolize branched-chain amino acids showed reduced branching in BfaGCs, and mice monocolonized with this mutant strain had impaired colonic natural killer T (NKT) cell regulation, implying structure-specific immunomodulatory activity. The sphinganine chain branching of BfaGCs is a critical determinant of NKT cell activation, which induces specific immunomodulatory gene expression signatures and effector functions. Co-crystal structure and affinity analyses of CD1d-BfaGC-NKT cell receptor complexes confirmed the interaction of BfaGCs as CD1d-restricted ligands. We present a structural and molecular-level paradigm of immunomodulatory control by interactions of endobiotic metabolites with diet, microbiota and the immune system.

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Organizational Affiliation: 
• Department of Immunology, Blavatnik Institute of Harvard Medical School, Boston, MA, USA. [e-mail].
Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA. [e-mail].
Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, Republic of Korea.
Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA.
Department of Immunology, Blavatnik Institute of Harvard Medical School, Boston, MA, USA.
Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. [e-mail].
Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia. [e-mail].
Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK. [e-mail].
CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, Republic of Korea. [e-mail].
Department of Immunology, Blavatnik Institute of Harvard Medical School, Boston, MA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 99.09 kDa 
• Atom Count: 6,843 
• Modeled Residue Count: 838 
• Deposited Residue Count: 850 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d1	A	302	Mus musculus	Mutation(s): 0  Gene Names: Cd1d1, Cd1.1
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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NKT Valpha14 (Mouse)-2C12 TCR	C	207	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NKT Vbeta8.2 (Mouse)-2C12 TCR	D	242	Mus musculus	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V8P (Subject of Investigation/LOI)	H [auth A], I [auth A]	(3R)-N-[(2S,3R)-1-(alpha-D-galactopyranosyloxy)-3-hydroxyheptadecan-2-yl]-3-hydroxyheptadecanamide C40 H79 N O9 BIVDLWPPMIZENJ-OGMOURDSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free:  0.277 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.338	α = 90
b = 80.661	β = 90
c = 242.797	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-11-10 
Deposition Author(s): Thirunavukkarasu, P., Le Nours, J., Rossjohn, J.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History  

• Version 1.0: 2021-11-10
  Type: Initial release
  
• Version 1.1: 2021-12-01
  Changes: Database references
• Version 1.2: 2021-12-22
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary