7M72 | pdb_00007m72

MHC-like protein complex structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.227 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

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

  • 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.


  • Organizational Affiliation
    • Department of Immunology, Blavatnik Institute of Harvard Medical School, Boston, MA, USA. soh2@bwh.harvard.edu.

Macromolecule Content 

  • Total Structure Weight: 98.47 kDa 
  • Atom Count: 6,942 
  • Modeled Residue Count: 840 
  • Deposited Residue Count: 850 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1d1302Mus musculusMutation(s): 0 
Gene Names: Cd1d1Cd1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11609 (Mus musculus)
Explore P11609 
Go to UniProtKB:  P11609
IMPC:  MGI:107674
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11609
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P11609-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Mus musculusMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01887
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
NKT Valpha14 (Mouse)-2C12 TCR,Human T-cell receptor sp3.4 alpha chain207Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Trav11Trav11d
UniProt
Find proteins for K7N5N2 (Homo sapiens)
Explore K7N5N2 
Go to UniProtKB:  K7N5N2
Entity Groups
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UniProt GroupK7N5N2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
NKT Vbeta8.2 (Mouse)-2C12 TCR,Human nkt tcr beta chain242Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
UniProt
Find proteins for K7N5M4 (Homo sapiens)
Explore K7N5M4 
Go to UniProtKB:  K7N5M4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK7N5M4
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, G
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QOD
(Subject of Investigation/LOI)

Query on QOD



Download:Ideal Coordinates CCD File
H [auth A](3R)-N-[(2S,3R)-1-(alpha-D-galactopyranosyloxy)-3-hydroxy-15-methylhexadecan-2-yl]-3-hydroxyheptadecanamide
C40 H79 N O9
OXDHWVALGDXDDK-OGMOURDSSA-N
HP6

Query on HP6



Download:Ideal Coordinates CCD File
I [auth A]HEPTANE
C7 H16
IMNFDUFMRHMDMM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.227 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.571α = 90
b = 80.92β = 90
c = 243.351γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • 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: 2024-10-16
    Changes: Structure summary