RCSB PDB - 8GLH: Crystal Structure of Human CD1b in Complex with Endogenous PC C40:5

 8GLH

Crystal Structure of Human CD1b in Complex with Endogenous PC C40:5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3IYClick on this verticalbar to view detailsBest fitted 3IVClick on this verticalbar to view details

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Literature

CD1 lipidomes reveal lipid-binding motifs and size-based antigen-display mechanisms.

Huang, S.Shahine, A.Cheng, T.Y.Chen, Y.L.Ng, S.W.Balaji, G.R.Farquhar, R.Gras, S.Hardman, C.S.Altman, J.D.Tahiri, N.Minnaard, A.J.Ogg, G.S.Mayfield, J.A.Rossjohn, J.Moody, D.B.

(2023) Cell 186: 4583-4596.e13

  • DOI: https://doi.org/10.1016/j.cell.2023.08.022
  • Primary Citation of Related Structures:  
    8GLE, 8GLF, 8GLG, 8GLH, 8GLI

  • PubMed Abstract: 

    The CD1 system binds lipid antigens for display to T cells. Here, we solved lipidomes for the four human CD1 antigen-presenting molecules, providing a map of self-lipid display. Answering a basic question, the detection of >2,000 CD1-lipid complexes demonstrates broad presentation of self-sphingolipids and phospholipids. Whereas peptide antigens are chemically processed, many lipids are presented in an unaltered form. However, each type of CD1 protein differentially edits the self-lipidome to show distinct capture motifs based on lipid length and chemical composition, suggesting general antigen display mechanisms. For CD1a and CD1d, lipid size matches the CD1 cleft volume. CD1c cleft size is more variable, and CD1b is the outlier, where ligands and clefts show an extreme size mismatch that is explained by uniformly seating two small lipids in one cleft. Furthermore, the list of compounds that comprise the integrated CD1 lipidome supports the ongoing discovery of lipid blockers and antigens for T cells.


  • Organizational Affiliation

    Division of Rheumatology, Immunity and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA. Electronic address: shouxiong.huang@uc.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD1b300Homo sapiensMutation(s): 0 
Gene Names: CD1B
UniProt & NIH Common Fund Data Resources
Find proteins for P29016 (Homo sapiens)
Explore P29016 
Go to UniProtKB:  P29016
PHAROS:  P29016
GTEx:  ENSG00000158485 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29016
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P29016-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin101Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
C
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G11460AB
GlyCosmos:  G11460AB
GlyGen:  G11460AB
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
D
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G92953ND
GlyCosmos:  G92953ND
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3IY (Subject of Investigation/LOI)
Query on 3IY

Download Ideal Coordinates CCD File 
G [auth A][(2~{R})-1-dodecanoyloxy-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propan-2-yl] (8~{Z},11~{Z},14~{Z},24~{Z},27~{Z})-triaconta-8,11,14,24,27-pentaenoate
C50 H91 N O8 P
JZJDDTSQGYPVAU-XFFLUJDDSA-O
3IV (Subject of Investigation/LOI)
Query on 3IV

Download Ideal Coordinates CCD File 
F [auth A](11E)-hexadec-11-enoic acid
C16 H30 O2
JGMYDQCXGIMHLL-AATRIKPKSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
N [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
K [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
M [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.447α = 90
b = 77.049β = 90
c = 91.445γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3IYClick on this verticalbar to view detailsBest fitted 3IVClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDE210101031

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Structure summary