5WKG

Crystal Structure of Human CD1b in Complex with PA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

A molecular basis of human T cell receptor autoreactivity toward self-phospholipids.

Shahine, A., Van Rhijn, I., Cheng, T.Y., Iwany, S., Gras, S., Moody, D.B., Rossjohn, J.

(2017) Sci Immunol 2: --

  • DOI: 10.1126/sciimmunol.aao1384
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Human T cell autoreactivity toward lipid antigens presented by CD1 proteins can manifest in numerous diseases, including psoriasis, contact hypersensitivities, and allergies. However, the molecular mechanisms for regulating T cell autoreactivity towa ...

    Human T cell autoreactivity toward lipid antigens presented by CD1 proteins can manifest in numerous diseases, including psoriasis, contact hypersensitivities, and allergies. However, the molecular mechanisms for regulating T cell autoreactivity toward lipid antigens remain unclear. We determined the basis for T cell receptor (TCR) autoreactivity toward CD1b bound to self-phospholipids. The spectrum of self-antigens captured by CD1b skews toward abundant membrane phospholipids such as phosphatidylcholine and phosphatidylethanolamine. However, TCRs can specifically recognize rare phospholipids, including phosphatidylglycerol (PG). The structure of an autoreactive TCR bound to CD1b-PG shows that discrimination occurs through a marked induced fit movement of PG so that its polar head group fits snugly into the cationic cup of the TCR. Conversely, TCR binding toward ubiquitous self-phospholipids was sterically or electrostatically repelled. Accordingly, we describe a mechanism of TCR autoreactivity toward rare phospholipids and avoidance of autoreactivity to the most abundant self-phospholipids.

    Organizational Affiliation: 

    Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD1b
A
300Homo sapiensMutation(s): 0 
Gene Names: CD1B
Find proteins for P29016 (Homo sapiens)
Go to Gene View: CD1B
Go to UniProtKB:  P29016
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
99Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D21
Query on D21
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A
(2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate
C37 H71 O8 P
OPVZUEPSMJNLOM-PGUFJCEWSA-N
 Ligand Interaction
NA
Query on NA
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B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD
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A, B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL
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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CUY
Query on CUY
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A
tetracosyl octadecanoate
C42 H84 O2
JKKQRJTZBKHHOI-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN
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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC
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A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
EDO
Query on EDO
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A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA
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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
PEG
Query on PEG
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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG
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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.190α = 90.00
b = 78.530β = 90.00
c = 84.710γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PHASERphasing
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release