4X6C

CD1a ternary complex with lysophosphatidylcholine and BK6 TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

alpha beta T cell antigen receptor recognition of CD1a presenting self lipid ligands.

Birkinshaw, R.W.Pellicci, D.G.Cheng, T.Y.Keller, A.N.Sandoval-Romero, M.Gras, S.de Jong, A.Uldrich, A.P.Moody, D.B.Godfrey, D.I.Rossjohn, J.

(2015) Nat Immunol 16: 258-266

  • DOI: 10.1038/ni.3098
  • Primary Citation of Related Structures:  
    4X6B, 4X6C, 4X6D, 4X6E, 4X6F

  • PubMed Abstract: 
  • A central paradigm in αβ T cell-mediated immunity is the simultaneous co-recognition of antigens and antigen-presenting molecules by the αβ T cell antigen receptor (TCR). CD1a presents a broad repertoire of lipid-based antigens. We found that a prototypical autoreactive TCR bound CD1a when it was presenting a series of permissive endogenous ligands, while other lipid ligands were nonpermissive to TCR binding ...

    A central paradigm in αβ T cell-mediated immunity is the simultaneous co-recognition of antigens and antigen-presenting molecules by the αβ T cell antigen receptor (TCR). CD1a presents a broad repertoire of lipid-based antigens. We found that a prototypical autoreactive TCR bound CD1a when it was presenting a series of permissive endogenous ligands, while other lipid ligands were nonpermissive to TCR binding. The structures of two TCR-CD1a-lipid complexes showed that the TCR docked over the A' roof of CD1a in a manner that precluded direct contact with permissive ligands. Nonpermissive ligands indirectly inhibited TCR binding by disrupting the TCR-CD1a contact zone. The exclusive recognition of CD1a by the TCR represents a previously unknown mechanism whereby αβ T cells indirectly sense self antigens that are bound to an antigen-presenting molecule.


    Organizational Affiliation

    1] Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Australia. [2] ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Australia. [3] Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD1aA, C281Homo sapiensMutation(s): 2 
Gene Names: CD1A
UniProt & NIH Common Fund Data Resources
Find proteins for P06126 (Homo sapiens)
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Go to UniProtKB:  P06126
PHAROS:  P06126
GTEx:  ENSG00000158477 
Entity Groups  
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UniProt GroupP06126
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, D105Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
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PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
TCR alphaE, G207Homo sapiensMutation(s): 0 
Gene Names: TRACTCRA
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Find proteins for P01848 (Homo sapiens)
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PHAROS:  P01848
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UniProt GroupP01848
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
TCR betaF, H245Homo sapiensMutation(s): 0 
Gene Names: TRBC1
UniProt
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UniProt GroupP01850
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
42H
Query on 42H

Download Ideal Coordinates CCD File 
K [auth A],
M [auth C]
(4R,7R,18Z)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium 4-oxide
C26 H53 N O7 P
YAMUFBLWGFFICM-PTGWMXDISA-O
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
L [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.273α = 90
b = 142.144β = 90
c = 175.752γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Database references
  • Version 1.2: 2015-02-25
    Changes: Database references
  • Version 1.3: 2015-03-04
    Changes: Structure summary
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Source and taxonomy, Structure summary