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5C9J

Non-classical MHC Class I molecule CD1b at 2.40Å resolution

Data provenance

Structure downloaded from PDB Europe using the Coordinate Server. Aligned to residues 1-180 of 1HHK2 using the CEALIGN3 function of PyMol4. Chain assigment using a Levenshtein distance5 method using data from the PDBe REST API6. Organism data from PDBe REST API. Data for both of these operations from the Molecules endpoint. Structure visualised with 3DMol7.

Information sections


Complex type

Cd1b

1. Beta 2 microglobulin
['B']
2. CD1b
['A']

Species


Locus / Allele group

Non-classical MHC Class I molecule

Publication

Cholesteryl esters stabilize human CD1c conformations for recognition by self-reactive T cells.

Mansour S, Tocheva AS, Cave-Ayland C, Machelett MM, Sander B, Lissin NM, Molloy PE, Baird MS, St��bs G, Schr��der NW, Schumann RR, Rademann J, Postle AD, Jakobsen BK, Marshall BG, Gosain R, Elkington PT, Elliott T, Skylaris CK, Essex JW, Tews I, Gadola SD
Proc. Natl. Acad. Sci. U.S.A. (2016) [doi:10.1073/pnas.1519246113]  [pubmed:26884207

Cluster of differentiation 1c (CD1c)-dependent self-reactive T cells are abundant in human blood, but self-antigens presented by CD1c to the T-cell receptors of these cells are poorly understood. Here we present a crystal structure of CD1c determined at 2.4 Å revealing an extended ligand binding potential of the antigen groove and a substantially different conformation compared with known CD1c structures. Computational simulations exploring different occupancy states of the groove reenacted these different CD1c conformations and suggested cholesteryl esters (CE) and acylated steryl glycosides (ASG) as new ligand classes for CD1c. Confirming this, we show that binding of CE and ASG to CD1c enables the binding of human CD1c self-reactive T-cell receptors. Hence, human CD1c adopts different conformations dependent on ligand occupancy of its groove, with CE and ASG stabilizing CD1c conformations that provide a footprint for binding of CD1c self-reactive T-cell receptors.

Structure deposition and release

Deposited: 2015-06-27
Released: 2016-03-02
Revised: 2016-03-09

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Chain sequences

1. Beta 2 microglobulin
Beta 2 microglobulin
        10        20        30        40        50        60
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
        70        80        90
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRD

2. CD1b
CD1b
        10        20        30        40        50        60
EHVSFHVIQIFSFVNQSWARGQGSGWLDELQTHGWDSESGTIIFLHNWSKGNFSNEELSD
        70        80        90       100       110       120
LELLFRFYLFGLTREIQDHASQDYSKYPFEVQVKAGCELHSGKSPEGFFQVAFNGLDLLS
       130       140       150       160       170       180
FQNTTWVPSPGCGSLAQSVCHLLNHQYEGVTETVYNLIRSTCPRFLLGLLDAGKMYVHRQ
       190       200       210       220       230       240
VKPEAWLSSGPSPGPGRLQLVCHVSGFYPKPVWVMWMRGEQEQQGTQLGDILPNANWTWY
       250       260       270       280
LRATLDVADGEAAGLSCRVKHSSLEGQDIILYWGPGSGGGL


Data provenance

Sequences are retrieved via the Uniprot method of the RSCB REST API. Sequences are then compared to those derived from the PDB file and matched against sequences retrieved from the IPD-IMGT/HLA database for human sequences, or the IPD-MHC database for other species. Mouse sequences are matched against FASTA files from Uniprot. Sequences for the mature extracellular protein (signal petide and cytoplasmic tail removed) are compared to identical length sequences from the datasources mentioned before using either exact matching or Levenshtein distance based matching.


Downloadable data

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Complete structures

Aligned structures [cif]
  1. 5C9J assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 5C9J assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 5C9J assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/5c9j

Data license

The data above is made available under a Creative Commons CC-BY 4.0 license. This means you can copy, remix, transform, build upon and redistribute the material, but you must give appropriate credit, provide a link to the license, and indicate if changes were made.
If you use any data downloaded from this site in a publication, please cite 'https://www.histo.fyi/'. A preprint is in preparation.

Footnotes