CD1

For the album by Throbbing Gristle, see CD1 (album).

CD1a molecule
Identifiers
Symbol	CD1A
Alt. symbols	CD1
NCBI gene	909
HGNC	1634
OMIM	188370
RefSeq	NM_001763
UniProt	P06126
Other data
Locus	Chr. 1 q22-q23
Search for Structures Swiss-model Domains InterPro

CD1b molecule
Identifiers
Symbol	CD1B
Alt. symbols	CD1
NCBI gene	910
HGNC	1635
OMIM	188360
RefSeq	NM_001764
UniProt	P29016
Other data
Locus	Chr. 1 q22-q23
Search for Structures Swiss-model Domains InterPro

CD1c molecule
Identifiers
Symbol	CD1C
Alt. symbols	CD1
NCBI gene	911
HGNC	1636
OMIM	188340
RefSeq	NM_001765
UniProt	P29017
Other data
Locus	Chr. 1 q22-q23
Search for Structures Swiss-model Domains InterPro

CD1d molecule
Identifiers
Symbol	CD1D
NCBI gene	912
HGNC	1637
OMIM	188410
RefSeq	NM_001766
UniProt	P15813
Other data
Locus	Chr. 1 q22-q23
Search for Structures Swiss-model Domains InterPro

CD1e molecule
Identifiers
Symbol	CD1E
NCBI gene	913
HGNC	1638
OMIM	188411
RefSeq	NM_030893
UniProt	P15812
Other data
Locus	Chr. 1 q22-q23
Search for Structures Swiss-model Domains InterPro

CD1 (cluster of differentiation 1) is a family of glycoproteins expressed on the surface of various human antigen-presenting cells. CD1 glycoproteins are structurally related to the class I MHC molecules, however, in contrast to MHC class 1 proteins, they present lipids, glycolipids and small molecules antigens, from both endogenous and pathogenic proteins, to T cells and activate an immune response.

T cells recognise CD1 using TCR αβ, γδ,^[1][2][3] or CD36 family members. T cells that are activated by CD1-antigen complexes are called CD1-restricted T cells.^[4] 10% of all αβ T lymphocytes in human peripheral blood are Cd1-restricted, out of which, the most abundant are the T cells specific for CD1c.^[5]

The human CD1 gene cluster is located on chromosome 1. Genes of the CD1 family were first cloned in 1986, by Franco Calabi and C. Milstein, whereas the first known lipid antigen for CD1 was discovered in 1994, during studies of Mycobacterium tuberculosis.^[6] The first antigen that was discovered to be able to bind CD1 and then be recognised by TCR is C80 mycolic acid. Even though their precise function is unknown, The CD1 system of lipid antigen recognition by TCR offers the prospect of discovering new approaches to therapy and developing immunomodulatory agents.^[7][1][8][2]

Types

CD1 glycoproteins can be classified primarily into two groups of CD1 isoforms which differ in their lipid anchoring, as well as their expression patterns of the CD1 genes (CD1d is constitutively expressed, whereas the group 1 CD1 genes are inducible and coordinately regulated by myeloid cells).^[9]

• CD1a, CD1b and CD1c (group 1 CD1 molecules) are expressed on cells specialized for antigen presentation.^[10]
  • CD1e is also considered a group 1 CD1 molecule, even though it does not function in antigen presentation, contrasting the other isoforms.^[2][6][11]
• CD1d (group 2 CD1) is expressed in a wider variety of cells.

CD1e is an intermediate form, a soluble lipid transfer protein that is expressed intracellularly. It does not present lipid antigens to T cells, rather plays a role in the processing of lipid antigens and loading them onto other CD1 molecules.^[12][13][6]

In humans

Group 1

Group 1 CD1 molecules have been shown to present foreign lipid antigens to CD1-specific T cells. Human CD1 cells can recognise and bind a large number of lipids, from monoacylated lipids or lipopeptides to tetra-acylated lipids. However, not all of the lipid ligands can be considered antigens for T-cells. Free fatty acids sphingolipids, phospholipids, sulfolipids, lysophospholipids, amphipathic small molecules and some oils function as natural antigens for T cells.^[1][12]

Group 2

The natural antigens of group 2 CD1 are not well characterized, but a synthetic glycolipid, alpha-galactosylceramide (α-GalCer), originally isolated from a compound found in a marine sponge, has strong biologic activity.

Group 2 CD1 molecules activate a group of T cells, known as natural killer T cells because of their expression of NK surface markers such as CD161. Natural Killer T (NKT) cells are activated by CD1d-presented antigens, and rapidly produce Th1 and Th2 cytokines, typically represented by interferon-gamma and IL-4 production. The group 2 (CD1d) ligand α-GalCer is currently in phase I clinical trials for the treatment of advanced non-hematologic cancers.

NKT cells that respond to α-GalCer are termed "type 1 NKTs". There exists another group of "type 2 NKTs" that do not respond to α-GalCer-CD1D. Instead, they respond to a diverse set of antigens such as sulfatide-CD1d and mycobacterial lipid-CD1d.^[3]

Diagnostic relevance

CD1 antigens are expressed on cortical thymocytes, but not on mature T cells. This often remains true in neoplastic cells from these populations, so that the presence of CD1 antigens can be used in diagnostic immunohistochemistry to identify some thymomas and malignancies arising from T cell precursors. CD1a, in particular, is a specific marker for Langerhans cells, and can therefore also be used in the diagnosis of Langerhans cell histiocytosis. Other conditions that may show CD1 positivity include myeloid leukaemia and some B cell lymphomas.^[14]

Structure

CD1 proteins consist of a heavy chain with α1, α2, and α3 domains and a transmembrane domain which anchors it to the cell membrane. Much like the MHC molecules, the CD1 heavy chain associates with β2-microglobulin and its binding groove consists of two antiparallel α-helices, placed atop a β-sheet platform. The antigen-binding cleft architecture of CD1 proteins consists of A', C', F' and T' binding pockets and C' and D'/E' accessory portals, which act to accommodate the aliphatic hydrocarbon chains present in lipid, glycolipid, phospholipid, or lipopeptide antigens. CD1 antigen binding clefts are defined by locations of named portals where antigens protrude.^[5][12]

The main difference in structure between MHC and CD1 proteins is that in MHC proteins, the contact region for TCR show lateral symmetry, whereas human CD1 proteins show left-right asymmetry. Another difference between MHC and CD1 proteins is that the antigen display platform of CD1 molecules is smaller than the antigen display groove of MHC molecules.^[6]

CD1-lipid TCR interactions

Three models of CD1 recognition by TCR have been described: "head group recognition" model, "absence of interference" model and "altered CD1" model. The "head group recognition" model is considered to be a classical mode of CD1-antigen recognition, whereas the other two models posit that TCR contacts CD1 and not lipid. They are believed to occur in different TCR-antigen-CD1 pairings.^{[5][8][1][12]} The two former models are proven by protein crystallography.^[3]

• The "Head group recognition" model, also called "headgroup discrimination" model, is attributed to CD1b and CD1d, and it refers to the fact that TCR do not only react to peptidic antigens, but can also recognise and bind to the structure of carbohydrate and other non-peptidic head groups of antigens that are carried by CD1.^[5][8] It is also called "corecognition" and is most similar to the recognition between TCR and traditional peptide-MHC.^[3]
• The "absence of interference" model emerged as a result of the identification of tissue-derived CD1a-presented autoantigens and the first CD1a-lipid-TCR structure, between an autoreactive TCR which bound the CD1a without contacting the lipid that CD1a was carrying. In accordance to the left-right asymmetry of CD1, the small hydrophobic lipid ligand emerges from the F' binding pocket (the right side of the CD1 binding cleft) and TCR binds to the A' binding pocket (the left side of CD1a). Sulfatide and sphingomyelin can be considered antagonists for CD1 autoreactive cells, as they have a large polar head group and can block the CD1a A' binding pocket.^[8][5]
• The "altered CD1" model is attributed to CD1c. CD1c has A' pole, F' roof and G' portal, which serve as points of access to the binding cleft. When it is loaded with fatty acids and lipids, CD1c alters its 3D surface in order to act as a TCR recognition surface.^[8][5]

The TCR3d database includes all examples of a CD1-family protein interacting with an TCR in the Protein Data Bank, updated periodically.

CD36 interactions

Although it is known that CD1 binds to CD36, there is currently (as of January 2026) no structural characterization of the nature of the interaction.

In other animals

Rodents

Mice lack the group 1 CD1 molecules, and instead have 2 copies of CD1d. Thus, mice have been used extensively to characterize the role of CD1d and CD1d-dependent NKT cells in a variety of disease models. Rats also lack group 1 CD1 molecules.

Guinea pigs have both groups of CD1 and are commonly used as the alternative model animal for CD1 research.^[15] Specifically, they express four orthologs of the group 1 CD1b protein and three orthologs of CD1c, as well as one ortholog of CD1d.^[16]

Ruminants

Cows have one copy each of CD1a and CD1e, several copies of CD1b, and no copies of CD1c.^[17] Ruminants including cows were previously thought to have no functional copies of CD1d (only pseudogenes) due to lack of reaction to αGalCer when tested using mouse iNKT cells, but later research has shown CD1d to be expressed and the genes for the NKT machinery to be present. It turns out bovine CD1d has an altered binding pocket causing a different binding "pose". The change also incurs a limit on the length of the glycosphingolipid antigen.^[18]

Because of the fact that cows are a natural host of Mycobacterium bovis, a pathogen in humans as well, it is hoped that studying cows will yield insights into the group 1 CD1 antigen-presenting system. M. bovis is also very similar to M. tuberculosis genetically. Cows are a valuable model organism for studying immune responses to tuberculosis with many similarities to humans. Nevertheless, they have their own special features such as the aforementioned CD1 repertoire and a special division of labor among δγ T cells by expression of WC1, a protein not found in primates.^[19]

References

1. Layre E, de Jong A, Moody DB (December 2014). "Human T cells use CD1 and MR1 to recognize lipids and small molecules". Current Opinion in Chemical Biology. Molecular immunology. 23: 31–38. doi:10.1016/j.cbpa.2014.09.007. PMID 25271021.
2. Tang Y, Ma S, Lin S, Wu Y, Chen S, Liu G, Ma L, Wang Z, Jiang L, Wang Y (2023-03-01). "Cell-free protein synthesis of CD1E and B2M protein and in vitro interaction". Protein Expression and Purification. 203 106209. doi:10.1016/j.pep.2022.106209. ISSN 1046-5928. PMID 36460227. S2CID 254180046.
3. Cao TP, Shahine A, Cox LR, Besra GS, Moody DB, Rossjohn J (August 2024). "A structural perspective of how T cell receptors recognize the CD1 family of lipid antigen-presenting molecules". The Journal of Biological Chemistry. 300 (8) 107511. doi:10.1016/j.jbc.2024.107511. PMC 11780374. PMID 38945451.
4. Gherardin NA, Redmond SJ, McWilliam HE, Almeida CF, Gourley KH, Seneviratna R, Li S, De Rose R, Ross FJ, Nguyen-Robertson CV, Su S, Ritchie ME, Villadangos JA, Moody DB, Pellicci DG, Uldrich AP, Godfrey DI (15 June 2021). "CD36 family members are TCR-independent ligands for CD1 antigen–presenting molecules". Science Immunology. 6 (60) eabg4176. doi:10.1126/sciimmunol.abg4176. PMC 8418821. PMID 34172588.
5. Moody DB, Cotton RN (2017-06-01). "Four pathways of CD1 antigen presentation to T cells". Current Opinion in Immunology. Antigen processing * Special section: Metabolism of T cells. 46: 127–133. doi:10.1016/j.coi.2017.07.013. ISSN 0952-7915. PMC 5599164. PMID 28756303.
6. Van Rhijn I, Godfrey DI, Rossjohn J, Moody DB (October 2015). "Lipid and small-molecule display by CD1 and MR1". Nature Reviews. Immunology. 15 (10): 643–654. doi:10.1038/nri3889. PMC 6944187. PMID 26388332.
7. Porcelli S, Brenner MB, Greenstein JL, Balk SP, Terhorst C, Bleicher PA (October 1989). "Recognition of cluster of differentiation 1 antigens by human CD4-CD8-cytolytic T lymphocytes". Nature. 341 (6241): 447–450. Bibcode:1989Natur.341..447P. doi:10.1038/341447a0. PMID 2477705. S2CID 4264602.
8. Moody DB, Suliman S (2017-10-30). "CD1: From Molecules to Diseases". F1000Research. 6: 1909. doi:10.12688/f1000research.12178.1. PMC 5664979. PMID 29152228.
9. Zajonc DM, Wilson IA (2007). "Architecture of CD1 Proteins". T Cell Activation by CD1 and Lipid Antigens. Current Topics in Microbiology and Immunology. Vol. 314. pp. 27–50. doi:10.1007/978-3-540-69511-0_2. ISBN 978-3-540-69510-3. PMID 17593656.
10. Sköld M, Behar SM (March 2005). "The role of group 1 and group 2 CD1-restricted T cells in microbial immunity". Microbes and Infection. 7 (3): 544–551. doi:10.1016/j.micinf.2004.12.012. PMID 15777730.
11. Mori L, Lepore M, De Libero G (2016-05-20). "The Immunology of CD1- and MR1-Restricted T Cells". Annual Review of Immunology. 34 (1): 479–510. doi:10.1146/annurev-immunol-032414-112008. ISSN 0732-0582. PMID 26927205.
12. Zajonc DM (August 2016). "The CD1 family: serving lipid antigens to T cells since the Mesozoic era". Immunogenetics. 68 (8): 561–576. doi:10.1007/s00251-016-0931-0. ISSN 0093-7711. PMC 5087154. PMID 27368414.
13. Angenieux C, Salamero J, Fricker D, Cazenave JP, Goud B, Hanau D, de La Salle H (December 2000). "Characterization of CD1e, a third type of CD1 molecule expressed in dendritic cells". The Journal of Biological Chemistry. 275 (48): 37757–37764. doi:10.1074/jbc.M007082200. PMID 10948205.
14. Kumarasen C, Anthony S-Y L (2003). Manual of diagnostic antibodies for immunohistology. London: Greenwich Medical Media. pp. 59–60. ISBN 1-84110-100-1.
15. Milton M, Mansour S (2025). "CD1-restricted T cells: are unconventional allies the key to future TB vaccines?". Frontiers in Immunology. 16 1629466. doi:10.3389/fimmu.2025.1629466. PMC 12286804. PMID 40709176.
16. Harris MC, Gary HE, Cooper SK, Ackart DF, DiLisio JE, Basaraba RJ, Cheng TY, van Rhijn I, Branch Moody D, Podell BK (10 December 2024). "Establishment of CD1b-restricted immunity to lipid antigens in the pulmonary response to Mycobacterium tuberculosis infection". Infection and Immunity. 92 (12): e0038024. doi:10.1128/iai.00380-24. PMC 11629625. PMID 39494875.
17. Van Rhijn I, Koets AP, Im JS, Piebes D, Reddington F, Besra GS, et al. (April 2006). "The bovine CD1 family contains group 1 CD1 proteins, but no functional CD1d". Journal of Immunology. 176 (8): 4888–4893. doi:10.4049/jimmunol.176.8.4888. PMID 16585584.
18. Wang J, Guillaume J, Pauwels N, Van Calenbergh S, Van Rhijn I, Zajonc DM (2012). "Crystal structures of bovine CD1d reveal altered αGalCer presentation and a restricted A' pocket unable to bind long-chain glycolipids". PLOS ONE. 7 (10) e47989. Bibcode:2012PLoSO...747989W. doi:10.1371/journal.pone.0047989. PMC 3479135. PMID 23110152.
19. Waters WR, Palmer MV, Thacker TC, Davis WC, Sreevatsan S, Coussens P, Meade KG, Hope JC, Estes DM (2011). "Tuberculosis immunity: opportunities from studies with cattle". Clinical & Developmental Immunology. 2011 768542. doi:10.1155/2011/768542. PMC 3004413. PMID 21197095.

External links

• CD1+Antigen at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
• Mouse CD Antigen Chart
• Human CD Antigen Chart
• The Human Protein Atlas - Additional Info
  • CD1a
  • CD1b
  • CD1c
  • CD1d
  • CD1e