ID CLM1_MOUSE Reviewed; 337 AA.
AC Q6SJQ7; A2A6Z1; A2A6Z3; Q6PEU7; Q8K4V9;
DT 25-JUL-2006, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 27-MAR-2024, entry version 132.
DE RecName: Full=CMRF35-like molecule 1;
DE Short=CLM-1;
DE AltName: Full=CD300 antigen-like family member F;
DE AltName: Full=Leukocyte mono-Ig-like receptor 3;
DE AltName: Full=Myeloid-associated immunoglobulin-like receptor 5;
DE Short=MAIR-5;
DE Short=MAIR-V;
DE AltName: CD_antigen=CD300f;
DE Flags: Precursor;
GN Name=Cd300lf; Synonyms=Clm1, Lmir3;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, TISSUE SPECIFICITY, AND
RP INTERACTION WITH PTPN6.
RC STRAIN=C57BL/6J;
RX PubMed=14662855; DOI=10.4049/jimmunol.171.12.6541;
RA Chung D.-H., Humphrey M.B., Nakamura M.C., Ginzinger D.G., Seaman W.E.,
RA Daws M.R.;
RT "CMRF-35-like molecule-1, a novel mouse myeloid receptor, can inhibit
RT osteoclast formation.";
RL J. Immunol. 171:6541-6548(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), AND FUNCTION.
RC STRAIN=CBA/J;
RX PubMed=17438331; DOI=10.1074/jbc.m701100200;
RA Izawa K., Kitaura J., Yamanishi Y., Matsuoka T., Oki T., Shibata F.,
RA Kumagai H., Nakajima H., Maeda-Yamamoto M., Hauchins J.P., Tybulewicz V.L.,
RA Takai T., Kitamura T.;
RT "Functional analysis of activating receptor LMIR4 as a counterpart of
RT inhibitory receptor LMIR3.";
RL J. Biol. Chem. 282:17997-18008(2007).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3).
RA Zhang W., Wan T., Li N., Chen T., Cao X.;
RL Submitted (APR-2000) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C57BL/6J;
RX PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA Eichler E.E., Ponting C.P.;
RT "Lineage-specific biology revealed by a finished genome assembly of the
RT mouse.";
RL PLoS Biol. 7:E1000112-E1000112(2009).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=129; TISSUE=Mammary gland;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [6]
RP FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=18097021; DOI=10.4049/jimmunol.180.1.207;
RA Can I., Tahara-Hanaoka S., Hitomi K., Nakano T., Nakahashi-Oda C.,
RA Kurita N., Honda S., Shibuya K., Shibuya A.;
RT "Caspase-independent cell death by CD300LF (MAIR-V), an inhibitory
RT immunoglobulin-like receptor on myeloid cells.";
RL J. Immunol. 180:207-213(2008).
RN [7]
RP FUNCTION, AND PHOSPHATIDYLSERINE-BINDING.
RX PubMed=21865548; DOI=10.4049/jimmunol.1101549;
RA Choi S.C., Simhadri V.R., Tian L., Gil-Krzewska A., Krzewski K.,
RA Borrego F., Coligan J.E.;
RT "Cutting edge: mouse CD300f (CMRF-35-like molecule-1) recognizes outer
RT membrane-exposed phosphatidylserine and can promote phagocytosis.";
RL J. Immunol. 187:3483-3487(2011).
RN [8]
RP FUNCTION, CERAMIDE-BINDING, AND PHOSPHORYLATION.
RX PubMed=23123064; DOI=10.1016/j.immuni.2012.08.018;
RA Izawa K., Yamanishi Y., Maehara A., Takahashi M., Isobe M., Ito S.,
RA Kaitani A., Matsukawa T., Matsuoka T., Nakahara F., Oki T., Kiyonari H.,
RA Abe T., Okumura K., Kitamura T., Kitaura J.;
RT "The receptor LMIR3 negatively regulates mast cell activation and allergic
RT responses by binding to extracellular ceramide.";
RL Immunity 37:827-839(2012).
RN [9]
RP FUNCTION, INDUCTION, TISSUE SPECIFICITY, AND INTERACTION WITH IL4R.
RX PubMed=26124135; DOI=10.1073/pnas.1507625112;
RA Moshkovits I., Karo-Atar D., Itan M., Reichman H., Rozenberg P.,
RA Morgenstern-Ben-Baruch N., Shik D., Ejarque-Ortiz A., Hershko A.Y.,
RA Tian L., Coligan J.E., Sayos J., Munitz A.;
RT "CD300f associates with IL-4 receptor alpha and amplifies IL-4-induced
RT immune cell responses.";
RL Proc. Natl. Acad. Sci. U.S.A. 112:8708-8713(2015).
RN [10]
RP FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=26768664; DOI=10.1038/cdd.2015.161;
RA Tian L., Choi S.C., Lee H.N., Murakami Y., Qi C.F., Sengottuvelu M.,
RA Voss O., Krzewski K., Coligan J.E.;
RT "Enhanced efferocytosis by dendritic cells underlies memory T-cell
RT expansion and susceptibility to autoimmune disease in CD300f-deficient
RT mice.";
RL Cell Death Differ. 23:1086-1096(2016).
RN [11]
RP FUNCTION (MICROBIAL INFECTION), AND MNV-BINDING REGION.
RX PubMed=27681626; DOI=10.1073/pnas.1605575113;
RA Haga K., Fujimoto A., Takai-Todaka R., Miki M., Doan Y.H., Murakami K.,
RA Yokoyama M., Murata K., Nakanishi A., Katayama K.;
RT "Functional receptor molecules CD300lf and CD300ld within the CD300 family
RT enable murine noroviruses to infect cells.";
RL Proc. Natl. Acad. Sci. U.S.A. 113:E6248-E6255(2016).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 20-138 (ISOFORM 2), AND DISULFIDE
RP BONDS.
RG Midwest center for structural genomics (MCSG);
RT "Crystal structure of the mouse CLM-1 ectodomain.";
RL Submitted (MAY-2005) to the PDB data bank.
RN [13]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 20-138 (ISOFORM 2), FUNCTION
RP (MICROBIAL INFECTION), AND DISULFIDE BONDS.
RX PubMed=27540007; DOI=10.1126/science.aaf1220;
RA Orchard R.C., Wilen C.B., Doench J.G., Baldridge M.T., McCune B.T.,
RA Lee Y.C., Lee S., Pruett-Miller S.M., Nelson C.A., Fremont D.H.,
RA Virgin H.W.;
RT "Discovery of a proteinaceous cellular receptor for a norovirus.";
RL Science 353:933-936(2016).
CC -!- FUNCTION: Acts as an inhibitory receptor for myeloid cells and mast
CC cells (PubMed:17438331). Positively regulates the phagocytosis of
CC apoptotic cells (efferocytosis) via phosphatidylserine (PS)
CC recognition; recognizes and binds PS as a ligand which is expressed on
CC the surface of apoptotic cells (PubMed:21865548). Plays an important
CC role in the maintenance of immune homeostasis, by promoting macrophage-
CC mediated efferocytosis and by inhibiting dendritic cell-mediated
CC efferocytosis (PubMed:26768664). Negatively regulates Fc epsilon
CC receptor-dependent mast cell activation and allergic responses via
CC binding to ceramide which acts as a ligand (PubMed:23123064). May act
CC as a coreceptor for interleukin 4 (IL-4). Associates with and regulates
CC IL-4 receptor alpha-mediated responses by augmenting IL-4- and IL-13-
CC induced signaling (PubMed:26124135). Negatively regulates the Toll-like
CC receptor (TLR) signaling mediated by MYD88 and TRIF through activation
CC of PTPN6/SHP-1 and PTPN11/SHP-2 (By similarity). Inhibits osteoclast
CC formation (PubMed:14662855). Induces macrophage cell death upon
CC engagement (PubMed:18097021). {ECO:0000250|UniProtKB:Q8TDQ1,
CC ECO:0000269|PubMed:14662855, ECO:0000269|PubMed:17438331,
CC ECO:0000269|PubMed:18097021, ECO:0000269|PubMed:21865548,
CC ECO:0000269|PubMed:23123064, ECO:0000269|PubMed:26124135,
CC ECO:0000269|PubMed:26768664}.
CC -!- FUNCTION: (Microbial infection) Acts as a functional murine norovirus
CC (MNV) receptor that mediates binding to the cell surface and is both
CC necessary and sufficient for viral entry and replication. Primary
CC determinant of MNV species tropism and is sufficient to render cells
CC permissive to infection by MNV. Can render nonmurine mammalian cells
CC susceptible to MNV infection (PubMed:27681626, PubMed:27540007).
CC {ECO:0000269|PubMed:27540007, ECO:0000269|PubMed:27681626}.
CC -!- SUBUNIT: Interacts with PTPN6/SHP-1 in a tyrosine phosphorylation
CC dependent manner (PubMed:14662855). Interacts with IL4R
CC (PubMed:26124135). {ECO:0000269|PubMed:14662855,
CC ECO:0000269|PubMed:26124135}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000305}; Single-pass type I
CC membrane protein {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q6SJQ7-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q6SJQ7-2; Sequence=VSP_020066;
CC Name=3;
CC IsoId=Q6SJQ7-3; Sequence=VSP_020067;
CC -!- TISSUE SPECIFICITY: Expressed in myeloid cells. Present on the surface
CC of macrophages (at protein level). Highly expressed by alveolar,
CC splenic macrophages and bone marrow-derived dendritic cells. Expression
CC is increased following aeroallergen challenge in macrophages, mast
CC cells, and eosinophils. {ECO:0000269|PubMed:14662855,
CC ECO:0000269|PubMed:18097021, ECO:0000269|PubMed:26124135,
CC ECO:0000269|PubMed:26768664}.
CC -!- INDUCTION: Up-regulated by interleukin-4/IL-4.
CC {ECO:0000269|PubMed:26124135}.
CC -!- PTM: Phosphorylated on tyrosine. {ECO:0000269|PubMed:23123064}.
CC -!- SIMILARITY: Belongs to the CD300 family. {ECO:0000305}.
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DR EMBL; AY457047; AAR27938.1; -; mRNA.
DR EMBL; AB292061; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; AF251703; AAM19096.1; -; mRNA.
DR EMBL; AL606487; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC057864; AAH57864.1; -; mRNA.
DR CCDS; CCDS25619.1; -. [Q6SJQ7-2]
DR CCDS; CCDS48980.1; -. [Q6SJQ7-1]
DR RefSeq; NP_001162624.1; NM_001169153.1. [Q6SJQ7-1]
DR RefSeq; NP_663609.2; NM_145634.3. [Q6SJQ7-2]
DR RefSeq; XP_017170042.1; XM_017314553.1.
DR PDB; 1ZOX; X-ray; 2.10 A; A=20-128.
DR PDB; 5FFL; X-ray; 1.60 A; A=20-128.
DR PDB; 5OR7; X-ray; 2.05 A; C=1-337.
DR PDB; 6C6Q; X-ray; 2.00 A; D/F=20-128.
DR PDB; 6C74; X-ray; 1.36 A; A=20-128.
DR PDB; 6E47; X-ray; 1.95 A; F/G=20-128.
DR PDB; 6E48; X-ray; 1.80 A; F/G=20-128.
DR PDB; 6H6L; X-ray; 2.50 A; E/F/G/H=20-128.
DR PDB; 6H6M; X-ray; 2.38 A; E/F=20-128.
DR PDBsum; 1ZOX; -.
DR PDBsum; 5FFL; -.
DR PDBsum; 5OR7; -.
DR PDBsum; 6C6Q; -.
DR PDBsum; 6C74; -.
DR PDBsum; 6E47; -.
DR PDBsum; 6E48; -.
DR PDBsum; 6H6L; -.
DR PDBsum; 6H6M; -.
DR AlphaFoldDB; Q6SJQ7; -.
DR SMR; Q6SJQ7; -.
DR BioGRID; 232945; 1.
DR IntAct; Q6SJQ7; 1.
DR STRING; 10090.ENSMUSP00000102171; -.
DR iPTMnet; Q6SJQ7; -.
DR PhosphoSitePlus; Q6SJQ7; -.
DR MaxQB; Q6SJQ7; -.
DR PaxDb; 10090-ENSMUSP00000102171; -.
DR ProteomicsDB; 281688; -. [Q6SJQ7-1]
DR ProteomicsDB; 281689; -. [Q6SJQ7-2]
DR ProteomicsDB; 281690; -. [Q6SJQ7-3]
DR ABCD; Q6SJQ7; 1 sequenced antibody.
DR DNASU; 246746; -.
DR Ensembl; ENSMUST00000051264.14; ENSMUSP00000053983.8; ENSMUSG00000047798.16. [Q6SJQ7-2]
DR Ensembl; ENSMUST00000106561.8; ENSMUSP00000102171.2; ENSMUSG00000047798.16. [Q6SJQ7-1]
DR GeneID; 246746; -.
DR KEGG; mmu:246746; -.
DR UCSC; uc007mgn.2; mouse. [Q6SJQ7-1]
DR UCSC; uc011yhh.1; mouse. [Q6SJQ7-2]
DR AGR; MGI:2442359; -.
DR CTD; 146722; -.
DR MGI; MGI:2442359; Cd300lf.
DR VEuPathDB; HostDB:ENSMUSG00000047798; -.
DR eggNOG; ENOG502S7MA; Eukaryota.
DR GeneTree; ENSGT00940000154332; -.
DR InParanoid; Q6SJQ7; -.
DR OMA; HEESMEY; -.
DR OrthoDB; 4204212at2759; -.
DR PhylomeDB; Q6SJQ7; -.
DR TreeFam; TF334441; -.
DR BioGRID-ORCS; 246746; 5 hits in 78 CRISPR screens.
DR ChiTaRS; Cd300lf; mouse.
DR EvolutionaryTrace; Q6SJQ7; -.
DR PRO; PR:Q6SJQ7; -.
DR Proteomes; UP000000589; Chromosome 11.
DR RNAct; Q6SJQ7; Protein.
DR Bgee; ENSMUSG00000047798; Expressed in granulocyte and 117 other cell types or tissues.
DR ExpressionAtlas; Q6SJQ7; baseline and differential.
DR Genevisible; Q6SJQ7; MM.
DR GO; GO:0005886; C:plasma membrane; IBA:GO_Central.
DR GO; GO:0097001; F:ceramide binding; IDA:UniProtKB.
DR GO; GO:0042802; F:identical protein binding; ISO:MGI.
DR GO; GO:0005136; F:interleukin-4 receptor binding; IDA:UniProtKB.
DR GO; GO:0001786; F:phosphatidylserine binding; IDA:UniProtKB.
DR GO; GO:0001618; F:virus receptor activity; IMP:UniProtKB.
DR GO; GO:0035772; P:interleukin-13-mediated signaling pathway; IMP:UniProtKB.
DR GO; GO:2000426; P:negative regulation of apoptotic cell clearance; IMP:UniProtKB.
DR GO; GO:0033004; P:negative regulation of mast cell activation; IMP:UniProtKB.
DR GO; GO:0034125; P:negative regulation of MyD88-dependent toll-like receptor signaling pathway; ISS:UniProtKB.
DR GO; GO:0030316; P:osteoclast differentiation; IDA:MGI.
DR GO; GO:2000427; P:positive regulation of apoptotic cell clearance; IDA:UniProtKB.
DR GO; GO:1902216; P:positive regulation of interleukin-4-mediated signaling pathway; IMP:UniProtKB.
DR GO; GO:0035666; P:TRIF-dependent toll-like receptor signaling pathway; ISS:UniProtKB.
DR CDD; cd05716; IgV_pIgR_like; 1.
DR DisProt; DP02478; -.
DR Gene3D; 2.60.40.10; Immunoglobulins; 1.
DR InterPro; IPR036179; Ig-like_dom_sf.
DR InterPro; IPR013783; Ig-like_fold.
DR InterPro; IPR003599; Ig_sub.
DR InterPro; IPR013106; Ig_V-set.
DR PANTHER; PTHR11860:SF83; CMRF35-LIKE MOLECULE 1; 1.
DR PANTHER; PTHR11860; POLYMERIC-IMMUNOGLOBULIN RECEPTOR; 1.
DR Pfam; PF15330; SIT; 1.
DR Pfam; PF07686; V-set; 1.
DR SMART; SM00409; IG; 1.
DR SUPFAM; SSF48726; Immunoglobulin; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Cell membrane; Disulfide bond;
KW Host cell receptor for virus entry; Immunity; Immunoglobulin domain;
KW Lipid-binding; Membrane; Phosphoprotein; Receptor; Reference proteome;
KW Signal; Transmembrane; Transmembrane helix.
FT SIGNAL 1..19
FT /evidence="ECO:0000255"
FT CHAIN 20..337
FT /note="CMRF35-like molecule 1"
FT /id="PRO_0000247826"
FT TOPO_DOM 20..193
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 194..214
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 215..337
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT DOMAIN 20..125
FT /note="Ig-like V-type"
FT REGION 39..45
FT /note="Plays an important role in murine norovirus (MNV)
FT binding"
FT /evidence="ECO:0000269|PubMed:27681626"
FT REGION 248..270
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 318..337
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 248..264
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 241
FT /note="Phosphatase-binding"
FT /evidence="ECO:0000250"
FT DISULFID 41..109
FT /evidence="ECO:0000269|PubMed:27540007, ECO:0000269|Ref.12"
FT DISULFID 55..63
FT /evidence="ECO:0000269|PubMed:27540007, ECO:0000269|Ref.12"
FT VAR_SEQ 129..135
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_020066"
FT VAR_SEQ 212..265
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|Ref.3"
FT /id="VSP_020067"
FT CONFLICT 20
FT /note="E -> Q (in Ref. 2; AB292061)"
FT /evidence="ECO:0000305"
FT CONFLICT 37
FT /note="L -> V (in Ref. 3; AAM19096)"
FT /evidence="ECO:0000305"
FT CONFLICT 56..65
FT /note="QGVPQRSCKT -> RGAYWKSCEI (in Ref. 2; AB292061)"
FT /evidence="ECO:0000305"
FT CONFLICT 71
FT /note="A -> K (in Ref. 2; AB292061)"
FT /evidence="ECO:0000305"
FT CONFLICT 114..116
FT /note="GGL -> AGP (in Ref. 2; AB292061)"
FT /evidence="ECO:0000305"
FT CONFLICT 123
FT /note="T -> A (in Ref. 2; AB292061)"
FT /evidence="ECO:0000305"
FT CONFLICT 166
FT /note="S -> G (in Ref. 2; AB292061)"
FT /evidence="ECO:0000305"
FT CONFLICT 337
FT /note="P -> H (in Ref. 2; AB292061)"
FT /evidence="ECO:0000305"
FT STRAND 22..24
FT /evidence="ECO:0007829|PDB:6C74"
FT STRAND 27..32
FT /evidence="ECO:0007829|PDB:6C74"
FT STRAND 37..43
FT /evidence="ECO:0007829|PDB:6C74"
FT HELIX 45..47
FT /evidence="ECO:0007829|PDB:6C74"
FT STRAND 52..59
FT /evidence="ECO:0007829|PDB:6C74"
FT HELIX 60..62
FT /evidence="ECO:0007829|PDB:6C74"
FT STRAND 64..68
FT /evidence="ECO:0007829|PDB:6C74"
FT STRAND 71..73
FT /evidence="ECO:0007829|PDB:6C74"
FT STRAND 76..78
FT /evidence="ECO:0007829|PDB:6C74"
FT STRAND 81..86
FT /evidence="ECO:0007829|PDB:6C74"
FT TURN 87..90
FT /evidence="ECO:0007829|PDB:6C74"
FT STRAND 91..96
FT /evidence="ECO:0007829|PDB:6C74"
FT HELIX 101..103
FT /evidence="ECO:0007829|PDB:6C74"
FT STRAND 105..111
FT /evidence="ECO:0007829|PDB:6C74"
FT STRAND 114..116
FT /evidence="ECO:0007829|PDB:6C74"
FT STRAND 119..127
FT /evidence="ECO:0007829|PDB:6C74"
SQ SEQUENCE 337 AA; 36715 MW; 0C6EB6E666223CD5 CRC64;
MHLSLLVPFL FWITGCCTAE DPVTGPEEVS GQEQGSLTVQ CRYTSGWKDY KKYWCQGVPQ
RSCKTLVETD ASEQLVKKNR VSIRDNQRDF IFTVTMEDLR MSDAGIYWCG ITKGGLDPMF
KVTVNIGPAI QVPITVPTMP PITSTTTIFT VTTTVKETSM FPTLTSYYSD NGHGGGDSGG
GEDGVGDGFL DLSVLLPVIS AVLLLLLLVA SLFAWRMVRR QKKAAGPPSE QAQSLEGDLC
YADLSLKQPR TSPGSSWKKG SSMSSSGKDH QEEVEYVTMA PFPREEVSYA ALTLAGLGQE
PTYGNTGCPI THVPRTGLEE ETTEYSSIRR PLPAAMP
//
