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Protein

C-type lectin domain family 4 member D

Gene

CLEC4D

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Functions as an endocytic receptor. May be involved in antigen uptake at the site of infection, either for clearance of the antigen, or for processing and further presentation to T cells.1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Adaptive immunity, Immunity, Innate immunity

Keywords - Ligandi

Lectin

Enzyme and pathway databases

ReactomeiR-HSA-5621480. Dectin-2 family.

Names & Taxonomyi

Protein namesi
Recommended name:
C-type lectin domain family 4 member D
Alternative name(s):
C-type lectin superfamily member 8
C-type lectin-like receptor 6
Short name:
CLEC-6
Gene namesi
Name:CLEC4D
Synonyms:CLECSF8, MCL
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

HGNCiHGNC:14554. CLEC4D.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 1717CytoplasmicSequence analysisAdd
BLAST
Transmembranei18 – 3821Helical; Signal-anchor for type II membrane proteinSequence analysisAdd
BLAST
Topological domaini39 – 215177ExtracellularSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134916109.

Polymorphism and mutation databases

BioMutaiCLEC4D.
DMDMi73916933.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 215215C-type lectin domain family 4 member DPRO_0000046616Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi45 – 451N-linked (GlcNAc...)Sequence analysis
Disulfide bondi84 ↔ 95PROSITE-ProRule annotation
Glycosylationi102 – 1021N-linked (GlcNAc...)Sequence analysis
Glycosylationi111 – 1111N-linked (GlcNAc...)Sequence analysis
Disulfide bondi112 ↔ 207PROSITE-ProRule annotation
Disulfide bondi182 ↔ 199PROSITE-ProRule annotation

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiQ8WXI8.
PRIDEiQ8WXI8.

PTM databases

PhosphoSiteiQ8WXI8.

Expressioni

Tissue specificityi

Expressed weakly in peripheral blood leukocytes, bone marrow and spleen. Expression is confined mostly in monocytes and macrophage and seems to be up-regulated by IL-6, IL-10, TNF-alpha and IFN-gamma.1 Publication

Inductioni

By autocrine inflammatory stimuli.1 Publication

Gene expression databases

BgeeiQ8WXI8.
CleanExiHS_CLEC4D.
ExpressionAtlasiQ8WXI8. baseline and differential.
GenevisibleiQ8WXI8. HS.

Organism-specific databases

HPAiHPA004906.

Interactioni

Protein-protein interaction databases

STRINGi9606.ENSP00000299665.

Structurei

Secondary structure

1
215
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi63 – 675Combined sources
Beta strandi81 – 855Combined sources
Beta strandi88 – 914Combined sources
Beta strandi94 – 10310Combined sources
Helixi105 – 1139Combined sources
Turni114 – 1163Combined sources
Beta strandi118 – 1203Combined sources
Helixi125 – 1328Combined sources
Beta strandi141 – 1477Combined sources
Beta strandi150 – 1523Combined sources
Beta strandi181 – 1877Combined sources
Beta strandi189 – 19810Combined sources
Beta strandi203 – 2108Combined sources
Beta strandi212 – 2143Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2LS8NMR-A84-215[»]
3WHDX-ray2.29A/C61-215[»]
ProteinModelPortaliQ8WXI8.
SMRiQ8WXI8. Positions 84-215.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini91 – 208118C-type lectinPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 C-type lectin domain.PROSITE-ProRule annotation

Keywords - Domaini

Signal-anchor, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IS3N. Eukaryota.
ENOG410XYR0. LUCA.
GeneTreeiENSGT00760000118924.
HOGENOMiHOG000059556.
HOVERGENiHBG050992.
InParanoidiQ8WXI8.
KOiK10058.
OMAiRAFQSNC.
PhylomeDBiQ8WXI8.
TreeFamiTF333341.

Family and domain databases

Gene3Di3.10.100.10. 1 hit.
InterProiIPR001304. C-type_lectin.
IPR016186. C-type_lectin-like.
IPR016187. C-type_lectin_fold.
[Graphical view]
PfamiPF00059. Lectin_C. 1 hit.
[Graphical view]
SMARTiSM00034. CLECT. 1 hit.
[Graphical view]
SUPFAMiSSF56436. SSF56436. 1 hit.
PROSITEiPS50041. C_TYPE_LECTIN_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8WXI8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGLEKPQSKL EGGMHPQLIP SVIAVVFILL LSVCFIASCL VTHHNFSRCK
60 70 80 90 100
RGTGVHKLEH HAKLKCIKEK SELKSAEGST WNCCPIDWRA FQSNCYFPLT
110 120 130 140 150
DNKTWAESER NCSGMGAHLM TISTEAEQNF IIQFLDRRLS YFLGLRDENA
160 170 180 190 200
KGQWRWVDQT PFNPRRVFWH KNEPDNSQGE NCVVLVYNQD KWAWNDVPCN
210
FEASRICKIP GTTLN
Length:215
Mass (Da):24,704
Last modified:May 10, 2005 - v2
Checksum:i938B68661AAC175B
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti32 – 321S → G.2 Publications
Corresponds to variant rs4304840 [ dbSNP | Ensembl ].
VAR_021261

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY297446 mRNA. Translation: AAQ63173.1.
AY486482 mRNA. Translation: AAS59161.1.
AY486483 mRNA. Translation: AAS59162.1.
AF411850 mRNA. Translation: AAL37713.1.
AY115592 mRNA. Translation: AAM75389.1.
BC032313 mRNA. Translation: AAH32313.1.
CCDSiCCDS8593.1.
RefSeqiNP_525126.2. NM_080387.4.
XP_011518934.1. XM_011520632.1.
UniGeneiHs.351811.

Genome annotation databases

EnsembliENST00000299665; ENSP00000299665; ENSG00000166527.
GeneIDi338339.
KEGGihsa:338339.
UCSCiuc001qun.4. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Web resourcesi

Functional Glycomics Gateway - Glycan Binding

MCL

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY297446 mRNA. Translation: AAQ63173.1.
AY486482 mRNA. Translation: AAS59161.1.
AY486483 mRNA. Translation: AAS59162.1.
AF411850 mRNA. Translation: AAL37713.1.
AY115592 mRNA. Translation: AAM75389.1.
BC032313 mRNA. Translation: AAH32313.1.
CCDSiCCDS8593.1.
RefSeqiNP_525126.2. NM_080387.4.
XP_011518934.1. XM_011520632.1.
UniGeneiHs.351811.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2LS8NMR-A84-215[»]
3WHDX-ray2.29A/C61-215[»]
ProteinModelPortaliQ8WXI8.
SMRiQ8WXI8. Positions 84-215.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9606.ENSP00000299665.

PTM databases

PhosphoSiteiQ8WXI8.

Polymorphism and mutation databases

BioMutaiCLEC4D.
DMDMi73916933.

Proteomic databases

PaxDbiQ8WXI8.
PRIDEiQ8WXI8.

Protocols and materials databases

DNASUi338339.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000299665; ENSP00000299665; ENSG00000166527.
GeneIDi338339.
KEGGihsa:338339.
UCSCiuc001qun.4. human.

Organism-specific databases

CTDi338339.
GeneCardsiCLEC4D.
HGNCiHGNC:14554. CLEC4D.
HPAiHPA004906.
MIMi609964. gene.
neXtProtiNX_Q8WXI8.
PharmGKBiPA134916109.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IS3N. Eukaryota.
ENOG410XYR0. LUCA.
GeneTreeiENSGT00760000118924.
HOGENOMiHOG000059556.
HOVERGENiHBG050992.
InParanoidiQ8WXI8.
KOiK10058.
OMAiRAFQSNC.
PhylomeDBiQ8WXI8.
TreeFamiTF333341.

Enzyme and pathway databases

ReactomeiR-HSA-5621480. Dectin-2 family.

Miscellaneous databases

GenomeRNAii338339.
PROiQ8WXI8.
SOURCEiSearch...

Gene expression databases

BgeeiQ8WXI8.
CleanExiHS_CLEC4D.
ExpressionAtlasiQ8WXI8. baseline and differential.
GenevisibleiQ8WXI8. HS.

Family and domain databases

Gene3Di3.10.100.10. 1 hit.
InterProiIPR001304. C-type_lectin.
IPR016186. C-type_lectin-like.
IPR016187. C-type_lectin_fold.
[Graphical view]
PfamiPF00059. Lectin_C. 1 hit.
[Graphical view]
SMARTiSM00034. CLECT. 1 hit.
[Graphical view]
SUPFAMiSSF56436. SSF56436. 1 hit.
PROSITEiPS50041. C_TYPE_LECTIN_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The human C-type lectin CLECSF8 is a novel monocyte/macrophage endocytic receptor."
    Arce I., Martinez-Munoz L., Roda-Navarro P., Fernandez-Ruiz E.
    Eur. J. Immunol. 34:210-220(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, INDUCTION.
  2. "Identification of lectin-like receptors expressed by antigen presenting cells and neutrophils and their mapping to a novel gene complex."
    Flornes L.M., Bryceson Y.T., Spurkland A., Lorentzen J.C., Dissen E., Fossum S.
    Immunogenetics 56:506-517(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Macrophage.
  3. "C-type lectin-like receptor."
    Colonna M.
    Submitted (JUL-2001) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT GLY-32.
  4. Ma J., Liew C.-C.
    Submitted (MAY-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT GLY-32.
    Tissue: Peripheral blood.
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Blood.

Entry informationi

Entry nameiCLC4D_HUMAN
AccessioniPrimary (citable) accession number: Q8WXI8
Secondary accession number(s): Q8N5J5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 15, 2005
Last sequence update: May 10, 2005
Last modified: June 8, 2016
This is version 112 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 12
    Human chromosome 12: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.