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Protein

C-type lectin domain family 4 member D

Gene

CLEC4D

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

Keywordsi

Biological processAdaptive immunity, Immunity, Innate immunity
LigandLectin

Enzyme and pathway databases

ReactomeiR-HSA-5621480 Dectin-2 family
R-HSA-6798695 Neutrophil degranulation

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

EuPathDBiHostDB:ENSG00000166527.7
HGNCiHGNC:14554 CLEC4D
MIMi609964 gene
neXtProtiNX_Q8WXI8

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 17CytoplasmicSequence analysisAdd BLAST17
Transmembranei18 – 38Helical; Signal-anchor for type II membrane proteinSequence analysisAdd BLAST21
Topological domaini39 – 215ExtracellularSequence analysisAdd BLAST177

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Organism-specific databases

DisGeNETi338339
OpenTargetsiENSG00000166527
PharmGKBiPA134916109

Polymorphism and mutation databases

BioMutaiCLEC4D
DMDMi73916933

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000466161 – 215C-type lectin domain family 4 member DAdd BLAST215

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi45N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi84 ↔ 95PROSITE-ProRule annotation
Glycosylationi102N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi111N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi112 ↔ 207PROSITE-ProRule annotation
Disulfide bondi182 ↔ 199PROSITE-ProRule annotation

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiQ8WXI8
PeptideAtlasiQ8WXI8
PRIDEiQ8WXI8

PTM databases

iPTMnetiQ8WXI8
PhosphoSitePlusiQ8WXI8

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

BgeeiENSG00000166527
CleanExiHS_CLEC4D
ExpressionAtlasiQ8WXI8 baseline and differential
GenevisibleiQ8WXI8 HS

Organism-specific databases

HPAiHPA004906

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
ACTN2P356093EBI-12703404,EBI-77797

GO - Molecular functioni

Protein-protein interaction databases

IntActiQ8WXI8, 1 interactor
STRINGi9606.ENSP00000299665

Structurei

Secondary structure

1215
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi63 – 67Combined sources5
Beta strandi81 – 85Combined sources5
Beta strandi88 – 91Combined sources4
Beta strandi94 – 103Combined sources10
Helixi105 – 113Combined sources9
Turni114 – 116Combined sources3
Beta strandi118 – 120Combined sources3
Helixi125 – 132Combined sources8
Beta strandi141 – 147Combined sources7
Beta strandi150 – 152Combined sources3
Beta strandi181 – 187Combined sources7
Beta strandi189 – 198Combined sources10
Beta strandi203 – 210Combined sources8
Beta strandi212 – 214Combined sources3

3D structure databases

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

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini91 – 208C-type lectinPROSITE-ProRule annotationAdd BLAST118

Keywords - Domaini

Signal-anchor, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IS3N Eukaryota
ENOG410XYR0 LUCA
GeneTreeiENSGT00910000144068
HOGENOMiHOG000059556
HOVERGENiHBG050992
InParanoidiQ8WXI8
KOiK10058
OMAiRAFQSNC
OrthoDBiEOG091G0K6R
PhylomeDBiQ8WXI8
TreeFamiTF333341

Family and domain databases

CDDicd03590 CLECT_DC-SIGN_like, 1 hit
Gene3Di3.10.100.10, 1 hit
InterProiView protein in InterPro
IPR001304 C-type_lectin-like
IPR016186 C-type_lectin-like/link_sf
IPR033989 CD209-like_CTLD
IPR016187 CTDL_fold
PfamiView protein in Pfam
PF00059 Lectin_C, 1 hit
SMARTiView protein in SMART
SM00034 CLECT, 1 hit
SUPFAMiSSF56436 SSF56436, 1 hit
PROSITEiView protein in PROSITE
PS50041 C_TYPE_LECTIN_2, 1 hit

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)DescriptionActionsGraphical viewLength
Natural variantiVAR_02126132S → G2 PublicationsCorresponds to variant dbSNP:rs4304840EnsemblClinVar.1

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_011520632.2
UniGeneiHs.351811

Genome annotation databases

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

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Entry informationi

Entry nameiCLC4D_HUMAN
AccessioniPrimary (citable) accession number: Q8WXI8
Secondary accession number(s): Q8N5J5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 15, 2005
Last sequence update: May 10, 2005
Last modified: February 28, 2018
This is version 124 of the entry and version 2 of the sequence. See 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

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