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Protein

C-type lectin domain family 2 member D

Gene

CLEC2D

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

Functioni

Receptor for KLRB1 that protects target cells against natural killer cell-mediated lysis. Inhibits osteoclast formation. Inhibits bone resorption. Modulates the release of interferon-gamma. Binds high molecular weight sulfated glycosaminoglycans.3 Publications

GO - Molecular functioni

  • carbohydrate binding Source: UniProtKB-KW
  • transmembrane signaling receptor activity Source: ProtInc

GO - Biological processi

  • cell surface receptor signaling pathway Source: ProtInc
  • regulation of immune response Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Receptor

Keywords - Ligandi

Lectin

Enzyme and pathway databases

ReactomeiR-HSA-198933. Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell.

Names & Taxonomyi

Protein namesi
Recommended name:
C-type lectin domain family 2 member D
Alternative name(s):
Lectin-like NK cell receptor
Lectin-like transcript 1
Short name:
LLT-1
Osteoclast inhibitory lectin
Gene namesi
Name:CLEC2D
Synonyms:CLAX, LLT1, OCIL
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

HGNCiHGNC:14351. CLEC2D.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 38CytoplasmicSequence analysisAdd BLAST38
Transmembranei39 – 59Helical; Signal-anchor for type II membrane proteinSequence analysisAdd BLAST21
Topological domaini60 – 191ExtracellularSequence analysisAdd BLAST132

GO - Cellular componenti

  • cell surface Source: UniProtKB
  • endoplasmic reticulum Source: UniProtKB
  • integral component of plasma membrane Source: ProtInc
  • membrane Source: ProtInc
  • plasma membrane Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Endoplasmic reticulum, Membrane

Pathology & Biotechi

Organism-specific databases

DisGeNETi29121.
OpenTargetsiENSG00000069493.
PharmGKBiPA142672100.

Polymorphism and mutation databases

BioMutaiCLEC2D.
DMDMi74753331.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003152851 – 191C-type lectin domain family 2 member DAdd BLAST191

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi75 ↔ 86PROSITE-ProRule annotation
Glycosylationi95N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi103 ↔ 184PROSITE-ProRule annotation

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PeptideAtlasiQ9UHP7.
PRIDEiQ9UHP7.

PTM databases

iPTMnetiQ9UHP7.
PhosphoSitePlusiQ9UHP7.

Expressioni

Tissue specificityi

Detected in peripheral blood leukocytes, osteoblasts, lymph node, thymus and spleen. Isoform 1, isoform 2 and isoform 4 are expressed in T- and B-lymphocytes, and at lower levels in NK cells. They are also expressed in B-cell lines and LPS-matured monocyte-derived dendritic cells.2 Publications

Inductioni

Up-regulated by IL1A/interleukin-1 alpha and prostaglandin E2 in cultured osteogenic sarcoma cells.1 Publication

Gene expression databases

BgeeiENSG00000069493.
CleanExiHS_CLEC2D.
ExpressionAtlasiQ9UHP7. baseline and differential.
GenevisibleiQ9UHP7. HS.

Organism-specific databases

HPAiHPA017649.
HPA047584.

Interactioni

Subunit structurei

Homodimer or heterodimer; disulfide-linked.

Protein-protein interaction databases

BioGridi118886. 73 interactors.
IntActiQ9UHP7. 1 interactor.

Structurei

Secondary structure

1191
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi80 – 82Combined sources3
Beta strandi85 – 89Combined sources5
Helixi96 – 105Combined sources10
Helixi116 – 126Combined sources11
Beta strandi131 – 136Combined sources6
Beta strandi148 – 150Combined sources3
Beta strandi157 – 160Combined sources4
Beta strandi162 – 166Combined sources5
Beta strandi168 – 174Combined sources7
Beta strandi180 – 187Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4QKGX-ray1.95A72-191[»]
4QKHX-ray1.80A/B72-191[»]
4QKIX-ray1.80A/B72-191[»]
4QKJX-ray2.75A72-191[»]
4WCOX-ray2.46A/B/C71-191[»]
ProteinModelPortaliQ9UHP7.
SMRiQ9UHP7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini82 – 185C-type lectinPROSITE-ProRule annotationAdd BLAST104

Sequence similaritiesi

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

Keywords - Domaini

Signal-anchor, Transmembrane, Transmembrane helix

Phylogenomic databases

GeneTreeiENSGT00710000106527.
HOVERGENiHBG107718.
InParanoidiQ9UHP7.
KOiK10072.
OMAiEWTRQFP.
OrthoDBiEOG091G0JRZ.
PhylomeDBiQ9UHP7.
TreeFamiTF351467.

Family and domain databases

Gene3Di3.10.100.10. 1 hit.
InterProiIPR001304. C-type_lectin-like.
IPR016186. C-type_lectin-like/link.
IPR016187. CTDL_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]

Sequences (6)i

Sequence statusi: Complete.

This entry describes 6 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9UHP7-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MHDSNNVEKD ITPSELPANP GCLHSKEHSI KATLIWRLFF LIMFLTIIVC
60 70 80 90 100
GMVAALSAIR ANCHQEPSVC LQAACPESWI GFQRKCFYFS DDTKNWTSSQ
110 120 130 140 150
RFCDSQDADL AQVESFQELN FLLRYKGPSD HWIGLSREQG QPWKWINGTE
160 170 180 190
WTRQFPILGA GECAYLNDKG ASSARHYTER KWICSKSDIH V
Length:191
Mass (Da):21,849
Last modified:May 1, 2000 - v1
Checksum:iE71F3E21DC361F10
GO
Isoform 3 (identifier: Q9UHP7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     155-191: Missing.

Show »
Length:154
Mass (Da):17,742
Checksum:i776D60662399E38D
GO
Isoform 2 (identifier: Q9UHP7-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     155-191: FPILGAGECA...WICSKSDIHV → LVMKEDGANL...PGSRRVCLFE

Show »
Length:194
Mass (Da):22,263
Checksum:i96982E9EEA0C3410
GO
Isoform 4 (identifier: Q9UHP7-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     120-191: NFLLRYKGPS...WICSKSDIHV → VSYPGSRRVCLFE

Show »
Length:132
Mass (Da):14,969
Checksum:i28BEC8140C9D7B96
GO
Isoform 5 (identifier: Q9UHP7-6) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     21-57: Missing.

Show »
Length:154
Mass (Da):17,703
Checksum:iBF7D57B198B8A7F9
GO
Isoform 6 (identifier: Q9UHP7-7) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     21-57: Missing.
     120-132: NFLLRYKGPSDHW → VSYPGSRRVCLFE
     133-191: Missing.

Show »
Length:95
Mass (Da):10,823
Checksum:iAA71B3302B66BD3A
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_03817219N → K.1 PublicationCorresponds to variant rs16914640dbSNPEnsembl.1
Natural variantiVAR_03817323L → V.2 PublicationsCorresponds to variant rs3764022dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_03967621 – 57Missing in isoform 5 and isoform 6. 1 PublicationAdd BLAST37
Alternative sequenceiVSP_039678120 – 191NFLLR…SDIHV → VSYPGSRRVCLFE in isoform 4. 2 PublicationsAdd BLAST72
Alternative sequenceiVSP_039680120 – 132NFLLR…PSDHW → VSYPGSRRVCLFE in isoform 6. 1 PublicationAdd BLAST13
Alternative sequenceiVSP_039681133 – 191Missing in isoform 6. 1 PublicationAdd BLAST59
Alternative sequenceiVSP_039683155 – 191FPILG…SDIHV → LVMKEDGANLYVAKVSQVPR MNPRPVMVSYPGSRRVCLFE in isoform 2. 1 PublicationAdd BLAST37
Alternative sequenceiVSP_039682155 – 191Missing in isoform 3. 1 PublicationAdd BLAST37

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF133299 mRNA. Translation: AAF22159.1.
AY144606 Genomic DNA. Translation: AAN59996.1.
FN813349 mRNA. Translation: CBL81070.1.
FN813350 mRNA. Translation: CBL81071.1.
FN813351 mRNA. Translation: CBL81072.1.
AF285087 mRNA. Translation: AAG00514.1.
AF285088 mRNA. Translation: AAG00515.1.
AF285089 mRNA. Translation: AAG00516.1.
AC007068 Genomic DNA. No translation available.
AC010186 Genomic DNA. No translation available.
CH471094 Genomic DNA. Translation: EAW96114.1.
BC019883 mRNA. Translation: AAH19883.1.
CCDSiCCDS31741.1. [Q9UHP7-3]
CCDS55800.1. [Q9UHP7-5]
CCDS55801.1. [Q9UHP7-6]
CCDS55802.1. [Q9UHP7-7]
CCDS8602.1. [Q9UHP7-1]
RefSeqiNP_001004419.1. NM_001004419.4. [Q9UHP7-3]
NP_001184246.1. NM_001197317.2. [Q9UHP7-6]
NP_001184247.1. NM_001197318.2. [Q9UHP7-5]
NP_001184248.1. NM_001197319.2. [Q9UHP7-7]
NP_037401.1. NM_013269.5. [Q9UHP7-1]
UniGeneiHs.268326.

Genome annotation databases

EnsembliENST00000261339; ENSP00000261339; ENSG00000069493. [Q9UHP7-6]
ENST00000261340; ENSP00000261340; ENSG00000069493. [Q9UHP7-3]
ENST00000290855; ENSP00000290855; ENSG00000069493. [Q9UHP7-1]
ENST00000479877; ENSP00000441653; ENSG00000069493. [Q9UHP7-2]
ENST00000543300; ENSP00000443065; ENSG00000069493. [Q9UHP7-5]
ENST00000545918; ENSP00000444818; ENSG00000069493. [Q9UHP7-7]
GeneIDi29121.
KEGGihsa:29121.
UCSCiuc001qwf.4. human. [Q9UHP7-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Web resourcesi

Functional Glycomics Gateway - Glycan Binding

LLT1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF133299 mRNA. Translation: AAF22159.1.
AY144606 Genomic DNA. Translation: AAN59996.1.
FN813349 mRNA. Translation: CBL81070.1.
FN813350 mRNA. Translation: CBL81071.1.
FN813351 mRNA. Translation: CBL81072.1.
AF285087 mRNA. Translation: AAG00514.1.
AF285088 mRNA. Translation: AAG00515.1.
AF285089 mRNA. Translation: AAG00516.1.
AC007068 Genomic DNA. No translation available.
AC010186 Genomic DNA. No translation available.
CH471094 Genomic DNA. Translation: EAW96114.1.
BC019883 mRNA. Translation: AAH19883.1.
CCDSiCCDS31741.1. [Q9UHP7-3]
CCDS55800.1. [Q9UHP7-5]
CCDS55801.1. [Q9UHP7-6]
CCDS55802.1. [Q9UHP7-7]
CCDS8602.1. [Q9UHP7-1]
RefSeqiNP_001004419.1. NM_001004419.4. [Q9UHP7-3]
NP_001184246.1. NM_001197317.2. [Q9UHP7-6]
NP_001184247.1. NM_001197318.2. [Q9UHP7-5]
NP_001184248.1. NM_001197319.2. [Q9UHP7-7]
NP_037401.1. NM_013269.5. [Q9UHP7-1]
UniGeneiHs.268326.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4QKGX-ray1.95A72-191[»]
4QKHX-ray1.80A/B72-191[»]
4QKIX-ray1.80A/B72-191[»]
4QKJX-ray2.75A72-191[»]
4WCOX-ray2.46A/B/C71-191[»]
ProteinModelPortaliQ9UHP7.
SMRiQ9UHP7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi118886. 73 interactors.
IntActiQ9UHP7. 1 interactor.

PTM databases

iPTMnetiQ9UHP7.
PhosphoSitePlusiQ9UHP7.

Polymorphism and mutation databases

BioMutaiCLEC2D.
DMDMi74753331.

Proteomic databases

PeptideAtlasiQ9UHP7.
PRIDEiQ9UHP7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000261339; ENSP00000261339; ENSG00000069493. [Q9UHP7-6]
ENST00000261340; ENSP00000261340; ENSG00000069493. [Q9UHP7-3]
ENST00000290855; ENSP00000290855; ENSG00000069493. [Q9UHP7-1]
ENST00000479877; ENSP00000441653; ENSG00000069493. [Q9UHP7-2]
ENST00000543300; ENSP00000443065; ENSG00000069493. [Q9UHP7-5]
ENST00000545918; ENSP00000444818; ENSG00000069493. [Q9UHP7-7]
GeneIDi29121.
KEGGihsa:29121.
UCSCiuc001qwf.4. human. [Q9UHP7-1]

Organism-specific databases

CTDi29121.
DisGeNETi29121.
GeneCardsiCLEC2D.
HGNCiHGNC:14351. CLEC2D.
HPAiHPA017649.
HPA047584.
MIMi605659. gene.
neXtProtiNX_Q9UHP7.
OpenTargetsiENSG00000069493.
PharmGKBiPA142672100.
GenAtlasiSearch...

Phylogenomic databases

GeneTreeiENSGT00710000106527.
HOVERGENiHBG107718.
InParanoidiQ9UHP7.
KOiK10072.
OMAiEWTRQFP.
OrthoDBiEOG091G0JRZ.
PhylomeDBiQ9UHP7.
TreeFamiTF351467.

Enzyme and pathway databases

ReactomeiR-HSA-198933. Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell.

Miscellaneous databases

GeneWikiiCLEC2D.
GenomeRNAii29121.
PROiQ9UHP7.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000069493.
CleanExiHS_CLEC2D.
ExpressionAtlasiQ9UHP7. baseline and differential.
GenevisibleiQ9UHP7. HS.

Family and domain databases

Gene3Di3.10.100.10. 1 hit.
InterProiIPR001304. C-type_lectin-like.
IPR016186. C-type_lectin-like/link.
IPR016187. CTDL_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...

Entry informationi

Entry nameiCLC2D_HUMAN
AccessioniPrimary (citable) accession number: Q9UHP7
Secondary accession number(s): D6CI39
, D6CI40, D6CI41, Q6YID5, Q8WUP7, Q9HD37, Q9HD38
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: May 1, 2000
Last modified: November 30, 2016
This is version 120 of the entry and version 1 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.