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Q5KU26 (COL12_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 82. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Collectin-12
Alternative name(s):
Collectin placenta protein 1
Short name=CL-P1
Short name=hCL-P1
Nurse cell scavenger receptor 2
Scavenger receptor class A member 4
Scavenger receptor with C-type lectin
Gene names
Name:COLEC12
Synonyms:CLP1, NSR2, SCARA4, SRCL
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length742 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Scavenger receptor that displays several functions associated with host defense. Promotes binding and phagocytosis of Gram-positive, Gram-negative bacteria and yeast. Mediates the recognition, internalization and degradation of oxidatively modified low density lipoprotein (oxLDL) by vascular endothelial cells. Binds to several carbohydrates including Gal-type ligands, D-galactose, L- and D-fucose, GalNAc, T and Tn antigens in a calcium-dependent manner and internalizes specifically GalNAc in nurse-like cells. Binds also to sialyl Lewis X or a trisaccharide and asialo-orosomucoid (ASOR). May also play a role in the clearance of amyloid beta in Alzheimer disease. Ref.1 Ref.2 Ref.3 Ref.8 Ref.9

Subunit structure

The extracellular domain forms a stable trimer. The extracellular domain interacts with fibrillar beta amyloid peptide. Ref.8 Ref.9

Subcellular location

Membrane; Single-pass type II membrane protein. Note: Forms clusters on the cell surface. Ref.1

Tissue specificity

Expressed in perivascular macrophages. Expressed in plaques-surrounding reactive astrocytes and in perivascular astrocytes associated with cerebral amyloid angiopathy (CAA) in the temporal cortex of Alzheimer patient (at protein level). Strongly expressed in placenta. Moderately expressed in heart, skeletal muscle, small intestine and lung. Weakly expressed in brain, colon, thymus and kidney. Expressed in nurse-like cells. Expressed in reactive astrocytes and vascular/perivascular cells in the brain of Alzheimer patient. Ref.1 Ref.2 Ref.3 Ref.9

Sequence similarities

Contains 1 C-type lectin domain.

Contains 3 collagen-like domains.

Sequence caution

The sequence BAB39148.1 differs from that shown. Reason: Probable cloning artifact.

Ontologies

Keywords
   Cellular componentMembrane
   Coding sequence diversityPolymorphism
   DomainCoiled coil
Collagen
Repeat
Signal-anchor
Transmembrane
Transmembrane helix
   LigandCalcium
Lectin
Metal-binding
   Molecular functionReceptor
   PTMDisulfide bond
Glycoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcarbohydrate mediated signaling

Non-traceable author statement Ref.2. Source: UniProtKB

defense response

Traceable author statement Ref.1. Source: UniProtKB

innate immune response

Traceable author statement Ref.2. Source: UniProtKB

pattern recognition receptor signaling pathway

Inferred from direct assay Ref.2. Source: GOC

phagocytosis, recognition

Inferred from direct assay Ref.2. Source: UniProtKB

protein homooligomerization

Non-traceable author statement Ref.2. Source: UniProtKB

receptor-mediated endocytosis

Traceable author statement Ref.1. Source: GOC

   Cellular_componentcollagen

Inferred from electronic annotation. Source: UniProtKB-KW

endocytic vesicle membrane

Traceable author statement. Source: Reactome

integral component of membrane

Traceable author statement Ref.1. Source: UniProtKB

plasma membrane

Traceable author statement. Source: Reactome

   Molecular_functiongalactose binding

Non-traceable author statement Ref.2. Source: UniProtKB

low-density lipoprotein particle binding

Inferred from direct assay Ref.2. Source: UniProtKB

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

scavenger receptor activity

Traceable author statement Ref.1. Source: UniProtKB

signaling pattern recognition receptor activity

Inferred from direct assay Ref.2. Source: UniProtKB

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 742742Collectin-12
PRO_0000318681

Regions

Topological domain1 – 3737Cytoplasmic Potential
Transmembrane38 – 5821Helical; Signal-anchor for type II membrane protein; Potential
Topological domain59 – 742684Extracellular Potential
Domain443 – 47230Collagen-like 1
Domain473 – 52957Collagen-like 2
Domain530 – 58960Collagen-like 3
Domain614 – 731118C-type lectin
Coiled coil73 – 14169 Potential
Coiled coil215 – 328114 Potential

Sites

Metal binding6441Calcium 1; via carbonyl oxygen
Metal binding6461Calcium 1
Metal binding6501Calcium 1
Metal binding6701Calcium 2
Metal binding6741Calcium 2
Metal binding6941Calcium 3
Metal binding6961Calcium 3
Metal binding6971Calcium 2
Metal binding7061Calcium 2; via carbonyl oxygen
Metal binding7061Calcium 3
Metal binding7071Calcium 2
Metal binding7181Calcium 3
Metal binding7191Calcium 3
Metal binding7311Calcium 1
Binding site6911Carbohydrate By similarity
Binding site6941Carbohydrate By similarity
Binding site6961Carbohydrate By similarity
Binding site7061Carbohydrate By similarity
Binding site7181Carbohydrate By similarity
Binding site7191Carbohydrate; via carbonyl oxygen By similarity

Amino acid modifications

Glycosylation671N-linked (GlcNAc...) Potential
Glycosylation1591N-linked (GlcNAc...) Potential
Glycosylation1681N-linked (GlcNAc...) Potential
Glycosylation2711N-linked (GlcNAc...) Potential
Disulfide bond607 ↔ 618 Ref.10
Disulfide bond635 ↔ 730 Ref.10
Disulfide bond708 ↔ 722 Ref.10

Natural variations

Natural variant911K → E. Ref.5
Corresponds to variant rs17855029 [ dbSNP | Ensembl ].
VAR_038853
Natural variant4871I → V.
Corresponds to variant rs8098850 [ dbSNP | Ensembl ].
VAR_038854
Natural variant5221S → P. Ref.1 Ref.2 Ref.3 Ref.5 Ref.7
Corresponds to variant rs2305025 [ dbSNP | Ensembl ].
VAR_038855
Natural variant6061G → S. Ref.1 Ref.5 Ref.7
Corresponds to variant rs2305027 [ dbSNP | Ensembl ].
VAR_038856

Experimental info

Sequence conflict121Q → P in BAB39148. Ref.1
Sequence conflict161Y → F in BAB39148. Ref.1
Sequence conflict221Q → H in BAB39148. Ref.1
Sequence conflict281T → P in BAB39148. Ref.1
Sequence conflict311K → H in BAB39148. Ref.1
Sequence conflict721M → V in BAD83592. Ref.3

Secondary structure

..................... 742
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q5KU26 [UniParc].

Last modified May 18, 2010. Version 3.
Checksum: 85A003C1D6A83949

FASTA74281,515
        10         20         30         40         50         60 
MKDDFAEEEE VQSFGYKRFG IQEGTQCTKC KNNWALKFSI ILLYILCALL TITVAILGYK 

        70         80         90        100        110        120 
VVEKMDNVTG GMETSRQTYD DKLTAVESDL KKLGDQTGKK AISTNSELST FRSDILDLRQ 

       130        140        150        160        170        180 
QLREITEKTS KNKDTLEKLQ ASGDALVDRQ SQLKETLENN SFLITTVNKT LQAYNGYVTN 

       190        200        210        220        230        240 
LQQDTSVLQG NLQNQMYSHN VVIMNLNNLN LTQVQQRNLI TNLQRSVDDT SQAIQRIKND 

       250        260        270        280        290        300 
FQNLQQVFLQ AKKDTDWLKE KVQSLQTLAA NNSALAKANN DTLEDMNSQL NSFTGQMENI 

       310        320        330        340        350        360 
TTISQANEQN LKDLQDLHKD AENRTAIKFN QLEERFQLFE TDIVNIISNI SYTAHHLRTL 

       370        380        390        400        410        420 
TSNLNEVRTT CTDTLTKHTD DLTSLNNTLA NIRLDSVSLR MQQDLMRSRL DTEVANLSVI 

       430        440        450        460        470        480 
MEEMKLVDSK HGQLIKNFTI LQGPPGPRGP RGDRGSQGPP GPTGNKGQKG EKGEPGPPGP 

       490        500        510        520        530        540 
AGERGPIGPA GPPGERGGKG SKGSQGPKGS RGSPGKPGPQ GSSGDPGPPG PPGKEGLPGP 

       550        560        570        580        590        600 
QGPPGFQGLQ GTVGEPGVPG PRGLPGLPGV PGMPGPKGPP GPPGPSGAVV PLALQNEPTP 

       610        620        630        640        650        660 
APEDNGCPPH WKNFTDKCYY FSVEKEIFED AKLFCEDKSS HLVFINTREE QQWIKKQMVG 

       670        680        690        700        710        720 
RESHWIGLTD SERENEWKWL DGTSPDYKNW KAGQPDNWGH GHGPGEDCAG LIYAGQWNDF 

       730        740 
QCEDVNNFIC EKDRETVLSS AL 

« Hide

References

« Hide 'large scale' references
[1]"Molecular cloning and functional characterization of a human scavenger receptor with C-type lectin (SRCL), a novel member of a scavenger receptor family."
Nakamura K., Funakoshi H., Miyamoto K., Tokunaga F., Nakamura T.
Biochem. Biophys. Res. Commun. 280:1028-1035(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, VARIANTS PRO-522 AND SER-606.
Tissue: Placenta.
[2]"The membrane-type collectin CL-P1 is a scavenger receptor on vascular endothelial cells."
Ohtani K., Suzuki Y., Eda S., Kawai T., Kase T., Keshi H., Sakai Y., Fukuoh A., Sakamoto T., Itabe H., Suzutani T., Ogasawara M., Yoshida I., Wakamiya N.
J. Biol. Chem. 276:44222-44228(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, VARIANT PRO-522.
Tissue: Lung and Placenta.
[3]"SRCL/CL-P1 recognizes GalNAc and a carcinoma-associated antigen, Tn antigen."
Yoshida T., Tsuruta Y., Iwasaki M., Yamane S., Ochi T., Suzuki R.
J. Biochem. 133:271-277(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, VARIANT PRO-522.
[4]"DNA sequence and analysis of human chromosome 18."
Nusbaum C., Zody M.C., Borowsky M.L., Kamal M., Kodira C.D., Taylor T.D., Whittaker C.A., Chang J.L., Cuomo C.A., Dewar K., FitzGerald M.G., Yang X., Abouelleil A., Allen N.R., Anderson S., Bloom T., Bugalter B., Butler J. expand/collapse author list , Cook A., DeCaprio D., Engels R., Garber M., Gnirke A., Hafez N., Hall J.L., Norman C.H., Itoh T., Jaffe D.B., Kuroki Y., Lehoczky J., Lui A., Macdonald P., Mauceli E., Mikkelsen T.S., Naylor J.W., Nicol R., Nguyen C., Noguchi H., O'Leary S.B., Piqani B., Smith C.L., Talamas J.A., Topham K., Totoki Y., Toyoda A., Wain H.M., Young S.K., Zeng Q., Zimmer A.R., Fujiyama A., Hattori M., Birren B.W., Sakaki Y., Lander E.S.
Nature 437:551-555(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[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], VARIANTS GLU-91; PRO-522 AND SER-606.
Tissue: Placenta.
[6]"The full-ORF clone resource of the German cDNA consortium."
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I.
BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 326-742.
Tissue: Brain.
[7]"Haplotype analysis of the human collectin placenta 1 (hCL-P1) gene."
Ohmori H., Makita Y., Funamizu M., Chiba S., Ohtani K., Suzuki Y., Wakamiya N., Hata A.
J. Hum. Genet. 48:82-85(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS PRO-522 AND SER-606.
[8]"Selective binding of the scavenger receptor C-type lectin to Lewis X trisaccharide and related glycan ligands."
Coombs P.J., Graham S.A., Drickamer K., Taylor M.E.
J. Biol. Chem. 280:22993-22999(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBUNIT.
[9]"Possible role of scavenger receptor SRCL in the clearance of amyloid-beta in Alzheimer's disease."
Nakamura K., Ohya W., Funakoshi H., Sakaguchi G., Kato A., Takeda M., Kudo T., Nakamura T.
J. Neurosci. Res. 84:874-890(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH FIBRILLAR BETA AMYLOID PEPTIDE, FUNCTION IN CLEARANCE OF AMYLOID BETA, TISSUE SPECIFICITY.
[10]"Scavenger receptor C-type lectin binds to the leukocyte cell surface glycan Lewis X by a novel mechanism."
Feinberg H., Taylor M.E., Weis W.I.
J. Biol. Chem. 282:17250-17258(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) OF 603-742 IN COMPLEX WITH CALCIUM IONS, DISULFIDE BONDS.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB038518 mRNA. Translation: BAB39147.1.
AB052103 mRNA. Translation: BAB39148.1. Sequence problems.
AB005145 mRNA. Translation: BAB72147.1.
AB034251 mRNA. Translation: BAD83592.1.
AP000915 Genomic DNA. No translation available.
AP005240 Genomic DNA. No translation available.
BC060789 mRNA. Translation: AAH60789.1.
AL713657 mRNA. Translation: CAD28466.1.
PIRJC7595.
RefSeqNP_569057.1. NM_130386.2.
UniGeneHs.464422.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2OX8X-ray2.50A/B/C/D603-742[»]
ProteinModelPortalQ5KU26.
SMRQ5KU26. Positions 107-157, 607-734.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid123353. 2 interactions.
IntActQ5KU26. 1 interaction.
STRING9606.ENSP00000383115.

PTM databases

PhosphoSiteQ5KU26.

Polymorphism databases

DMDM296439391.

Proteomic databases

PaxDbQ5KU26.
PRIDEQ5KU26.

Protocols and materials databases

DNASU81035.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000400256; ENSP00000383115; ENSG00000158270.
GeneID81035.
KEGGhsa:81035.
UCSCuc002kkm.3. human.

Organism-specific databases

CTD81035.
GeneCardsGC18M000309.
HGNCHGNC:16016. COLEC12.
HPAHPA047917.
MIM607621. gene.
neXtProtNX_Q5KU26.
PharmGKBPA26738.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG147335.
HOGENOMHOG000111886.
HOVERGENHBG107745.
InParanoidQ5KU26.
KOK10062.
OMAEQQWIKK.
OrthoDBEOG74XS65.
PhylomeDBQ5KU26.
TreeFamTF332426.

Enzyme and pathway databases

ReactomeREACT_160300. Binding and Uptake of Ligands by Scavenger Receptors.

Gene expression databases

BgeeQ5KU26.
CleanExHS_CLP1.
HS_COLEC12.
GenevestigatorQ5KU26.

Family and domain databases

Gene3D3.10.100.10. 1 hit.
InterProIPR001304. C-type_lectin.
IPR016186. C-type_lectin-like.
IPR018378. C-type_lectin_CS.
IPR016187. C-type_lectin_fold.
IPR008160. Collagen.
[Graphical view]
PfamPF01391. Collagen. 2 hits.
PF00059. Lectin_C. 1 hit.
[Graphical view]
SMARTSM00034. CLECT. 1 hit.
[Graphical view]
SUPFAMSSF56436. SSF56436. 1 hit.
PROSITEPS00615. C_TYPE_LECTIN_1. 1 hit.
PS50041. C_TYPE_LECTIN_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSCOLEC12. human.
EvolutionaryTraceQ5KU26.
GenomeRNAi81035.
NextBio71376.
PROQ5KU26.
SOURCESearch...

Entry information

Entry nameCOL12_HUMAN
AccessionPrimary (citable) accession number: Q5KU26
Secondary accession number(s): Q6P9F2 expand/collapse secondary AC list , Q8TCR2, Q8WZA4, Q9BY85, Q9BYH7
Entry history
Integrated into UniProtKB/Swiss-Prot: February 26, 2008
Last sequence update: May 18, 2010
Last modified: April 16, 2014
This is version 82 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 18

Human chromosome 18: entries, gene names and cross-references to MIM