Q5KU26 (COL12_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	742 AA.
Sequence status	Complete.
Protein existence	Evidence 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 component	Membrane
Coding sequence diversity	Polymorphism
Domain	Coiled coil Collagen Repeat Signal-anchor Transmembrane Transmembrane helix
Ligand	Calcium Lectin Metal-binding
Molecular function	Receptor
PTM	Disulfide bond Glycoprotein Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	carbohydrate mediated signaling Non-traceable author statement Ref.2. Source: UniProtKB innate immune response Traceable author statement Ref.2. Source: UniProtKB phagocytosis, recognition Inferred from direct assay Ref.2. Source: UniProtKB protein homooligomerization Non-traceable author statement Ref.2. Source: UniProtKB
Cellular_component	collagen Inferred from electronic annotation. Source: UniProtKB-KW integral to membrane Traceable author statement Ref.1. Source: UniProtKB
Molecular_function	galactose 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 pattern recognition receptor activity Inferred from direct assay Ref.2. Source: UniProtKB scavenger receptor activity Traceable author statement Ref.1. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 742

742

Collectin-12

PRO_0000318681

Regions

Topological domain

1 – 37

37

Cytoplasmic Potential

Transmembrane

38 – 58

21

Helical; Signal-anchor for type II membrane protein; Potential

Topological domain

59 – 742

684

Extracellular Potential

Domain

443 – 472

30

Collagen-like 1

Domain

473 – 529

57

Collagen-like 2

Domain

530 – 589

60

Collagen-like 3

Domain

614 – 731

118

C-type lectin

Coiled coil

73 – 141

69

Potential

Coiled coil

215 – 328

114

Potential

Sites

Metal binding

644

1

Calcium 1; via carbonyl oxygen

Metal binding

646

1

Calcium 1

Metal binding

650

1

Calcium 1

Metal binding

670

1

Calcium 2

Metal binding

674

1

Calcium 2

Metal binding

694

1

Calcium 3

Metal binding

696

1

Calcium 3

Metal binding

697

1

Calcium 2

Metal binding

706

1

Calcium 2; via carbonyl oxygen

Metal binding

706

1

Calcium 3

Metal binding

707

1

Calcium 2

Metal binding

718

1

Calcium 3

Metal binding

719

1

Calcium 3

Metal binding

731

1

Calcium 1

Binding site

691

1

Carbohydrate By similarity

Binding site

694

1

Carbohydrate By similarity

Binding site

696

1

Carbohydrate By similarity

Binding site

706

1

Carbohydrate By similarity

Binding site

718

1

Carbohydrate By similarity

Binding site

719

1

Carbohydrate; via carbonyl oxygen By similarity

Amino acid modifications

Modified residue

126

1

Phosphothreonine By similarity

Modified residue

359

1

Phosphothreonine By similarity

Modified residue

361

1

Phosphothreonine By similarity

Modified residue

362

1

Phosphoserine By similarity

Glycosylation

67

1

N-linked (GlcNAc...) Potential

Glycosylation

159

1

N-linked (GlcNAc...) Potential

Glycosylation

168

1

N-linked (GlcNAc...) Potential

Glycosylation

271

1

N-linked (GlcNAc...) Potential

Disulfide bond

607 ↔ 618

Ref.10

Disulfide bond

635 ↔ 730

Ref.10

Disulfide bond

708 ↔ 722

Ref.10

Natural variations

Natural variant

91

1

K → E. Ref.5
Corresponds to variant rs17855029 [ dbSNP | Ensembl ].

VAR_038853

Natural variant

487

1

I → V.
Corresponds to variant rs8098850 [ dbSNP | Ensembl ].

VAR_038854

Natural variant

522

1

S → P. Ref.1 Ref.2 Ref.3 Ref.5 Ref.7
Corresponds to variant rs2305025 [ dbSNP | Ensembl ].

VAR_038855

Natural variant

606

1

G → S. Ref.1 Ref.5 Ref.7
Corresponds to variant rs2305027 [ dbSNP | Ensembl ].

VAR_038856

Experimental info

Sequence conflict

12

1

Q → P in BAB39148. Ref.1

Sequence conflict

16

1

Y → F in BAB39148. Ref.1

Sequence conflict

22

1

Q → H in BAB39148. Ref.1

Sequence conflict

28

1

T → P in BAB39148. Ref.1

Sequence conflict

31

1

K → H in BAB39148. Ref.1

Sequence conflict

72

1

M → V in BAD83592. Ref.3

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

742

Helix Strand Turn

Details...

Beta strand

612 – 614

3

Beta strand

617 – 621

5

Helix

628 – 637

10

Helix

648 – 657

10

Beta strand

664 – 669

6

Beta strand

671 – 673

3

Turn

692 – 700

9

Beta strand

708 – 711

4

Beta strand

717 – 720

4

Beta strand

726 – 733

8

Sequences

	Sequence		Length	Mass (Da)
	Q5KU26 [UniParc]. Last modified May 18, 2010. Version 3. Checksum: 85A003C1D6A83949	FASTA	742	81,515
	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

References

	« Hide 'large scale' referencesShow '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. , 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.

IPI

IPI00414467.
IPI00885028.

PIR

JC7595.

RefSeq

NP_569057.1. NM_130386.2.

UniGene

Hs.464422.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2OX8	X-ray	2.50	A/B/C/D	603-742	[»]

ProteinModelPortal

Q5KU26.

SMR

Q5KU26. Positions 607-734.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q5KU26. 1 interaction.

STRING

9606.ENSP00000383115.

PTM databases

PhosphoSite

Q5KU26.

Polymorphism databases

DMDM

296439391.

Proteomic databases

PaxDb

Q5KU26.

PRIDE

Q5KU26.

Protocols and materials databases

DNASU

81035.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000400256; ENSP00000383115; ENSG00000158270.

GeneID

81035.

KEGG

hsa:81035.

UCSC

uc002kkm.3. human.

Organism-specific databases

CTD

81035.

GeneCards

GC18M000309.

HGNC

HGNC:16016. COLEC12.

MIM

607621. gene.

neXtProt

NX_Q5KU26.

PharmGKB

PA26738.

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG147335.

HOGENOM

HOG000111886.

HOVERGEN

HBG107745.

InParanoid

Q5KU26.

KO

K10062.

OMA

NGCPPHW.

OrthoDB

EOG4KH2TV.

PhylomeDB

Q5KU26.

Gene expression databases

Bgee

Q5KU26.

CleanEx

HS_CLP1.
HS_COLEC12.

Genevestigator

Q5KU26.

Family and domain databases

Gene3D

3.10.100.10. 1 hit.

InterPro

IPR001304. C-type_lectin.
IPR016186. C-type_lectin-like.
IPR018378. C-type_lectin_CS.
IPR016187. C-type_lectin_fold.
IPR008160. Collagen.
[Graphical view]

Pfam

PF01391. Collagen. 2 hits.
PF00059. Lectin_C. 1 hit.
[Graphical view]

SMART

SM00034. CLECT. 1 hit.
[Graphical view]

SUPFAM

SSF56436. C-type_lectin_fold. 1 hit.

PROSITE

PS00615. C_TYPE_LECTIN_1. 1 hit.
PS50041. C_TYPE_LECTIN_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChiTaRS

COLEC12. human.

EvolutionaryTrace

Q5KU26.

GenomeRNAi

81035.

NextBio

71376.

SOURCE

Search...

Entry information

Entry name

COL12_HUMAN

Accession

Primary (citable) accession number: Q5KU26
Secondary accession number(s): Q6P9F2 , Q8TCR2, Q8WZA4, Q9BY85, Q9BYH7

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 26, 2008
Last sequence update:	May 18, 2010
Last modified:	May 1, 2013
This is version 74 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.