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Protein

Collectin-12

Gene

Colec12

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

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) (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi644 – 6441Calcium 1; via carbonyl oxygenBy similarity
Metal bindingi646 – 6461Calcium 1By similarity
Metal bindingi650 – 6501Calcium 1By similarity
Metal bindingi670 – 6701Calcium 2By similarity
Metal bindingi674 – 6741Calcium 2By similarity
Binding sitei691 – 6911CarbohydrateBy similarity
Metal bindingi694 – 6941Calcium 3By similarity
Binding sitei694 – 6941CarbohydrateBy similarity
Metal bindingi696 – 6961Calcium 3By similarity
Binding sitei696 – 6961CarbohydrateBy similarity
Metal bindingi697 – 6971Calcium 2By similarity
Metal bindingi706 – 7061Calcium 2; via carbonyl oxygenBy similarity
Metal bindingi706 – 7061Calcium 3By similarity
Binding sitei706 – 7061CarbohydrateBy similarity
Metal bindingi707 – 7071Calcium 2By similarity
Metal bindingi718 – 7181Calcium 3By similarity
Binding sitei718 – 7181CarbohydrateBy similarity
Metal bindingi719 – 7191Calcium 3By similarity
Binding sitei719 – 7191Carbohydrate; via carbonyl oxygenBy similarity
Metal bindingi731 – 7311Calcium 1By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Receptor

Keywords - Ligandi

Calcium, Lectin, Metal-binding

Enzyme and pathway databases

ReactomeiR-RNO-3000480. Scavenging by Class A Receptors.

Names & Taxonomyi

Protein namesi
Recommended name:
Collectin-12
Alternative name(s):
Collectin placenta protein 1
Short name:
CL-P1
Nurse cell scavenger receptor 2
Gene namesi
Name:Colec12
Synonyms:Clp1, Nsr2
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 18

Organism-specific databases

RGDi735039. Colec12.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 3737CytoplasmicSequence analysisAdd
BLAST
Transmembranei38 – 5821Helical; Signal-anchor for type II membrane proteinSequence analysisAdd
BLAST
Topological domaini59 – 742684ExtracellularSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 742742Collectin-12PRO_0000318683Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi159 – 1591N-linked (GlcNAc...)Sequence analysis
Glycosylationi168 – 1681N-linked (GlcNAc...)Sequence analysis
Glycosylationi271 – 2711N-linked (GlcNAc...)Sequence analysis
Disulfide bondi607 ↔ 618PROSITE-ProRule annotation
Disulfide bondi635 ↔ 730PROSITE-ProRule annotation
Disulfide bondi708 ↔ 722PROSITE-ProRule annotation

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiQ4V885.
PRIDEiQ4V885.

Expressioni

Tissue specificityi

Highly expressed in lung, spleen, small and large intestine, stomach and brain. Expressed in neonatal microglia.1 Publication

Gene expression databases

BgeeiENSRNOG00000016366.
GenevisibleiQ4V885. RN.

Interactioni

Subunit structurei

The extracellular domain forms a stable trimer. The extracellular domain interacts with fibrillar beta amyloid peptide (By similarity).By similarity

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000059663.

Structurei

3D structure databases

ProteinModelPortaliQ4V885.
SMRiQ4V885. Positions 607-737.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini452 – 51160Collagen-like 1Add
BLAST
Domaini527 – 58660Collagen-like 2Add
BLAST
Domaini614 – 731118C-type lectinPROSITE-ProRule annotationAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili104 – 14239Sequence analysisAdd
BLAST
Coiled coili220 – 30182Sequence analysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi7 – 104Poly-Glu

Sequence similaritiesi

Contains 1 C-type lectin domain.PROSITE-ProRule annotation
Contains 2 collagen-like domains.Curated

Keywords - Domaini

Coiled coil, Collagen, Repeat, Signal-anchor, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IIUI. Eukaryota.
ENOG41101BT. LUCA.
GeneTreeiENSGT00820000126981.
HOGENOMiHOG000111886.
HOVERGENiHBG107745.
InParanoidiQ4V885.
KOiK10062.
OMAiEQQWIKK.
OrthoDBiEOG091G0OLC.
PhylomeDBiQ4V885.
TreeFamiTF332426.

Family and domain databases

Gene3Di3.10.100.10. 2 hits.
InterProiIPR001304. C-type_lectin.
IPR016186. C-type_lectin-like.
IPR018378. C-type_lectin_CS.
IPR016187. C-type_lectin_fold.
IPR008160. Collagen.
[Graphical view]
PfamiPF01391. Collagen. 3 hits.
PF00059. Lectin_C. 1 hit.
[Graphical view]
SMARTiSM00034. CLECT. 1 hit.
[Graphical view]
SUPFAMiSSF56436. SSF56436. 1 hit.
PROSITEiPS00615. C_TYPE_LECTIN_1. 1 hit.
PS50041. C_TYPE_LECTIN_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q4V885-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKDDFAEEEE VQSFGYKRFG IQEGTQCTKC KNNWALKFSI ILLYVLCALL
60 70 80 90 100
TITVAILGYK VVEKMDTVTD GMETSRQTYD NKLIAVESDL KKLGDQTGKK
110 120 130 140 150
ALSTNSELST FRSDILDLRQ QLQEITEKTS KNKDMLEKLQ ANGDSLVDRQ
160 170 180 190 200
SQLKETLQNN SFLITTVNKT LQAYNGYVTN LQQDTSVLQG NLQSQMYSQN
210 220 230 240 250
VVIMNLNNLN LTQVQQRNLI TNLQRSVDDT SLAIQQIKND FQNLQQVFLQ
260 270 280 290 300
AKKDTDWLKE KVQSLQTLAA NNSALAKANN DTLEDMNNQL SSFTGQMDNI
310 320 330 340 350
TTISQANEQS MKDLQDLHKD TENRTAVKFS QLEERFQVFE TDIVNIINNI
360 370 380 390 400
SYTAHHLRTL TSNLNDVRTT CTDTLTRHTD DLTSLNNTLV NIRLDSISLR
410 420 430 440 450
MQQDMMRSRL DTEVANLSVV MEEMKLVDSK HGQLIKNFTI LQGPPGPRGP
460 470 480 490 500
KGDRGSQGPP GPTGNKGQKG EKGEPGPPGP AGERGTIGPV GPPGERGSKG
510 520 530 540 550
SKGSQGPKGS RGSPGKPGPQ GPSGDPGPPG PPGKDGLPGP QGPPGFQGLQ
560 570 580 590 600
GTVGEPGVPG PRGLPGLPGV PGMPGPKGPP GPPGPSGAME PLALQNEPTP
610 620 630 640 650
ASEVNGCPPH WKNFTDKCYY FSVEKEIFED AKLFCEDKSS HLVFINSREE
660 670 680 690 700
QQWIKKQTMG RESHWIGLTD SEQESEWKWL DGTPVDYKNW KAGQPDNWGS
710 720 730 740
GHGPGEDCAG LIYAGQWNDF QCDEINNFIC EKEREAVPSS IL
Length:742
Mass (Da):81,546
Last modified:July 5, 2005 - v1
Checksum:iB1EB2768DB1C39F0
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti248 – 2481F → S in BAD06456 (PubMed:16868960).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC097495 mRNA. Translation: AAH97495.1.
AB080968 mRNA. Translation: BAD06456.1.
RefSeqiNP_001020892.1. NM_001025721.1.
UniGeneiRn.31273.

Genome annotation databases

EnsembliENSRNOT00000065494; ENSRNOP00000059663; ENSRNOG00000016366.
GeneIDi361289.
KEGGirno:361289.
UCSCiRGD:735039. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC097495 mRNA. Translation: AAH97495.1.
AB080968 mRNA. Translation: BAD06456.1.
RefSeqiNP_001020892.1. NM_001025721.1.
UniGeneiRn.31273.

3D structure databases

ProteinModelPortaliQ4V885.
SMRiQ4V885. Positions 607-737.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000059663.

Proteomic databases

PaxDbiQ4V885.
PRIDEiQ4V885.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000065494; ENSRNOP00000059663; ENSRNOG00000016366.
GeneIDi361289.
KEGGirno:361289.
UCSCiRGD:735039. rat.

Organism-specific databases

CTDi81035.
RGDi735039. Colec12.

Phylogenomic databases

eggNOGiENOG410IIUI. Eukaryota.
ENOG41101BT. LUCA.
GeneTreeiENSGT00820000126981.
HOGENOMiHOG000111886.
HOVERGENiHBG107745.
InParanoidiQ4V885.
KOiK10062.
OMAiEQQWIKK.
OrthoDBiEOG091G0OLC.
PhylomeDBiQ4V885.
TreeFamiTF332426.

Enzyme and pathway databases

ReactomeiR-RNO-3000480. Scavenging by Class A Receptors.

Miscellaneous databases

PROiQ4V885.

Gene expression databases

BgeeiENSRNOG00000016366.
GenevisibleiQ4V885. RN.

Family and domain databases

Gene3Di3.10.100.10. 2 hits.
InterProiIPR001304. C-type_lectin.
IPR016186. C-type_lectin-like.
IPR018378. C-type_lectin_CS.
IPR016187. C-type_lectin_fold.
IPR008160. Collagen.
[Graphical view]
PfamiPF01391. Collagen. 3 hits.
PF00059. Lectin_C. 1 hit.
[Graphical view]
SMARTiSM00034. CLECT. 1 hit.
[Graphical view]
SUPFAMiSSF56436. SSF56436. 1 hit.
PROSITEiPS00615. C_TYPE_LECTIN_1. 1 hit.
PS50041. C_TYPE_LECTIN_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCOL12_RAT
AccessioniPrimary (citable) accession number: Q4V885
Secondary accession number(s): Q76LC3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 26, 2008
Last sequence update: July 5, 2005
Last modified: September 7, 2016
This is version 86 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. 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.