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(-) Description

Authors :  I. Ohki, T. Ishigaki, T. Oyama, S. Matsunaga, Q. Xie, M. Ohnishi- Kameyama, T. Murata, D. Tsuchiya, S. Machida, K. Morikawa, S. Tate
Date :  22 Feb 05  (Deposition) - 14 Jun 05  (Release) - 24 Feb 09  (Revision)
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  C-Type Lectin-Like Domain, Lox-1, Ctld, Scavenger Receptor, Oxidized Ldl Receptor, Nk Cell Receptor, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  I. Ohki, T. Ishigaki, T. Oyama, S. Matsunaga, Q. Xie, M. Ohnishi-Kameyama, T. Murata, D. Tsuchiya, S. Machida, K. Morikawa, S. Tate
Crystal Structure Of Human Lectin-Like, Oxidized Low-Density Lipoprotein Receptor 1 Ligand Binding Domain And Its Ligand Recognition Mode To Oxldl.
Structure V. 13 905 2005
PubMed-ID: 15939022  |  Reference-DOI: 10.1016/J.STR.2005.03.016
(for further references see the PDB file header)

(-) Compounds

    ChainsA, B
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1YXK)

(-) Sites  (0, 0)

(no "Site" information available for 1YXK)

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
1A:144 -A:155
2A:172 -A:264
3A:243 -A:256
4B:144 -B:155
5B:172 -B:264
6B:243 -B:256

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YXK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.OLR1_HUMAN151-265

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:130
 aligned with OLR1_HUMAN | P78380 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:130
                                   150       160       170       180       190       200       210       220       230       240       250       260       270
               SCOP domains d1yxka_ A: automated matches                                                                                                       SCOP domains
               CATH domains 1yxkA00 A:141-270 Mannose-Binding Protein A, subunit A                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) --------------------------N------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------C_TYPE_LECTIN_2  PDB: A:151-265 UniProt: 151-265                                                                   ----- PROSITE
           Transcript 1 (1) 1.----------------------------------------------Exon 1.5  PDB: A:189-227               ------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -Exon 1.4  PDB: A:142-188 UniProt: 142-188      --------------------------------------Exon 1.6  PDB: A:227-270 UniProt: 227-273    Transcript 1 (2)
                                   150       160       170       180       190       200       210       220       230       240       250       260       270

Chain B from PDB  Type:PROTEIN  Length:135
 aligned with OLR1_HUMAN | P78380 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:135
                                   145       155       165       175       185       195       205       215       225       235       245       255       265     
               SCOP domains d1yxkb_ B: automated matches                                                                                                            SCOP domains
               CATH domains 1yxkB00 B:136-270 Mannose-Binding Protein A, subunit A                                                                                  CATH domains
           Pfam domains (1) -------------------------Lectin_C-1yxkB01 B:161-266                                                                                ---- Pfam domains (1)
           Pfam domains (2) -------------------------Lectin_C-1yxkB02 B:161-266                                                                                ---- Pfam domains (2)
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) -------------------------------N------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------C_TYPE_LECTIN_2  PDB: B:151-265 UniProt: 151-265                                                                   ----- PROSITE
           Transcript 1 (1) 1.3    ----------------------------------------------Exon 1.5  PDB: B:189-227               ------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------Exon 1.4  PDB: B:142-188 UniProt: 142-188      --------------------------------------Exon 1.6  PDB: B:227-270 UniProt: 227-273    Transcript 1 (2)
                                   145       155       165       175       185       195       205       215       225       235       245       255       265     

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
Clan: C_Lectin (98)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (OLR1_HUMAN | P78380)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0005041    low-density lipoprotein receptor activity    Combining with a low-density lipoprotein particle and delivering the low-density lipoprotein into the cell via endocytosis.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0008015    blood circulation    The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0008219    cell death    Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0007159    leukocyte cell-cell adhesion    The attachment of a leukocyte to another cell via adhesion molecules.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0042157    lipoprotein metabolic process    The chemical reactions and pathways involving any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    GO:0042542    response to hydrogen peroxide    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0043235    receptor complex    Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.


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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

        OLR1_HUMAN | P783801ypo 1ypq 1ypu 1yxj 3vlg

(-) Related Entries Specified in the PDB File