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(-) Description

Title :  SOLUTION STRUCTURE OF DOMAIN 3 OF RAP
 
Authors :  D. Lee, J. D. Walsh, Y. -X. Wang
Date :  24 Jan 06  (Deposition) - 09 May 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Domain 3; Rap; Receptor-Associated Protein, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Lee, J. D. Walsh, I. Mikhailenko, P. Yu, M. Migliorini, Y. Wu, S. Krueger, J. E. Curtis, B. Harris, S. Lockett, S. C. Blacklow, D. K. Strickland, Y. X. Wang
Rap Uses A Histidine Switch To Regulate Its Interaction With Lrp In The Er And Golgi.
Mol. Cell V. 22 423 2006
PubMed-ID: 16678114  |  Reference-DOI: 10.1016/J.MOLCEL.2006.04.011
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-2-MACROGLOBULIN RECEPTOR-ASSOCIATED PROTEIN, DOMAIN 3
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 240-357
    GeneLRPAP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2FTU)

(-) Sites  (0, 0)

(no "Site" information available for 2FTU)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FTU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FTU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011821V311MAMRP_HUMANPolymorphism1800493AV72M

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ER_TARGETPS00014 Endoplasmic reticulum targeting sequence.AMRP_HUMAN354-357  1A:115-118

(-) Exons   (0, 0)

(no "Exon" information available for 2FTU)

(-) Sequences/Alignments

NMR Structure
   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:118
 aligned with AMRP_HUMAN | P30533 from UniProtKB/Swiss-Prot  Length:357

    Alignment length:118
                                   249       259       269       279       289       299       309       319       329       339       349        
           AMRP_HUMAN   240 RVSHQGYSTEAEFEEPRVIDLWDLAQSANLTDKELEAFREELKHFEAKIEKHNHYQKQLEIAHEKLRHAESVGDGERVSRSREKHALLEGRTKELGYTVKKHLQDLSGRISRARHNEL 357
               SCOP domains d2ftua1 A:1-118 alpha-2-Macroglobulin receptor associated protein (RAP)                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------M---------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ER_T PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 2ftu A   1 RVSHQGYSTEAEFEEPRVIDLWDLAQSANLTDKELEAFREELKHFEAKIEKHNHYQKQLEIAHEKLRHAESVGDGERVSRSREKHALLEGRTKELGYTVKKHLQDLSGRISRARHNEL 118
                                    10        20        30        40        50        60        70        80        90       100       110        

   Legend:   → Mismatch (orange background)
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    → 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, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FTU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FTU)

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (AMRP_HUMAN | P30533)
molecular function
    GO:0004873    asialoglycoprotein receptor activity    Receiving an asialoglycoprotein, and delivering the asialoglycoprotein into the cell via endocytosis. An asialoglycoprotein is a plasma glycoproteins from which the terminal sialic acid residue on their complex carbohydrate groups has been removed. The asialoglycoprotein receptor recognizes the terminal galactose and N-acetylgalactosamine units of the asialoglycoprotein, the receptor-ligand complex is internalized and transported to a sorting organelle where disassociation occurs before the receptor is recycled to the cell membrane.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0035473    lipase binding    Interacting selectively and non-covalently with any lipase.
    GO:0050750    low-density lipoprotein particle receptor binding    Interacting selectively and non-covalently with a low-density lipoprotein receptor.
    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).
    GO:0048019    receptor antagonist activity    Interacts with receptors to reduce the action of another ligand, the agonist.
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
    GO:0070326    very-low-density lipoprotein particle receptor binding    Interacting selectively and non-covalently with a very-low-density lipoprotein receptor.
biological process
    GO:1900116    extracellular negative regulation of signal transduction    Any negative regulation of signal transduction that takes place in extracellular region.
    GO:1900222    negative regulation of amyloid-beta clearance    Any process that stops, prevents or reduces the frequency, rate or extent of amyloid-beta clearance.
    GO:0032091    negative regulation of protein binding    Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
    GO:0010916    negative regulation of very-low-density lipoprotein particle clearance    Any process that decreases the rate, frequency or extent of very-low-density lipoprotein particle clearance. Very-low-density lipoprotein particle clearance is the process in which a very-low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    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:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    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: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:0048237    rough endoplasmic reticulum lumen    The volume enclosed by the membranes of the rough endoplasmic reticulum.
    GO:0031982    vesicle    Any small, fluid-filled, spherical organelle enclosed by membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AMRP_HUMAN | P305331lre 1nre 1op1 1ov2 2fcw 2fyl 2p01 2p03

(-) Related Entries Specified in the PDB File

2fft 2ffv