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(-) Description

Title :  RECEPTOR ASSOCIATED PROTEIN (RAP) DOMAIN 1, NMR, MINIMIZED AVERAGE STRUCTURE
 
Authors :  P. R. Nielsen, F. M. Poulsen
Date :  08 May 97  (Deposition) - 20 Aug 97  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Alpha2Macroglobulin Receptor Associated Protein, Low Density Lipoprotein Receptor Family Associated Protein, Ldlr Family Associated Protein, Helix Bundle, Cell Surface Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. R. Nielsen, L. Ellgaard, M. Etzerodt, H. C. Thogersen, F. M. Poulsen
The Solution Structure Of The N-Terminal Domain Of Alpha2-Macroglobulin Receptor-Associated Protein.
Proc. Natl. Acad. Sci. Usa V. 94 7521 1997
PubMed-ID: 9207124  |  Reference-DOI: 10.1073/PNAS.94.14.7521
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RECEPTOR-ASSOCIATED PROTEIN
    Cell Line: BL21
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7H6UB
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Fragment: N-TERMINAL DOMAIN, DOMAIN 1, RESIDUES 17 - 97
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RAP, LOW DENSITY LIPOPROTEIN RECEPTOR RELATED PROTEIN, ALPHA2MACROGLOBULIN RECEPTOR ASSOCIATED PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1NRE)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NRE)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_050660N114SAMRP_HUMANPolymorphism2228158AN80S
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NRE)

(-) Exons   (0, 0)

(no "Exon" information available for 1NRE)

(-) 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:81
 aligned with AMRP_HUMAN | P30533 from UniProtKB/Swiss-Prot  Length:357

    Alignment length:81
                                    60        70        80        90       100       110       120       130 
           AMRP_HUMAN    51 GEEFRMEKLNQLWEKAQRLHLPPVRLAELHADLKIQERDELAWKKLKLDGLDEDGEKEARLIRNLNVILAKYGLDGKKDAR 131
               SCOP domains d1nrea_ A: alpha-2-Macroglobulin receptor associated protein (RAP)                SCOP domains
               CATH domains 1nreA00 A:17-97 Receptor-associated Protein                                       CATH domains
               Pfam domains Alpha-2-MRAP_N-1nreA01 A:17-97                                                    Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------S----------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 1nre A  17 GEEFRMEKLNQLWEKAQRLHLPPVRLAELHADLKIQERDELAWKKLKLDGLDEDGEKEARLIRNLNVILAKYGLDGKKDAR  97
                                    26        36        46        56        66        76        86        96
   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, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: Alpha-2-MRAP_N] (6)

(-) 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 | P30533: 1lre 1op1 1ov2 2fcw 2ftu 2fyl 2p01 2p03

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