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(-) Description

Title :  STRUCTURE OF MODULE 2 FROM THE E1 DOMAIN OF C. ELEGANS APL-1
 
Authors :  M. G. Hinds, S. Leong
Date :  20 Oct 12  (Deposition) - 23 Oct 13  (Release) - 01 Jan 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Apl-1, Amyloid Precursor Protein, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. L. Leong, T. R. Young, K. J. Barnham, A. G. Wedd, M. G. Hinds, Z. Xiao, R. Cappai
Quantification Of Copper Binding To Amyloid Precursor Protein Domain 2 And Its Caenorhabditis Elegans Ortholog. Implications For Biological Function.
Metallomics V. 6 105 2013
PubMed-ID: 24276282  |  Reference-DOI: 10.1039/C3MT00258F

(-) Compounds

Molecule 1 - BETA-AMYLOID-LIKE PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemKOMAGATAELLA PASTORIS
    Expression System CommonPICHIA PASTORIS
    Expression System Taxid4922
    FragmentMODULE 2 OF E1 DOMAIN
    GeneAPL-1, C42D8.8
    Organism CommonNEMATODE
    Organism ScientificCAENORHABDITIS ELEGANS
    Organism Taxid6239

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2M05)

(-) Sites  (0, 0)

(no "Site" information available for 2M05)

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:135 -A:195
2A:146 -A:182
3A:160 -A:194

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2M05)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2M05)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1A4_EXTRAPS00319 Amyloidogenic glycoprotein extracellular domain signature.A4_CAEEL189-196  1A:189-196
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1A4_EXTRAPS00319 Amyloidogenic glycoprotein extracellular domain signature.A4_CAEEL189-196  1A:189-196

(-) Exons   (0, 0)

(no "Exon" information available for 2M05)

(-) 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:65
 aligned with A4_CAEEL | Q10651 from UniProtKB/Swiss-Prot  Length:686

    Alignment length:65
                                   142       152       162       172       182       192     
             A4_CAEEL   133 HDCQFSHVNSRDQCNDYQHWKDEAGKQCKTKKSKGNKDMIVRSFAVLEPCALDMFTGVEFVCCPN 197
               SCOP domains d2m05a_ A: automated matches                                      SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee......hhhhhhhhhhhhhhhh........eeeeeee..........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------A4_EXTRA- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 2m05 A 133 EACQFSHVNSRDQCNDYQHWKDEAGKQCKTKKSKGNKDMIVRSFAVLEPCALDMFTGVEFVCCPN 197
                                   142       152       162       172       182       192     

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2M05)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2M05)

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (A4_CAEEL | Q10651)
molecular function
    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:0046914    transition metal ion binding    Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
biological process
    GO:0010171    body morphogenesis    The process in which the anatomical structures of the soma are generated and organized.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0042395    ecdysis, collagen and cuticulin-based cuticle    The shedding of the old collagen and cuticulin-based cuticle fragments during the molting cycle. Examples of this process are found in invertebrates.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0002119    nematode larval development    The process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
cellular component
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.

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 Related Entries

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        A4_CAEEL | Q106513k66 3k6b

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