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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF THE E2 DOMAIN OF APL-1 FROM C. ELEGANS, IN COMPLEX WITH SUCROSE OCTASULFATE (SOS)
 
Authors :  J. T. Hoopes, Y. Ha
Date :  08 Oct 09  (Deposition) - 10 Nov 09  (Release) - 02 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  X-Ray Crystal Structure, Amyloid Precursor Protein, Heparin Binding, Alternative Splicing, Amyloid, Developmental Protein, Differentiation, Glycoprotein, Membrane, Neurogenesis, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. T. Hoopes, X. Liu, X. Xu, B. Demeler, E. Folta-Stogniew, C. Li, Y. Ha
Structural Characterization Of The E2 Domain Of Apl-1, A Caenorhabditis Elegans Homolog Of Human Amyloid Precursor Protein, And Its Heparin Binding Site
J. Biol. Chem. V. 285 2165 2010
PubMed-ID: 19906646  |  Reference-DOI: 10.1074/JBC.M109.018432
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-AMYLOID-LIKE PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneAPL-1, C42D8.8
    Organism CommonNEMATODE
    Organism ScientificCAENORHABDITIS ELEGANS
    Organism Taxid6239

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NT21Ligand/Ion2,3,4,6-TETRA-O-SULFOHEXOPYRANOSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:16 , THR A:245 , ASN A:246 , GLU A:247 , HIS A:248 , ASP A:249 , LYS A:372 , MET A:375 , HIS A:376BINDING SITE FOR RESIDUE NT2 A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K6B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K6B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K6B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K6B)

(-) Exons   (0, 0)

(no "Exon" information available for 3K6B)

(-) 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:218
 aligned with A4_CAEEL | Q10651 from UniProtKB/Swiss-Prot  Length:686

    Alignment length:218
                                   249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449        
             A4_CAEEL   240 SQDPYFKIANWTNEHDDFKKAEMRMDEKHRKKVDKVMKEWGDLETRYNEQKAKDPKGAEKFKSQMNARFQKTVSSLEEEHKRMRKEIEAVHEERVQAMLNEKKRDATHDYRQALATHVNKPNKHSVLQSLKAYIRAEEKDRMHTLNRYRHLLKADSKEAAAYKPTVIHRLRYIDLRINGTLAMLRDFPDLEKYVRPIAVTYWKDYRDEVSPDISVEDS 457
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k6b A 234 SQDPYFKIANWTNEHDDFKKAEMRMDEKHRKKVDKVMKEWGDLETRYNEQKAKDPKGAEKFKSQMNARFQKTVSSLEEEHKRMRKEIEAVHEERVQAMLNEKKRDATHDYRQALATHVNKPNKHSVLQSLKAYIRAEEKDRMHTLNRYRHLLKADSKEAAAYKPTVIHRLRYIDLRINGTLAMLRDFPDLEKYVRPIAVTYWKDYRDEVSPDISVEDS 451
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443        

   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  (0, 0)

(no "SCOP Domain" information available for 3K6B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K6B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3K6B)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(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

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

UniProtKB/Swiss-Prot
        A4_CAEEL | Q106512m05 3k66

(-) Related Entries Specified in the PDB File

1rw6 THE E2 DOMAIN OF HUMAN AMYLOID PRECURSOR PROTEIN
3k66 CRYSTAL STRUCTURE OF THE E2 DOMAIN OF C. ELEGANS APL-1