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(-) Description

Title :  CRYSTAL STRUCTURE OF APPL1 PTB DOMAIN AT 1.8A
 
Authors :  H. Tanabe, T. Hosaka, K. Murayama, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  15 Mar 07  (Deposition) - 18 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Tanabe, T. Hosaka, K. Murayama, T. Terada, M. Shirouzu, S. Yokoyama
Crystal Structure Of Appl1 Ptb Domain At 1. 8A
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DCC-INTERACTING PROTEIN 13 ALPHA
    ChainsA, B
    EngineeredYES
    Expression System Vector TypePLASMID
    GeneAPPL1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsE.COLI CELL-FREE EXPRESSION SYSTEM
    SynonymDIP13 ALPHA, ADAPTER PROTEIN CONTAINING PH DOMAIN, PTB DOMAIN AND LEUCINE ZIPPER MOTIF 1

 Structural Features

(-) Chains, Units

  12
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 2EJ8)

(-) Sites  (0, 0)

(no "Site" information available for 2EJ8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EJ8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EJ8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EJ8)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PIDPS01179 Phosphotyrosine interaction domain (PID) profile.DP13A_HUMAN502-638
 
  2A:18-146
B:18-148

(-) Exons   (6, 11)

Asymmetric/Biological Unit (6, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002882661aENSE00001277615chr3:57261765-57261965201DP13A_HUMAN1-18180--
1.3ENST000002882663ENSE00001032931chr3:57269594-5726969299DP13A_HUMAN19-51330--
1.4ENST000002882664ENSE00001032953chr3:57271520-5727157960DP13A_HUMAN52-71200--
1.5aENST000002882665aENSE00001277569chr3:57272073-5727214472DP13A_HUMAN72-95240--
1.6ENST000002882666ENSE00001277563chr3:57274493-5727458088DP13A_HUMAN96-125300--
1.7ENST000002882667ENSE00002171063chr3:57276129-5727617042DP13A_HUMAN125-139150--
1.8bENST000002882668bENSE00001032951chr3:57276884-5727694259DP13A_HUMAN139-158200--
1.9ENST000002882669ENSE00001032966chr3:57280104-57280250147DP13A_HUMAN159-207490--
1.10ENST0000028826610ENSE00001032930chr3:57281423-5728150583DP13A_HUMAN208-235280--
1.11ENST0000028826611ENSE00001032938chr3:57282221-57282379159DP13A_HUMAN235-288540--
1.12ENST0000028826612ENSE00001032944chr3:57283388-57283576189DP13A_HUMAN288-351640--
1.13ENST0000028826613ENSE00001032948chr3:57286297-5728633943DP13A_HUMAN351-365150--
1.14ENST0000028826614ENSE00001632937chr3:57287710-5728776657DP13A_HUMAN366-384190--
1.15ENST0000028826615ENSE00001032937chr3:57290985-5729107995DP13A_HUMAN385-416320--
1.16ENST0000028826616ENSE00001032934chr3:57291274-57291456183DP13A_HUMAN416-477620--
1.17bENST0000028826617bENSE00001032928chr3:57293056-5729310853DP13A_HUMAN477-495192A:8-11
B:11-11
4
1
1.18bENST0000028826618bENSE00001032967chr3:57293873-57294047175DP13A_HUMAN495-553592A:11-69
B:11-69
59
59
1.19aENST0000028826619aENSE00001032959chr3:57294145-5729418137DP13A_HUMAN553-565132A:69-81
B:69-81
13
13
1.20ENST0000028826620ENSE00001032964chr3:57294656-57294802147DP13A_HUMAN566-614492A:82-130 (gaps)
B:82-130 (gaps)
49
49
1.21aENST0000028826621aENSE00001032935chr3:57301770-5730182051DP13A_HUMAN615-631172A:131-146
B:131-147
16
17
1.22ENST0000028826622ENSE00001032946chr3:57302426-5730251590DP13A_HUMAN632-661301-
B:148-148
-
1
1.23ENST0000028826623ENSE00001121992chr3:57303569-573074963928DP13A_HUMAN662-709480--

(-) 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:133
 aligned with DP13A_HUMAN | Q9UKG1 from UniProtKB/Swiss-Prot  Length:709

    Alignment length:139
                                   501       511       521       531       541       551       561       571       581       591       601       611       621         
          DP13A_HUMAN   492 ETEDSILHQLFIVRFLGSMEVKSDDHPDVVYETMRQILAARAIHNIFRMTESHLLVTCDCLKLIDPQTQVTRLTFPLPCVVLYATHQENKRLFGFVLRTSSGRSESNLSSVCYIFESNNEGEKICDSVGLAKQIALHAE 630
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeeee.....hhhhhhhhhhhhhhhhhh......eeeeeee..eeeee......eeeeee...eeeeeee..eeeeeeeeeee..------.eeeeeeeee..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------PID  PDB: A:18-146 UniProt: 502-638                                                                                               PROSITE
           Transcript 1 (1) 1.17---------------------------------------------------------Exon 1.19a   Exon 1.20  PDB: A:82-130 (gaps) UniProt: 566-614 Exon 1.21a       Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.18b  PDB: A:11-69 UniProt: 495-553                  ----------------------------------------------------------------------------- Transcript 1 (2)
                 2ej8 A   8 ETEDSILHQLFIVRFLGSMEVKSDDHPDVVYETMRQILAARAIHNIFRMTESHLLVTCDCLKLIDPQTQVTRLTFPLPCVVLYATHQENKRLFGFVLRTSS------LSSVCYIFESNNEGEKICDSVGLAKQIALHAE 146
                                    17        27        37        47        57        67        77        87        97       107|      117       127       137         
                                                                                                                              108    115                               

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with DP13A_HUMAN | Q9UKG1 from UniProtKB/Swiss-Prot  Length:709

    Alignment length:138
                                   504       514       524       534       544       554       564       574       584       594       604       614       624        
          DP13A_HUMAN   495 DSILHQLFIVRFLGSMEVKSDDHPDVVYETMRQILAARAIHNIFRMTESHLLVTCDCLKLIDPQTQVTRLTFPLPCVVLYATHQENKRLFGFVLRTSSGRSESNLSSVCYIFESNNEGEKICDSVGLAKQIALHAELD 632
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeeeeeee......hhhhhhhhhhhhhhhhh......eeeeee...eeeee......eeeeee...eeeeeee..eeeeeeeeeee.-------.eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------PID  PDB: B:18-148 UniProt: 502-638                                                                                                 PROSITE
           Transcript 1 (1) 1---------------------------------------------------------Exon 1.19a   Exon 1.20  PDB: B:82-130 (gaps) UniProt: 566-614 Exon 1.21a       1 Transcript 1 (1)
           Transcript 1 (2) Exon 1.18b  PDB: B:11-69 UniProt: 495-553                  ------------------------------------------------------------------------------- Transcript 1 (2)
                 2ej8 B  11 DSILHQLFIVRFLGSMEVKSDDHPDVVYETMRQILAARAIHNIFRMTESHLLVTCDCLKLIDPQTQVTRLTFPLPCVVLYATHQENKRLFGFVLRTS-------LSSVCYIFESNNEGEKICDSVGLAKQIALHAELD 148
                                    20        30        40        50        60        70        80        90       100      |  -    |  120       130       140        
                                                                                                                          107     115                                 

   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 2EJ8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2EJ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EJ8)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DP13A_HUMAN | Q9UKG1)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0043422    protein kinase B binding    Interacting selectively and non-covalently with protein kinase B, an intracellular kinase that is important in regulating glucose metabolism.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0097192    extrinsic apoptotic signaling pathway in absence of ligand    A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with withdrawal of a ligand from a cell surface receptor, and ends when the execution phase of apoptosis is triggered.
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    GO:0090003    regulation of establishment of protein localization to plasma membrane    Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location in the plasma membrane.
    GO:0046324    regulation of glucose import    Any process that modulates the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0016581    NuRD complex    An approximately 2 MDa multi-subunit complex that exhibits ATP-dependent chromatin remodeling activity in addition to histone deacetylase (HDAC) activity, and has been shown to establish transcriptional repression of a number of target genes in vertebrates, invertebrates and fungi. Amongst its subunits, the NuRD complex contains histone deacetylases, histone binding proteins and Mi-2-like proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0012506    vesicle membrane    The lipid bilayer surrounding any membrane-bounded vesicle in the cell.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DP13A_HUMAN | Q9UKG12ela 2elb 2q12 2q13 2z0n 2z0o 5c5b

(-) Related Entries Specified in the PDB File

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