Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE PTB DOMAIN OF HUMAN APPL1
 
Authors :  J. Li, X. Mao, L. Q. Dong, F. Liu, L. Tong
Date :  27 Mar 07  (Deposition) - 29 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Appl, Ptb Domain, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Li, X. Mao, L. Q. Dong, F. Liu, L. Tong
Crystal Structures Of The Bar-Ph And Ptb Domains Of Human Appl1
Structure V. 15 525 2007
PubMed-ID: 17502098  |  Reference-DOI: 10.1016/J.STR.2007.03.011
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADAPTER PROTEIN CONTAINING PH DOMAIN, PTB DOMAIN AND LEUCINE ZIPPER MOTIF 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentPTB DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPPL1, DIP13 ALPHA, DCC-INTERACTING PROTEIN 13 ALPHA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2ELA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_035909E643QDP13A_HUMANUnclassified  ---BE643Q
2CancerSNPVAR_DP13A_HUMAN_CCDS2882_1_01 *E643QDP13A_HUMANDisease (Breast cancer)  ---BE643Q
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (0, 0)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_035909E643QDP13A_HUMANUnclassified  ---BE643Q
2CancerSNPVAR_DP13A_HUMAN_CCDS2882_1_01 *E643QDP13A_HUMANDisease (Breast cancer)  ---BE643Q
   * ID not provided by source

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PIDPS01179 Phosphotyrosine interaction domain (PID) profile.DP13A_HUMAN502-638
 
  2A:502-633
B:502-638
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PIDPS01179 Phosphotyrosine interaction domain (PID) profile.DP13A_HUMAN502-638
 
  1A:502-633
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PIDPS01179 Phosphotyrosine interaction domain (PID) profile.DP13A_HUMAN502-638
 
  1-
B:502-638

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 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_HUMAN477-495190--
1.18bENST0000028826618bENSE00001032967chr3:57293873-57294047175DP13A_HUMAN495-553592A:496-553
B:499-553
58
55
1.19aENST0000028826619aENSE00001032959chr3:57294145-5729418137DP13A_HUMAN553-565132A:553-565
B:553-565
13
13
1.20ENST0000028826620ENSE00001032964chr3:57294656-57294802147DP13A_HUMAN566-614492A:566-614 (gaps)
B:566-614 (gaps)
49
49
1.21aENST0000028826621aENSE00001032935chr3:57301770-5730182051DP13A_HUMAN615-631172A:615-631
B:615-631
17
17
1.22ENST0000028826622ENSE00001032946chr3:57302426-5730251590DP13A_HUMAN632-661302A:632-633
B:632-645
2
14
1.23ENST0000028826623ENSE00001121992chr3:57303569-573074963928DP13A_HUMAN662-709480--

(-) Sequences/Alignments

Asymmetric 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:131
 aligned with DP13A_HUMAN | Q9UKG1 from UniProtKB/Swiss-Prot  Length:709

    Alignment length:138
                                   505       515       525       535       545       555       565       575       585       595       605       615       625        
          DP13A_HUMAN   496 SILHQLFIVRFLGSMEVKSDDHPDVVYETMRQILAARAIHNIFRMTESHLLVTCDCLKLIDPQTQVTRLTFPLPCVVLYATHQENKRLFGFVLRTSSGRSESNLSSVCYIFESNNEGEKICDSVGLAKQIALHAELDR 633
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeeeeee.....hhhhhhhhhhhhhhhhhh.....eeeeeee...eeeee......eeeeee...eeeeeee..eeeeeeeeeee.-------.eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------PID  PDB: A:502-633 UniProt: 502-638                                                                                                 PROSITE
           Transcript 1 (1) Exon 1.18b  PDB: A:496-553 UniProt: 495-553 [INCOMPLETE]  ------------Exon 1.20  PDB: A:566-614 (gaps) UniProt: 566-614Exon 1.21a       1. Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------Exon 1.19a   -------------------------------------------------------------------- Transcript 1 (2)
                 2ela A 496 SILHQLFIVRFLGSMEVKSDDHPDVVYETMRQILAARAIHNIFRMTESHLLVTCDCLKLIDPQTQVTRLTFPLPCVVLYATHQENKRLFGFVLRTS-------LSSVCYIFESNNEGEKICDSVGLAKQIALHAELDR 633
                                   505       515       525       535       545       555       565       575       585     |   -   |   605       615       625        
                                                                                                                         591     599                                  

Chain B from PDB  Type:PROTEIN  Length:141
 aligned with DP13A_HUMAN | Q9UKG1 from UniProtKB/Swiss-Prot  Length:709

    Alignment length:147
                                   508       518       528       538       548       558       568       578       588       598       608       618       628       638       
          DP13A_HUMAN   499 HQLFIVRFLGSMEVKSDDHPDVVYETMRQILAARAIHNIFRMTESHLLVTCDCLKLIDPQTQVTRLTFPLPCVVLYATHQENKRLFGFVLRTSSGRSESNLSSVCYIFESNNEGEKICDSVGLAKQIALHAELDRRASEKQKEIERV 645
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.....hhhhhhhhhhhhhhhhhh.....eeeeeee...eeeee......eeeeee...eeeeeee..eeeeeeeeeee..------.eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) ------------------------------------------------------------------------------------------------------------------------------------------------Q-- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------------Q-- SAPs(SNPs) (2)
                    PROSITE ---PID  PDB: B:502-638 UniProt: 502-638                                                                                                     ------- PROSITE
           Transcript 1 (1) Exon 1.18b  PDB: B:499-553 UniProt: 495-553            ------------Exon 1.20  PDB: B:566-614 (gaps) UniProt: 566-614Exon 1.21a       Exon 1.22      Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.19a   -------------------------------------------------------------------------------- Transcript 1 (2)
                 2ela B 499 HQLFIVRFLGSMEVKSDDHPDVVYETMRQILAARAIHNIFRMTESHLLVTCDCLKLIDPQTQVTRLTFPLPCVVLYATHQENKRLFGFVLRTSS------LSSVCYIFESNNEGEKICDSVGLAKQIALHAELDRRASEKQKEIERV 645
                                   508       518       528       538       548       558       568       578       588   |     -|      608       618       628       638       
                                                                                                                       592    599                                              

   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 2ELA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric 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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2ela)
 
  Sites
(no "Sites" information available for 2ela)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ela)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2ela
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DP13A_HUMAN | Q9UKG1
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  DP13A_HUMAN | Q9UKG1
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DP13A_HUMAN | Q9UKG12ej8 2elb 2q12 2q13 2z0n 2z0o 5c5b

(-) Related Entries Specified in the PDB File

2elb