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
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF APPL1-BAR DOMAIN
 
Authors :  K. Murayama, M. Kato-Murayama, A. Sakamoto, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  07 May 07  (Deposition) - 13 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Helix Bundle, Cell Cycle, Coiled Coil, Endosome, Membrane, Nucleus, Phosphorylation, Signaling Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Murayama, M. Kato-Murayama, A. Sakamoto, M. Shirouzu, S. Yokoyama
Crystal Structure Of Appl1-Bar Domain
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DCC-INTERACTING PROTEIN 13-ALPHA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentREISDUES 1-275
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPPL1, DIP13-ALPHA, ADAPTER PROTEIN CONTAINING PH DOMAIN, PTB DOMAIN AND LEUCINE ZIPPER MOTIF 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 11)

Asymmetric Unit (1, 11)
No.NameCountTypeFull Name
1MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 22)
No.NameCountTypeFull Name
1MSE22Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2Z0N)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z0N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z0N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_075857D94NDP13A_HUMANDisease (MODY14)796065047AD94N
2UniProtVAR_050958A108VDP13A_HUMANPolymorphism4381906AA108V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_075857D94NDP13A_HUMANDisease (MODY14)796065047AD94N
2UniProtVAR_050958A108VDP13A_HUMANPolymorphism4381906AA108V

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z0N)

(-) Exons   (10, 10)

Asymmetric Unit (10, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002882661aENSE00001277615chr3:57261765-57261965201DP13A_HUMAN1-18181A:13-186
1.3ENST000002882663ENSE00001032931chr3:57269594-5726969299DP13A_HUMAN19-51331A:19-5133
1.4ENST000002882664ENSE00001032953chr3:57271520-5727157960DP13A_HUMAN52-71201A:52-7120
1.5aENST000002882665aENSE00001277569chr3:57272073-5727214472DP13A_HUMAN72-95241A:80-9516
1.6ENST000002882666ENSE00001277563chr3:57274493-5727458088DP13A_HUMAN96-125301A:96-12530
1.7ENST000002882667ENSE00002171063chr3:57276129-5727617042DP13A_HUMAN125-139151A:125-13915
1.8bENST000002882668bENSE00001032951chr3:57276884-5727694259DP13A_HUMAN139-158201A:139-15820
1.9ENST000002882669ENSE00001032966chr3:57280104-57280250147DP13A_HUMAN159-207491A:159-20749
1.10ENST0000028826610ENSE00001032930chr3:57281423-5728150583DP13A_HUMAN208-235281A:208-23528
1.11ENST0000028826611ENSE00001032938chr3:57282221-57282379159DP13A_HUMAN235-288541A:235-25521
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_HUMAN495-553590--
1.19aENST0000028826619aENSE00001032959chr3:57294145-5729418137DP13A_HUMAN553-565130--
1.20ENST0000028826620ENSE00001032964chr3:57294656-57294802147DP13A_HUMAN566-614490--
1.21aENST0000028826621aENSE00001032935chr3:57301770-5730182051DP13A_HUMAN615-631170--
1.22ENST0000028826622ENSE00001032946chr3:57302426-5730251590DP13A_HUMAN632-661300--
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:235
 aligned with DP13A_HUMAN | Q9UKG1 from UniProtKB/Swiss-Prot  Length:709

    Alignment length:243
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252   
          DP13A_HUMAN    13 LEDSPQTRSLLGVFEEDATAISNYMNQLYQAMHRIYDAQNELSAATHLTSKLLKEYEKQRFPLGGDDEVMSSTLQQFSKVIDELSSCHAVLSTQLADAMMFPITQFKERDLKEILTLKEVFQIASNDHDAAINRYSRLSKKRENDKVKYEVTEDVYTSRKKQHQTMMHYFCALNTLQYKKKIALLEPLLGYMQAQISFFKMGSENLNEQLEEFLANIGTSVQNVRREMDSDIETMQQTIEDLE 255
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh--------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------N-------------V--------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1a  Exon 1.3  PDB: A:19-51           Exon 1.4            Exon 1.5a  PDB: A:80-95 Exon 1.6  PDB: A:96-125       -------------Exon 1.8b           Exon 1.9  PDB: A:159-207 UniProt: 159-207        Exon 1.10  PDB: A:208-235   -------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------Exon 1.7       -----------------------------------------------------------------------------------------------Exon 1.11             Transcript 1 (2)
                 2z0n A  13 LEDSPQTRSLLGVFEEDATAISNYmNQLYQAmHRIYDAQNELSAATHLTSKLLKEYEKQ--------EVmSSTLQQFSKVIDELSSCHAVLSTQLADAmmFPITQFKERDLKEILTLKEVFQIASNDHDAAINRYSRLSKKRENDKVKYEVTEDVYTSRKKQHQTmmHYFCALNTLQYKKKIALLEPLLGYmQAQISFFKmGSENLNEQLEEFLANIGTSVQNVRREmDSDIETmQQTIEDLE 255
                                    22        32    |   42 |      52        62        |-       |82        92       102       112       122       132       142       152       162       172     ||182       192       202 |     212|      222       232       242    |  252   
                                                   37-MSE 44-MSE                     71       80 |                          111-MSE                                                            178-MSE                   204-MSE  213-MSE                    240-MSE  |        
                                                                                                82-MSE                       112-MSE                                                            179-MSE                                                             247-MSE    

   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 2Z0N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z0N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Z0N)

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A   (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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2z0n)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2z0n)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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
  2z0n
    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)
  616511
    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 2ela 2elb 2q12 2q13 2z0o 5c5b

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2Z0N)