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(-) Description

Title :  CRYSTAL STRUCTURE OF APPL1-BAR-PH DOMAIN
 
Authors :  K. Murayama, M. Kato-Murayama, T. Terada, 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 :  2.58
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, T. Terada, M. Shirouzu, S. Yokoyama
Crystal Structure Of Appl1-Bar-Ph 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 SystemCELL-FREE PROTEIN SYNTHESIS
    Expression System PlasmidPX061018-05
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-385
    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, 15)

Asymmetric Unit (1, 15)
No.NameCountTypeFull Name
1MSE15Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 30)
No.NameCountTypeFull Name
1MSE30Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2Z0O)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z0O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z0O)

 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  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.DP13A_HUMAN277-375  1A:277-372
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.DP13A_HUMAN277-375  2A:277-372

(-) Exons   (13, 13)

Asymmetric Unit (13, 13)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002882661aENSE00001277615chr3:57261765-57261965201DP13A_HUMAN1-18181A:1-1818
1.3ENST000002882663ENSE00001032931chr3:57269594-5726969299DP13A_HUMAN19-51331A:19-5133
1.4ENST000002882664ENSE00001032953chr3:57271520-5727157960DP13A_HUMAN52-71201A:52-7120
1.5aENST000002882665aENSE00001277569chr3:57272073-5727214472DP13A_HUMAN72-95241A:72-95 (gaps)24
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:235-28753
1.12ENST0000028826612ENSE00001032944chr3:57283388-57283576189DP13A_HUMAN288-351641A:298-34649
1.13ENST0000028826613ENSE00001032948chr3:57286297-5728633943DP13A_HUMAN351-365151A:352-36514
1.14ENST0000028826614ENSE00001632937chr3:57287710-5728776657DP13A_HUMAN366-384191A:366-3727
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:354
 aligned with DP13A_HUMAN | Q9UKG1 from UniProtKB/Swiss-Prot  Length:709

    Alignment length:372
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370  
          DP13A_HUMAN     1 MPGIDKLPIEETLEDSPQTRSLLGVFEEDATAISNYMNQLYQAMHRIYDAQNELSAATHLTSKLLKEYEKQRFPLGGDDEVMSSTLQQFSKVIDELSSCHAVLSTQLADAMMFPITQFKERDLKEILTLKEVFQIASNDHDAAINRYSRLSKKRENDKVKYEVTEDVYTSRKKQHQTMMHYFCALNTLQYKKKIALLEPLLGYMQAQISFFKMGSENLNEQLEEFLANIGTSVQNVRREMDSDIETMQQTIEDLEVASDPLYVPDPDPTKFPVNRNLTRKAGYLNARNKTGLVSSTWDRQFYFTQGGNLMSQARGDVAGGLAMDIDNCSVMAVDCEDRRYCFQITSFDGKKSSILQAESKKDHEEWICTINN 372
               SCOP domains d2z0oa1 A:1-273 automated matches                                                                                                                                                                                                                                                d2z0oa2 A:274-          372 automated matches                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......---hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................eeeeee.----------.eeeeeee..eeeee.......eeeee....eeeee.......eeeee.-----...ee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------N-------------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PH_DOMAIN  PDB: A:277-372 UniProt: 277-375                                                       PROSITE
           Transcript 1 (1) Exon 1.1a         Exon 1.3  PDB: A:19-51           Exon 1.4            Exon 1.5a UniProt: 72-95Exon 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   ----------------------------------------------------Exon 1.12  PDB: A:298-346 UniProt: 288-351 [INCOMPLETE]         --------------1.14    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------Exon 1.7       -----------------------------------------------------------------------------------------------Exon 1.11  PDB: A:235-287 UniProt: 235-288            --------------------------------------------------------------Exon 1.13      ------- Transcript 1 (2)
                 2z0o A   1 mPGIDKLPIEETLEDSPQTRSLLGVFEEDATAISNYmNQLYQAmHRIYDAQNELSAATHLTSKLLKEYEKQRFPL---DEVmSSTLQQFSKVIDELSSCHAVLSTQLADAmmFPITQFKERDLKEILTLKEVFQIASNDHDAAINRYSRLSKKRENDKVKYEVTEDVYTSRKKQHQTmmHYFCALNTLQYKKKIALLEPLLGYmQAQISFFKmGSENLNEQLEEFLANIGTSVQNVRREmDSDIETmQQTIEDLEVASDPLYVPDPDPTKFPVNRNLTRKAGYLNAR----------DRQFYFTQGGNLmSQARGDVAGGLAmDIDNCSVmAVDCEDRRYCFQITS-----SSILQAESKKDHEEWICTINN 372
                            |       10        20        30      | 40   |    50        60        70    |   80 |      90       100       110||     120       130       140       150       160       170       180       190       200   |   210  |    220       230       240      |250       260       270       280      |  -       300       310       320  |    330|      340     |   - |     360       370  
                            |                                  37-MSE 44-MSE                         75  79  |                          111-MSE                                                            178-MSE                   204-MSE  213-MSE                    240-MSE  |                                     287        298         310-MSE      323-MSE 331-MSE        346   352                    
                            1-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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z0O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Z0O)

(-) 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.

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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