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(-) Description

Title :  CRYSTAL STRUCTURE OF ERBB3 BINDING PROTEIN 1 (EBP1)
 
Authors :  T. P. Monie, A. J. Perrin, J. R. Birtley, S. Curry
Date :  16 Jul 07  (Deposition) - 21 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Translation Regulation, Translational Regulator, Rna-Binding, Acetylation, Rna Binding, Transcription, Cobalt, Nucleus, Repressor, Hydrolase, Cytoplasm, Transcription Regulator, Transcription Regulation, Phosphorylation, Rrna Processing, Ribonucleoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. P. Monie, A. J. Perrin, J. R. Birtley, T. R. Sweeney, I. Karakasiliotis, Y. Chaudry, L. O. Roberts, S. Matthews, I. G. Goodfellow, S. Curry
Structural Insights Into The Transcriptional And Translational Roles Of Ebp1
Embo J. V. 26 3936 2007
PubMed-ID: 17690690  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601817

(-) Compounds

Molecule 1 - PROLIFERATION-ASSOCIATED PROTEIN 2G4
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA (NOVAGEN)
    Expression System VectorPETM-11
    FragmentRESIDUES 7-359
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymERBB3 BINDING PROTEIN 1, PROLIFERATION-ASSOCIATED PROTEIN 1, PROTEIN P38-2G4, MPP1, IRES-SPECIFIC CELLULAR TRANS-ACTING FACTOR 45 KDA, ITAF45

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2V6C)

(-) Sites  (0, 0)

(no "Site" information available for 2V6C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V6C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V6C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V6C)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MAP_2PS01202 Methionine aminopeptidase subfamily 2 signature.PA2G4_MOUSE104-120  1A:104-120

(-) Exons   (11, 11)

Asymmetric/Biological Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENSMUST000000264251aENSMUSE00000150156chr10:128002990-128002796195PA2G4_MOUSE1-30301A:8-3023
1.2aENSMUST000000264252aENSMUSE00000150160chr10:128000761-128000633129PA2G4_MOUSE30-73441A:30-7344
1.2dENSMUST000000264252dENSMUSE00000150159chr10:128000385-128000280106PA2G4_MOUSE73-108361A:73-10836
1.3ENSMUST000000264253ENSMUSE00000268016chr10:128000191-12800012270PA2G4_MOUSE108-131241A:108-13124
1.4ENSMUST000000264254ENSMUSE00000150163chr10:127999975-12799988393PA2G4_MOUSE132-162311A:132-16231
1.5ENSMUST000000264255ENSMUSE00000150165chr10:127998038-12799797564PA2G4_MOUSE163-184221A:163-18422
1.6ENSMUST000000264256ENSMUSE00000150162chr10:127997793-12799771579PA2G4_MOUSE184-210271A:184-21027
1.7bENSMUST000000264257bENSMUSE00000479971chr10:127997350-127997138213PA2G4_MOUSE210-281721A:210-28172
1.8ENSMUST000000264258ENSMUSE00000885083chr10:127996588-12799649495PA2G4_MOUSE281-313331A:281-31333
1.9ENSMUST000000264259ENSMUSE00000150157chr10:127996413-127996286128PA2G4_MOUSE313-355431A:313-35543
1.10ENSMUST0000002642510ENSMUSE00000150161chr10:127996171-12799611854PA2G4_MOUSE356-373181A:356-3605
1.11ENSMUST0000002642511ENSMUSE00000150153chr10:127996027-1279948221206PA2G4_MOUSE374-394210--

(-) 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:353
 aligned with PA2G4_MOUSE | P50580 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:353
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357   
          PA2G4_MOUSE     8 QEQTIAEDLVVTKYKMGGDIANRVLRSLVEASSSGVSVLSLCEKGDAMIMEETGKIFKKEKEMKKGIAFPTSISVNNCVCHFSPLKSDQDYILKEGDLVKIDLGVHVDGFIANVAHTFVIGVAQGTQVTGRKADVIKAAHLCAEAALRLVKPGNQNTQVTEAWNKVAHSFNCTPIEGMLSHQLKQHVIDGEKTIIQNPTDQQKKDHEKAEFEVHEVYAVDVLVSSGEGKAKDAGQRTTIYKRDPSKQYGLKMKTSRAFFSEVERRFDAMPFTLRAFEDEKKARMGVVECAKHELLQPFNVLYEKEGEFVAQFKFTVLLMPNGPMRITSGPFEPDLYKSEMEVQDAELKALLQS 360
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------Peptidase_M24-2v6cA01 A:19-263                                                                                                                                                                                                                       ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..........eeeeeeeeeee..eee.................eeeeeeeeee..eeeeeeeeee..........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..ee....eeee..........eee...hhhhhhhh.........eeeeeeeee......ee......eeee.........hhhhhhhhhhhhhhh....ee.hhh.hhhhhhhhhhhhhhh..eeee..ee......eeeeeeeeeee..eeee......hhhh........hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------MAP_2            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:8-30 ------------------------------------------Exon 1.2d  PDB: A:73-108            -----------------------Exon 1.4  PDB: A:132-162       Exon 1.5              -------------------------Exon 1.7b  PDB: A:210-281 UniProt: 210-281                              -------------------------------Exon 1.9  PDB: A:313-355 UniProt: 313-355  1.10  Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.2a  PDB: A:30-73 UniProt: 30-73      ----------------------------------Exon 1.3  PDB: A:108-131----------------------------------------------------Exon 1.6  PDB: A:184-210   ----------------------------------------------------------------------Exon 1.8  PDB: A:281-313         ----------------------------------------------- Transcript 1 (2)
                 2v6c A   8 EEQTIAEDLVVTKYKMGGDIANRVLRSLVEASSSGVSVLSLCEKGDAMIMEETGKIFKKEKEMKKGIAFPTSISVNNCVCHFSPLKSDQDYILKEGDLVKIDLGVHVDGFIANVAHTFVIGVAQGTQVTGRKADVIKAAHLCAEAALRLVKPGNQNTQVTEAWNKVAHSFNCTPIEGMLSHQLKQHVIDGEKTIIQNPTDQQKKDHEKAEFEVHEVYAVDVLVSSGEGKAKDAGQRTTIYKRDPSKQYGLKMKTSRAFFSEVERRFDAMPFALRAFEDEKKARMGVVECAKHELLQPFNVLYEREGEFVAQFKFTVLLMPNGPMRITSGPFEPDLYKSEMEVQDAELKALLQS 360
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357   

   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 2V6C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V6C)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PA2G4_MOUSE | P50580)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045597    positive regulation of cell differentiation    Any process that activates or increases the frequency, rate or extent of cell differentiation.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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