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(-) Description

Title :  P1 CRYSTAL STRUCTURE OF THE N-TERMINAL R1-R7 OF MURINE MVP
 
Authors :  J. Querol-Audi, A. Casanas, I. Uson, D. Luque, J. R. Caston, I. Fita, N. V
Date :  17 Mar 09  (Deposition) - 10 Nov 09  (Release) - 22 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  B
Keywords :  Beta Sheets, Phosphoprotein, Ribonucleoprotein, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Querol-Audi, A. Casanas, I. Uson, D. Luque, J. R. Caston, I. Fita, N. Verdaguer
The Mechanism Of Vault Opening From The High Resolution Structure Of The N-Terminal Repeats Of Mvp
Embo J. V. 28 3450 2009
PubMed-ID: 19779459  |  Reference-DOI: 10.1038/EMBOJ.2009.274

(-) Compounds

Molecule 1 - MAJOR VAULT PROTEIN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P1
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentR1-R7 DOMAIN, UNP RESIDUES 1-383
    GeneMVP
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymMVP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3GNF)

(-) Sites  (0, 0)

(no "Site" information available for 3GNF)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GNF)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly B:31 -Pro B:32
2Gly B:147 -Pro B:148

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GNF)

(-) PROSITE Motifs  (1, 6)

Asymmetric/Biological Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MVPPS51224 MVP (vault) repeat profile.MVP_MOUSE4-54
56-116
117-169
170-222
223-277
279-327
328-383
384-436
  6-
B:56-116
B:117-169
B:170-222
B:223-277
B:279-327
B:328-380
-

(-) Exons   (0, 0)

(no "Exon" information available for 3GNF)

(-) 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 B from PDB  Type:PROTEIN  Length:365
 aligned with MVP_MOUSE | Q9EQK5 from UniProtKB/Swiss-Prot  Length:861

    Alignment length:376
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374      
            MVP_MOUSE     5 EAIIRIPPYHYIHVLDQNSNVSRVEVGPKTYIRQDNERVLFAPVRMVTVPPRHYCIVANPVSRDAQSSVLFDVTGQVRLRHADQEIRLAQDPFPLYPGELLEKDITPLQVVLPNTALHLKALLDFEDKNGDKVMAGDEWLFEGPGTYIPQKEVEVVEIIQATVIKQNQALRLRARKECFDRDGKERVTGEEWLVRSVGAYLPAVFEEVLDLVDAVILTEKTALHLRARQNFKDLRGVAHRTGEEWLVTVQDTEAHVPDVYEEVLGVVPITTLGPRHYCVILDPMGPDGKNQLGQKRVVKGEKSFFLQPGERLERGIQDVYVLSEQQGLLLKALQPLEEGEGEEKVAHQAGDRWLIRGPLEYVPSAKVEVVEERQAI 380
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeeee.....eeeee..eeee....eee....ee.eee...eeeeee.........................eeee..eeee......eeeeeeee.eee...eeeeeee...ee.....ee....eeeee..eee.....eeeeeeee.eee...eeeeeee...ee.....ee....eeee...eee.....eeeeeeee.ee....eeeeeee...ee.....ee....eeee......ee.....eeeeeeee.eee...eeeeee.............eeeee..eee......ee....ee.eee....eeeeee..-----------......eeee...eee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE MVP  PDB: - UniProt: 4-54                         -MVP  PDB: B:56-116 UniProt: 56-116                           MVP  PDB: B:117-169 UniProt: 117-169                 MVP  PDB: B:170-222 UniProt: 170-222                 MVP  PDB: B:223-277 UniProt: 223-277                   -MVP  PDB: B:279-327 UniProt: 279-327             MVP  PDB: B:328-380 UniProt: 328-383                  PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gnf B   5 EAIIRIPPYHYIHVLDQNSNVSRVEVGPKTYIRQDNERVLFAPVRMVTVPPRHYCIVANPVSRDAQSSVLFDVTGQVRLRHADQEIRLAQDPFPLYPGELLEKDITPLQVVLPNTALHLKALLDFEDKNGDKVMAGDEWLFEGPGTYIPQKEVEVVEIIQATVIKQNQALRLRARKECFDRDGKERVTGEEWLVRSVGAYLPAVFEEVLDLVDAVILTEKTALHLRARQNFKDLRGVAHRTGEEWLVTVQDTEAHVPDVYEEVLGVVPITTLGPRHYCVILDPMGPDGKNQLGQKRVVKGEKSFFLQPGERLERGIQDVYVLSEQQGLLLKALQ-----------AHQAGDRWLIRGPLEYVPSAKVEVVEERQAI 380
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334   |     -     | 354       364       374      
                                                                                                                                                                                                                                                                                                                                                                       338         350                              

   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 3GNF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GNF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GNF)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (MVP_MOUSE | Q9EQK5)
molecular function
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
biological process
    GO:0038127    ERBB signaling pathway    A series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptor tyrosine kinases on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0031953    negative regulation of protein autophosphorylation    Any process that stops, prevents or decreases the rate of the phosphorylation by a protein of one or more of its own residues.
    GO:0061099    negative regulation of protein tyrosine kinase activity    Any process that decreases the rate, frequency, or extent of protein tyrosine kinase activity.
    GO:0023057    negative regulation of signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process.
    GO:0072376    protein activation cascade    A response to a stimulus that consists of a sequential series of modifications to a set of proteins where the product of one reaction acts catalytically in the following reaction. The magnitude of the response is typically amplified at each successive step in the cascade. Modifications typically include proteolysis or covalent modification, and may also include binding events.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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: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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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  Cis Peptide Bonds
    Gly B:147 - Pro B:148   [ RasMol ]  
    Gly B:31 - Pro B:32   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        MVP_MOUSE | Q9EQK53gf5 3gng

(-) Related Entries Specified in the PDB File

3gf5 P21 CRYSTAL STRUCTURE OF MURINE R1-R7 MVP FRAGMENT
3gng P21B CRYSTAL STRUCTURE OF R1-R7 OF MURINE MVP