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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MABP DOMAIN OF MVB12B OF HUMAN ESCRT-I COMPLEX
 
Authors :  E. Boura, J. H. Hurley
Date :  06 Sep 11  (Deposition) - 11 Jan 12  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.34
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Prism, Membrane Binding Domain, Negatively Charged Membrane, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Boura, J. H. Hurley
Structural Basis For Membrane Targeting By The Mvb12-Associated Beta-Prism Domain Of The Human Escrt-I Mvb12 Subunit.
Proc. Natl. Acad. Sci. Usa V. 109 1901 2012
PubMed-ID: 22232651  |  Reference-DOI: 10.1073/PNAS.1117597109

(-) Compounds

Molecule 1 - MULTIVESICULAR BODY SUBUNIT 12B
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRSFD
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 47-192
    GeneC9ORF28, FAM125B, MVB12B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymESCRT-I COMPLEX SUBUNIT MVB12B, PROTEIN FAM125B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

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(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MABPPS51498 MABP domain profile.MB12B_HUMAN47-193  1A:47-192

(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:152
 aligned with MB12B_HUMAN | Q9H7P6 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:152
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196  
          MB12B_HUMAN    47 MDPITGVGVVASRNRAPTGYDVVAQTADGVDADLWKDGLFKSKVTRYLCFTRSFSKENSHLGNVLVDMKLIDIKDTLPVGFIPIQETVDTQEVAFRKKRLCIKFIPRDSTEAAICDIRIMGRTKQAPPQYTFIGELNSMGIWYRMGRVPRNH 198
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..........ee........................eeeee......hhhh.eeeeeeeeee.........ee..............eeeeeeeee.hhh..eeeeeeeee........eeeeeee..eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE MABP  PDB: A:47-192 UniProt: 47-193                                                                                                                ----- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tow A  47 MDPITGVGVVASRNRAPTGYDVVAQTADGVDADLWKDGLFKSKVTRYLCFTRSFSKENSHLGNVLVDMKLIDIKDTLPVGFIPIQETVDTQEVAFRKKRLCIKFIPRDSTEAAICDIRIMGRTKQAPPQYTFIGELNSMGIWYRMGHHHHHH 198
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196  

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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MB12B_HUMAN | Q9H7P6)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    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:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
    GO:0048524    positive regulation of viral process    Any process that activates or increases the frequency, rate or extent of a multi-organism process in which a virus is a participant.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0042058    regulation of epidermal growth factor receptor signaling pathway    Any process that modulates the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0043162    ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway    The chemical reactions and pathways resulting in the breakdown of a protein or peptide covalently tagged with ubiquitin, via the multivesicular body (MVB) sorting pathway; ubiquitin-tagged proteins are sorted into MVBs, and delivered to a lysosome/vacuole for degradation.
    GO:0019075    virus maturation    The refolding and structural rearrangements of virion parts to transition from the intermediate virion to the more mature virion. Maturation usually involves proteolysis events and changes in the folding of the virion proteins. Can occur inside the host cell or after release.
cellular component
    GO:0000813    ESCRT I complex    An endosomal sorting complex required for transport. It consists of the class E vacuolar protein sorting (Vps) proteins and interacts with ubiquitinated cargoes.
    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:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    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:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    GO:0031902    late endosome membrane    The lipid bilayer surrounding a late endosome.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0031982    vesicle    Any small, fluid-filled, spherical organelle enclosed by membrane.

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