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(-) Description

Title :  LIP5-CHMP5
 
Authors :  J. J. Skalicky, W. I. Sundquist
Date :  29 Aug 12  (Deposition) - 28 Nov 12  (Release) - 27 Apr 16  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (10x)
NMR Structure *:  A,B  (1x)
Keywords :  Mit, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. J. Skalicky, J. Arii, D. M. Wenzel, W. M. Stubblefield, A. Katsuyama N. T. Uter, M. Bajorek, D. G. Myszka, W. I. Sundquist
Interactions Of The Human Lip5 Regulatory Protein With Endosomal Sorting Complexes Required For Transport.
J. Biol. Chem. V. 287 43910 2012
PubMed-ID: 23105106  |  Reference-DOI: 10.1074/JBC.M112.417899

(-) Compounds

Molecule 1 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VTA1 HOMOLOG
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPGEX
    FragmentUNP RESIDUES 1-168
    GeneC6ORF55, HSPC228, MY012, VTA1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDOPAMINE-RESPONSIVE GENE 1 PROTEIN, DRG-1, LYST-INTERACTING PROTEIN 5, LIP5, SKD1-BINDING PROTEIN 1, SBP1
 
Molecule 2 - CHARGED MULTIVESICULAR BODY PROTEIN 5
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET16B
    FragmentUNP RESIDUES 139-195
    GeneC9ORF83, CGI-34, CHMP5, HSPC177, PNAS-114, PNAS-2, SNF7DC2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCHROMATIN-MODIFYING PROTEIN 5, SNF7 DOMAIN-CONTAINING PROTEIN 2, VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 60, VPS60, HVPS60

 Structural Features

(-) Chains, Units

  12
NMR Structure (10x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2LXM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2LXM)

(-) Sequences/Alignments

NMR Structure
   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:163
 aligned with VTA1_HUMAN | Q9NP79 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   
           VTA1_HUMAN     1 MAALAPLPPLPAQFKSIQHHLRTAQEHDKRDPVVAYYCRLYAMQTGMKIDSKTPECRKFLSKLMDQLEALKKQLGDNEAITQEIVGCAHLENYALKMFLYADNEDRAGRFHKNMIKSFYTASLLIDVITVFGELTDENVKHRKYARWKATYIHNCLKNGETPQ 163
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2lxm A   1 MAALAPLPPLPAQFKSIQHHLRTAQEHDKRDPVVAYYCRLYAMQTGMKIDSKTPECRKFLSKLMDQLEALKKQLGDNEAITQEIVGCAHLENYALKMFLYADNEDRAGRFHKNMIKSFYTASLLIDVITVFGELTDENVKHRKYARWKATYIHNCLKNGETPQ 163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   

Chain B from PDB  Type:PROTEIN  Length:36
 aligned with CHMP5_HUMAN | Q9NZZ3 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:36
                                   163       173       183      
          CHMP5_HUMAN   154 GTPELDEDDLEAELDALGDELLADEDSSYLDEAASA 189
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                 2lxm B 154 GTPELDEDDLEAELDALGDELLADEDSSYLDEAASA 189
                                   163       173       183      

   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 2LXM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 42)

NMR Structure(hide GO term definitions)
Chain A   (VTA1_HUMAN | Q9NP79)
molecular function
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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).
biological process
    GO:1904903    ESCRT III complex disassembly    The disaggregation of an ESCRT III complex into its constituent components.
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0016197    endosomal transport    The directed movement of substances into, out of, or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation.
    GO:0036258    multivesicular body assembly    The aggregation, arrangement and bonding together of a set of components to form a multivesicular body, a type of late endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.
    GO:0071985    multivesicular body sorting pathway    A vesicle-mediated transport process in which transmembrane proteins are ubiquitylated to facilitate their entry into luminal vesicles of multivesicular bodies (MVBs); upon subsequent fusion of MVBs with lysosomes or vacuoles, the cargo proteins are degraded.
    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: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:0046755    viral budding    A viral process by which enveloped viruses acquire a host-derived membrane enriched in viral proteins to form their external envelope. The process starts when nucleocapsids, assembled or in the process of being built, induce formation of a membrane curvature in the host plasma or organelle membrane and wrap up in the forming bud. The process ends when the bud is eventually pinched off by membrane scission to release the enveloped particle into the lumenal or extracellular space.
    GO:0019058    viral life cycle    A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
cellular component
    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: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.

Chain B   (CHMP5_HUMAN | Q9NZZ3)
molecular function
    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).
biological process
    GO:1904903    ESCRT III complex disassembly    The disaggregation of an ESCRT III complex into its constituent components.
    GO:0000920    cell separation after cytokinesis    The process of physically separating progeny cells after cytokinesis; this may involve enzymatic digestion of septum or cell wall components.
    GO:0016197    endosomal transport    The directed movement of substances into, out of, or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation.
    GO:0008333    endosome to lysosome transport    The directed movement of substances from endosomes to lysosomes.
    GO:0007040    lysosome organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lysosome. A lysosome is a cytoplasmic, membrane-bounded organelle that is found in most animal cells and that contains a variety of hydrolases.
    GO:0007080    mitotic metaphase plate congression    The cell cycle process in which chromosomes are aligned at the metaphase plate, a plane halfway between the poles of the mitotic spindle, during mitosis.
    GO:0036258    multivesicular body assembly    The aggregation, arrangement and bonding together of a set of components to form a multivesicular body, a type of late endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.
    GO:0071985    multivesicular body sorting pathway    A vesicle-mediated transport process in which transmembrane proteins are ubiquitylated to facilitate their entry into luminal vesicles of multivesicular bodies (MVBs); upon subsequent fusion of MVBs with lysosomes or vacuoles, the cargo proteins are degraded.
    GO:0006997    nucleus organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
    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:0010824    regulation of centrosome duplication    Any process that modulates the frequency, rate or extent of centrosome duplication. Centrosome duplication is the replication of a centrosome, a structure comprised of a pair of centrioles and peri-centriolar material from which a microtubule spindle apparatus is organized.
    GO:1901673    regulation of mitotic spindle assembly    Any process that modulates the frequency, rate or extent of mitotic spindle assembly.
    GO:0001919    regulation of receptor recycling    Any process that modulates the frequency, rate, or extent of receptor recycling.
    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:0007034    vacuolar transport    The directed movement of substances into, out of or within a vacuole.
    GO:0046755    viral budding    A viral process by which enveloped viruses acquire a host-derived membrane enriched in viral proteins to form their external envelope. The process starts when nucleocapsids, assembled or in the process of being built, induce formation of a membrane curvature in the host plasma or organelle membrane and wrap up in the forming bud. The process ends when the bud is eventually pinched off by membrane scission to release the enveloped particle into the lumenal or extracellular space.
    GO:0019058    viral life cycle    A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
cellular component
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CHMP5_HUMAN | Q9NZZ33uly 3um0 3um1 3um2 4txr
        VTA1_HUMAN | Q9NP792lxl 4txp 4txq 4txr 4u7e

(-) Related Entries Specified in the PDB File

2lxl