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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN VPS25-VPS20 SUBCOMPLEX
 
Authors :  Y. J. Im, J. H. Hurley
Date :  12 Jun 09  (Deposition) - 25 Aug 09  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Escrt-Ii, Escrt-Iii, Vps20, Vps25, Mvb, Cytoplasm, Nucleus, Polymorphism, Protein Transport, Transcription, Transcription Regulation, Transport, Coiled Coil, Endosome, Lipoprotein, Membrane, Myristate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. J. Im, T. Wollert, E. Boura, J. H. Hurley
Structure And Function Of The Escrt-Ii-Iii Interface In Multivesicular Body Biogenesis.
Dev. Cell V. 17 234 2009
PubMed-ID: 19686684  |  Reference-DOI: 10.1016/J.DEVCEL.2009.07.008
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VACUOLAR PROTEIN-SORTING-ASSOCIATED PROTEIN 25
    Chains: A, C, E, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PST39
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: THE C-TERMINAL WH2 DOMAIN OF VPS25: UNP RESIDUES 102-176
    Gene: DERP9, EAP20, VPS25
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HVPS25, ESCRT-II COMPLEX SUBUNIT VPS25, ELL- ASSOCIATED PROTEIN OF 20 KDA, DERMAL PAPILLA-DERIVED PROTEIN 9
 
Molecule 2 - VACUOLAR PROTEIN-SORTING-ASSOCIATED PROTEIN 20
    Chains: B, D, F, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PST39
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: THE FIRST HELIX OF VPS20: UNP RESIDUES 11-48
    Gene: CHMP6, VPS20
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CHROMATIN-MODIFYING PROTEIN 6, CHARGED MULTIVESICULAR BODY PROTEIN 6, VPS20, HVPS20

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3HTU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HTU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HTU)

(-) Exons   (0, 0)

(no "Exon" information available for 3HTU)

(-) 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:75
 aligned with VPS25_HUMAN | Q9BRG1 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:75
                                   111       121       131       141       151       161       171     
          VPS25_HUMAN   102 RRPEEWGKLIYQWVSRSGQNNSVFTLYELTNGEDTEDEEFHGLDEATLLRALQALQQEHKAEIITVSDGRGVKFF 176
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh......eehhhhhhhh...........hhhhhhhhhhhhhhh..eeee......eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 3htu A 102 RRPEEWGKLIYQWVSRSGQNNSVFTLYELTNGEDTEDEEFHGLDEATLLRALQALQQEHKAEIITVSDGRGVKFF 176
                                   111       121       131       141       151       161       171     


Chain B from PDB  Type:PROTEIN  Length:35
 aligned with CHMP6_HUMAN | Q96FZ7 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:39
                                    15        25        35         
          CHMP6_HUMAN     6 GRKKQSRVTEQDKAILQLKQQRDKLRQYQKRIAQQLERE  44
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author .----...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                 3htu B  10 G----SRVTEQDKAILQLKQQRDKLRQYQKRIAQQLERE  44
                            |    |  15        25        35         
                            |   11                                 
                           10                                      


Chain C from PDB  Type:PROTEIN  Length:75
 aligned with VPS25_HUMAN | Q9BRG1 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:75
                                   111       121       131       141       151       161       171     
          VPS25_HUMAN   102 RRPEEWGKLIYQWVSRSGQNNSVFTLYELTNGEDTEDEEFHGLDEATLLRALQALQQEHKAEIITVSDGRGVKFF 176
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....eeehhhhhhh...........hhhhhhhhhhhhh....eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 3htu C 102 RRPEEWGKLIYQWVSRSGQNNSVFTLYELTNGEDTEDEEFHGLDEATLLRALQALQQEHKAEIITVSDGRGVKFF 176
                                   111       121       131       141       151       161       171     


Chain D from PDB  Type:PROTEIN  Length:36
 aligned with CHMP6_HUMAN | Q96FZ7 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:40
                                    15        25        35        45
          CHMP6_HUMAN     6 GRKKQSRVTEQDKAILQLKQQRDKLRQYQKRIAQQLERER  45
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author .----...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 3htu D  10 G----SRVTEQDKAILQLKQQRDKLRQYQKRIAQQLERER  45
                            |    |  15        25        35        45
                           10   11                                  


Chain E from PDB  Type:PROTEIN  Length:75
 aligned with VPS25_HUMAN | Q9BRG1 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:75
                                   111       121       131       141       151       161       171     
          VPS25_HUMAN   102 RRPEEWGKLIYQWVSRSGQNNSVFTLYELTNGEDTEDEEFHGLDEATLLRALQALQQEHKAEIITVSDGRGVKFF 176
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh......eeehhhhhhhhhhh.......hhhhhhhhhhhhhhh..eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 3htu E 102 RRPEEWGKLIYQWVSRSGQNNSVFTLYELTNGEDTEDEEFHGLDEATLLRALQALQQEHKAEIITVSDGRGVKFF 176
                                   111       121       131       141       151       161       171     


Chain F from PDB  Type:PROTEIN  Length:32
 aligned with CHMP6_HUMAN | Q96FZ7 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:36
                                    15        25        35      
          CHMP6_HUMAN     6 GRKKQSRVTEQDKAILQLKQQRDKLRQYQKRIAQQL  41
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author .----...hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                 3htu F  10 G----SRVTEQDKAILQLKQQRDKLRQYQKRIAQQL  41
                            |    |  15        25        35      
                           10   11                              


Chain G from PDB  Type:PROTEIN  Length:75
 aligned with VPS25_HUMAN | Q9BRG1 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:75
                                   111       121       131       141       151       161       171     
          VPS25_HUMAN   102 RRPEEWGKLIYQWVSRSGQNNSVFTLYELTNGEDTEDEEFHGLDEATLLRALQALQQEHKAEIITVSDGRGVKFF 176
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....eeehhhhhhh...........hhhhhhhhhhhhhhh..eeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 3htu G 102 RRPEEWGKLIYQWVSRSGQNNSVFTLYELTNGEDTEDEEFHGLDEATLLRALQALQQEHKAEIITVSDGRGVKFF 176
                                   111       121       131       141       151       161       171     


Chain H from PDB  Type:PROTEIN  Length:36
 aligned with CHMP6_HUMAN | Q96FZ7 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:40
                                    15        25        35        45
          CHMP6_HUMAN     6 GRKKQSRVTEQDKAILQLKQQRDKLRQYQKRIAQQLERER  45
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author .----...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 3htu H  10 G----SRVTEQDKAILQLKQQRDKLRQYQKRIAQQLERER  45
                            |    |  15        25        35        45
                           10   11
   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 3HTU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 46)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E,G   (VPS25_HUMAN | Q9BRG1)
molecular function
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) 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).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    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: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:0043328    protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway    The process of directing proteins towards the vacuole that contributes to protein catabolism via the multivesicular body (MVB) pathway.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:1903900    regulation of viral life cycle    Any process that modulates the frequency, rate or extent of viral life cycle.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    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.
cellular component
    GO:0000814    ESCRT II complex    An endosomal sorting complex required for transport and functions downstream of ESCRT I complex. It consists of the class E vacuolar protein sorting (Vps) proteins and is required for the membrane recruitment of ESCRT III complex and binds to ubiquitinated cargoes.
    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: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.

Chain B,D,F,H   (CHMP6_HUMAN | Q96FZ7)
molecular function
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) 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:1904902    ESCRT III complex assembly    The aggregation, arrangement and bonding together of a set of components to form an ESCRT III complex.
    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: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: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: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:1903541    regulation of exosomal secretion    Any process that modulates the frequency, rate or extent of exosomal secretion.
    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:0039702    viral budding via host ESCRT complex    Viral budding which uses a host ESCRT protein complex, or complexes, to mediate the budding process.
    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:0000815    ESCRT III complex    An endosomal sorting complex required for transport. Consists of two soluble subcomplexes of highly charged coiled-coil proteins and is required for sorting and/or concentration of multivesicular body (MVB) 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:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    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: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.

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  3htu
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  CHMP6_HUMAN | Q96FZ7
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  VPS25_HUMAN | Q9BRG1
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 Related Entries

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

UniProtKB/Swiss-Prot
        CHMP6_HUMAN | Q96FZ7: 2k3w
        VPS25_HUMAN | Q9BRG1: 2zme 3cuq

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3HTU)