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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TSG101 UEV DOMAIN IN COMPLEX WITH A HIV-1 PTAP PEPTIDE
 
Authors :  Y. J. Im, J. H. Hurley
Date :  09 Aug 10  (Deposition) - 01 Dec 10  (Release) - 01 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Tranport, Ubiquitin, Hiv-1 Gag, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. J. Im, L. Kuo, X. Ren, P. V. Burgos, X. Z. Zhao, F. Liu, T. R. Burke, J. S. Bonifacino, E. O. Freed, J. H. Hurley
Crystallographic And Functional Analysis Of The Escrt-I /Hiv-1 Gag Ptap Interaction.
Structure V. 18 1536 2010
PubMed-ID: 21070952  |  Reference-DOI: 10.1016/J.STR.2010.08.010

(-) Compounds

Molecule 1 - TUMOR SUSCEPTIBILITY GENE 101 PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGST2
    Expression System Strain: BL21(DE3) STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL UEV DOMAIN (UNP RESIDUES 2 TO 145)
    Gene: TSG101
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ESCRT-I COMPLEX SUBUNIT TSG101
 
Molecule 2 - GAG POLYPROTEIN
    Chains: B
    Engineered: YES
    Fragment: HIV-1 GAG PTAP MOTIF (5-13)
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMAN IMMUNODEFICIENCY VIRUS TYPE 1.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3OBU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:80 -Pro A:81
2His A:119 -Pro A:120

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UEVPS51322 UEV domain profile.TS101_HUMAN2-145  1A:2-145

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002519681aENSE00001129196chr11:18548489-18548322168TS101_HUMAN1-14141A:1-1414
1.2ENST000002519682ENSE00001106778chr11:18541150-1854106685TS101_HUMAN15-43291A:15-4329
1.3ENST000002519683ENSE00001615198chr11:18537711-1853764666TS101_HUMAN43-65231A:43-65 (gaps)23
1.4ENST000002519684ENSE00001604894chr11:18536388-18536225164TS101_HUMAN65-119551A:65-11955
1.5ENST000002519685ENSE00001631564chr11:18531212-18531089124TS101_HUMAN120-161421A:120-14526
1.6ENST000002519686ENSE00001601359chr11:18528470-1852840467TS101_HUMAN161-183230--
1.7bENST000002519687bENSE00001106774chr11:18524124-1852403392TS101_HUMAN183-214320--
1.8ENST000002519688ENSE00001106772chr11:18505619-18505417203TS101_HUMAN214-281680--
1.9ENST000002519689ENSE00001106782chr11:18503416-18503177240TS101_HUMAN282-361800--
1.10aENST0000025196810aENSE00001106781chr11:18502182-18501862321TS101_HUMAN362-390290--

(-) 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:142
 aligned with TS101_HUMAN | Q99816 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     
          TS101_HUMAN     1 MAVSESQLKKMVSKYKYRDLTVRETVNVITLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFSRP 145
               SCOP domains d3obua_ A: Tumor susceptibility gene 101 (TS   G101)                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh....hhhhhhhhhhhhhhhh..eeeeeee...---...eeeeeeeeeeeee..eeeeeeeeeee.........eeee.....eee.............hhhhhh......hhhhhhhhhhhhhhhh..eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -UEV  PDB: A:2-145 UniProt: 2-145                                                                                                                 PROSITE
           Transcript 1 (1) Exon 1.1a     Exon 1.2  PDB: A:15-43       ---------------------Exon 1.4  PDB: A:65-119 UniProt: 65-119                Exon 1.5  PDB: A:120-145   Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.3 UniProt: 43-65-------------------------------------------------------------------------------- Transcript 1 (2)
                 3obu A   1 SAVSESQLKKMVSKYKYRDLTVRETVNVITLYKDLKPVLDSYGT---GSRELMNLTGTIPVPYRGNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFSRP 145
                                    10        20        30        40   |   |50        60        70        80        90       100       110       120       130       140     
                                                                      44  48                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:9
 aligned with Q72497_9HIV1 | Q72497 from UniProtKB/TrEMBL  Length:500

    Alignment length:9
         Q72497_9HIV1   453 PEPTAPPEE 461
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 3obu B   5 PEPTAPPEE  13
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (66, 70)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TS101_HUMAN | Q99816)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0048306    calcium-dependent 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), in the presence of calcium.
    GO:0030374    ligand-dependent nuclear receptor transcription coactivator activity    The function of a transcription cofactor that activates transcription in conjuction with a ligand-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself.
    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:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    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.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
    GO:0046790    virion binding    Interacting selectively and non-covalently with a virion, either by binding to components of the capsid or the viral envelope.
biological process
    GO:0097352    autophagosome maturation    Removal of PI3P and Atg8/LC3 after the closure of the phagophore and before the fusion with the endosome/lysosome (e.g. mammals and insects) or vacuole (yeast), and that very likely destabilizes other Atg proteins and thus enables their efficient dissociation and recycling.
    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:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    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:0075733    intracellular transport of virus    The directed movement of a virus, or part of a virus, within the host cell.
    GO:0030216    keratinocyte differentiation    The process in which a relatively unspecialized cell acquires specialized features of a keratinocyte.
    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:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    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:1903543    positive regulation of exosomal secretion    Any process that activates or increases the frequency, rate or extent of exosomal secretion.
    GO:2000397    positive regulation of ubiquitin-dependent endocytosis    Any process that activates or increases the frequency, rate or extent of ubiquitin-dependent endocytosis.
    GO:1903774    positive regulation of viral budding via host ESCRT complex    Any process that activates or increases the frequency, rate or extent of viral budding via host ESCRT complex.
    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:1902188    positive regulation of viral release from host cell    Any process that activates or increases the frequency, rate or extent of viral release from host cell.
    GO:0006513    protein monoubiquitination    Addition of a single ubiquitin group to a protein.
    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:0043405    regulation of MAP kinase activity    Any process that modulates the frequency, rate or extent of MAP kinase activity.
    GO:0001558    regulation of cell growth    Any process that modulates the frequency, rate, extent or direction of cell growth.
    GO:1903551    regulation of extracellular exosome assembly    Any process that modulates the frequency, rate or extent of extracellular vesicular exosome assembly.
    GO:0040008    regulation of growth    Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.
    GO:1903772    regulation of viral budding via host ESCRT complex    Any process that modulates the frequency, rate or extent of viral budding via host ESCRT complex.
    GO:1902186    regulation of viral release from host cell    Any process that modulates the frequency, rate or extent of viral release from host cell.
    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: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: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.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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: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:0005771    multivesicular body    A type of 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: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: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.

Chain B   (Q72497_9HIV1 | Q72497)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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: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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    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:0039702    viral budding via host ESCRT complex    Viral budding which uses a host ESCRT protein complex, or complexes, to mediate the budding process.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019013    viral nucleocapsid    The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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  TS101_HUMAN | Q99816
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q72497_9HIV1 | Q72497: 1m9d 2buo 2jmg 2lf4 2nv3 3dph 3ds0 3ds1 3ds2 3ds3 3ds4 3ds5 3dtj 3p05 4dga 4dge
        TS101_HUMAN | Q99816: 1kpp 1kpq 1m4p 1m4q 1s1q 2f0r 3iv1 3obq 3obs 3obx 3p9g 3p9h 4eje 4yc1 4zny
UniProtKB/TrEMBL
        Q72497_9HIV1 | Q72497: 1l6n 1m9c 1m9e 1m9f 1m9x 1m9y 3obx 3p0a 5i4t 5mcz 5md0 5md1 5md2 5md3 5md4 5md5 5md6 5md7 5md8 5md9 5mda 5mdb 5mdc 5mdd 5mde 5mdf 5mdg

(-) Related Entries Specified in the PDB File

1m4q NMR STRUCTURE OF THE SAME PROTEIN COMPLEX
3obq CRYSTAL STRUCTURE OF THE TSG101 UEV DOMAIN IN COMPLEX WITH A HUMAN HRS PSAP PEPTIDE
3obs
3obx