Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE BROX BRO1 DOMAIN IN COMPLEX WITH THE C-TERMINAL TAIL OF CHMP4B
 
Authors :  J. S. Jiang, R. L. Mu, T. Xiao
Date :  12 Nov 11  (Deposition) - 18 Apr 12  (Release) - 23 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Helix Of C-Terminal Tail Of Chmp4B, Escrt-Iii, Chmps, Membrane Protein-Transport Protein Complex, Brox (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Mu, V. Dussupt, J. Jiang, P. Sette, V. Rudd, W. Chuenchor, N. F. Bello F. Bouamr, T. S. Xiao
Two Distinct Binding Modes Define The Interaction Of Brox With The C-Terminal Tails Of Chmp5 And Chmp4B.
Structure V. 20 887 2012
PubMed-ID: 22484091  |  Reference-DOI: 10.1016/J.STR.2012.03.001

(-) Compounds

Molecule 1 - BRO1 DOMAIN-CONTAINING PROTEIN BROX
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentBROX BRO1 DOMAIN 2-377
    GeneBROFTI, BROX, C1ORF58
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBRO1 DOMAIN- AND CAAX MOTIF-CONTAINING PROTEIN
 
Molecule 2 - CHARGED MULTIVESICULAR BODY PROTEIN 4B
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentC-TERMINAL TAIL OF CHMP4B 121-224
    GeneC20ORF178, CHMP4B, SHAX1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCHROMATIN-MODIFYING PROTEIN 4B, CHMP4B, SNF7 HOMOLOG ASSOCIATED WITH ALIX 1, SNF7-2, HSNF7-2, VACUOLAR PROTEIN SORTING- ASSOCIATED PROTEIN 32-2, VPS32-2, HVPS32-2

 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 3UM3)

(-) Sites  (0, 0)

(no "Site" information available for 3UM3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UM3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3UM3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UM3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UM3)

(-) Exons   (0, 0)

(no "Exon" information available for 3UM3)

(-) 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:377
 aligned with BROX_HUMAN | Q5VW32 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:377
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       
           BROX_HUMAN     1 MTHWFHRNPLKATAPVSFNYYGVVTGPSASKICNDLRSSRARLLELFTDLSCNPEMMKNAADSYFSLLQGFINSLDESTQESKLRYIQNFKWTDTLQGQVPSAQQDAVFELISMGFNVALWYTKYASRLAGKENITEDEAKEVHRSLKIAAGIFKHLKESHLPKLITPAEKGRDLESRLIEAYVIQCQAEAQEVTIARAIELKHAPGLIAALAYETANFYQKADHTLSSLEPAYSAKWRKYLHLKMCFYTAYAYCYHGETLLASDKCGEAIRSLQEAEKLYAKAEALCKEYGETKGPGPTVKPSGHLFFRKLGNLVKNTLEKCQRENGFIYFQKIPTEAPQLELKANYGLVEPIPFEFPPTSVQWTPETLAAFDLTK 377
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhh.hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.................eee.........eee.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh...................................hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3um3 A   1 DTHWFHRNPLKATAPVSFNYYGVVTGPSASKICNDLRSSRARLLELFTDLSCNPEMMKNAADSYFSLLQGFINSLDESTQESKLRYIQNFKWTDTLQGQVPSAQQDAVFELISMGFNVALWYTKYASRLAGKENITEDEAKEVHRSLKIAAGIFKHLKESHLPKLITPAEKGRDLESRLIEAYVIQCQAEAQEVTIARAIELKHAPGLIAALAYETANFYQKADHTLSSLEPAYSAKWRKYLHLKMCFYTAYAYCYHGETLLASDKCGEAIRSLQEAEKLYAKAEALCKEYGETKGPGPTVKPSGHLFFRKLGNLVKNTLEKCQRENGFIYFQKIPTEAPQLELKANYGLVEPIPFEFPPTSVQWTPETLAAFDLTK 377
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       

Chain B from PDB  Type:PROTEIN  Length:18
 aligned with CHM4B_HUMAN | Q9H444 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:18
                                   216        
          CHM4B_HUMAN   207 KEEEDDDMKELENWAGSM 224
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 3um3 B 207 KEEEDDDMKELENWAGSM 224
                                   216        

   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 3UM3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UM3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UM3)

(-) Gene Ontology  (42, 44)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BROX_HUMAN | Q5VW32)
cellular component
    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   (CHM4B_HUMAN | Q9H444)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.
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: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:0010458    exit from mitosis    The cell cycle transition where a cell leaves M phase and enters a new G1 phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place.
    GO:0036438    maintenance of lens transparency    A homeostatic process in which the lens is maintained in a highly refractive, transparent state to allow for optimal focusing of light on the retina.
    GO:0090148    membrane fission    A process that is carried out at the cellular level which results in the separation of a single continuous membrane into two membranes.
    GO:0000281    mitotic cytokinesis    A cell cycle process that results in the division of the cytoplasm of a cell after mitosis, resulting in the separation of the original cell into two daughter cells.
    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:1902902    negative regulation of autophagosome assembly    Any process that stops, prevents or reduces the frequency, rate or extent of autophagosome assembly.
    GO:0060548    negative regulation of cell death    Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:1901215    negative regulation of neuron death    Any process that stops, prevents or reduces the frequency, rate or extent of neuron death.
    GO:0031468    nuclear envelope reassembly    The reformation of the nuclear envelope following its breakdown in the context of a normal process.
    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: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:0006620    posttranslational protein targeting to endoplasmic reticulum membrane    The targeting of proteins to a membrane that occurs after their translation. Some secretory proteins exhibit posttranslational transport into the endoplasmic reticulum (ER) lumen: they are synthesized in their entirety on free cytosolic ribosomes and then released into the cytosol, where they are bound by chaperones which keep them in an unfolded state, and subsequently are translocated across the ER membrane.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    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:0050792    regulation of viral process    Any process that modulates the rate or extent of the viral life cycle, the set of processes by which a virus reproduces and spreads among hosts.
    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:0090611    ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway    The chemical reactions and pathways resulting in the breakdown of a protein or peptide, via the multivesicular body (MVB) sorting pathway; proteins are sorted into MVBs, and delivered to a lysosome/vacuole for degradation. This process is independent of ubiquitination.
    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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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: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.
    GO:0030117    membrane coat    Any of several different proteinaceous coats that can associate with membranes. Membrane coats include those formed by clathrin plus an adaptor complex, the COPI and COPII complexes, and possibly others. They are found associated with membranes on many vesicles as well as other membrane features such as pits and perhaps tubules.
    GO:0030496    midbody    A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3um3)
 
  Sites
(no "Sites" information available for 3um3)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3um3)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3um3
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  BROX_HUMAN | Q5VW32
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  CHM4B_HUMAN | Q9H444
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  BROX_HUMAN | Q5VW32
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CHM4B_HUMAN | Q9H444
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        BROX_HUMAN | Q5VW323r9m 3uly 3um0 3um1 3um2 3zxp
        CHM4B_HUMAN | Q9H4443c3q 4abm

(-) Related Entries Specified in the PDB File

3r9m 3uly 3um0 3um1 3um2