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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HD-PTP BRO1 DOMAIN
 
Authors :  R. L. Mu, J. S. Jiang, G. Snyder, P. Smith, T. Xiao
Date :  28 Mar 11  (Deposition) - 14 Sep 11  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bro1 Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Sette, R. Mu, V. Dussupt, J. Jiang, G. Snyder, P. Smith, T. S. Xiao, F. Bouamr
The Phe105 Loop Of Alix Bro1 Domain Plays A Key Role In Hiv-1 Release.
Structure V. 19 1485 2011
PubMed-ID: 21889351  |  Reference-DOI: 10.1016/J.STR.2011.07.016

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 23
    ChainsA, B
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 2-361
    GenePTPN23, KIAA1471
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHIS DOMAIN-CONTAINING PROTEIN TYROSINE PHOSPHATASE, HD-PTP, PROTEIN TYROSINE PHOSPHATASE TD14, PTP-TD14

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1ACT8Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA B:208 , ALA B:249 , ALA B:252 , HIS B:253 , VAL B:333 , ACT B:365 , HOH B:470BINDING SITE FOR RESIDUE GOL B 362
02AC2SOFTWARELEU B:12 , ASP B:13 , PHE B:100BINDING SITE FOR RESIDUE ACT B 363
03AC3SOFTWARELEU A:12 , ASP A:13 , ILE A:99 , TRP A:237 , HOH A:508 , HOH A:531BINDING SITE FOR RESIDUE ACT A 362
04AC4SOFTWAREGLN B:209 , ASP B:212 , GLU B:216BINDING SITE FOR RESIDUE ACT B 364
05AC5SOFTWAREGLN A:209 , ASP A:212 , GLU A:216BINDING SITE FOR RESIDUE ACT A 363
06AC6SOFTWARELYS B:215 , ILE B:245 , TYR B:246 , LYS B:279 , GOL B:362BINDING SITE FOR RESIDUE ACT B 365
07AC7SOFTWARELYS A:215 , ILE A:245 , TYR A:246 , ALA A:249BINDING SITE FOR RESIDUE ACT A 364
08AC8SOFTWAREARG A:6 , HOH A:375 , LYS B:103BINDING SITE FOR RESIDUE ACT A 365
09AC9SOFTWAREHIS B:76 , GLN B:114 , TYR B:156BINDING SITE FOR RESIDUE ACT B 366
10BC1SOFTWAREGLY A:85 , SER A:86 , LYS A:111 , HOH A:371BINDING SITE FOR RESIDUE EDO A 366
11BC2SOFTWARELYS A:359 , ARG B:198BINDING SITE FOR RESIDUE EDO A 367

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BRO1PS51180 BRO1 domain profile.PTN23_HUMAN8-394
 
  2A:8-361
B:8-361

(-) Exons   (0, 0)

(no "Exon" information available for 3RAU)

(-) 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:358
 aligned with PTN23_HUMAN | Q9H3S7 from UniProtKB/Swiss-Prot  Length:1636

    Alignment length:358
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353        
          PTN23_HUMAN     4 VPRMPMIWLDLKEAGDFHFQPAVKKFVLKNYGENPEAYNEELKKLELLRQNAVRVPRDFEGCSVLRKYLGQLHYLQSRVPMGSGQEAAVPVTWTEIFSGKSVAHEDIKYEQACILYNLGALHSMLGAMDKRVSEEGMKVSCTHFQCAAGAFAYLREHFPQAYSVDMSRQILTLNVNLMLGQAQECLLEKSMLDNRKSFLVARISAQVVDYYKEACRALENPDTASLLGRIQKDWKKLVQMKIYYFAAVAHLHMGKQAEEQQKFGERVAYFQSALDKLNEAIKLAKGQPDTVQDALRFTMDVIGGKYNSAKKDNDFIYHEAVPALDTLQPVKGAPLVKPLPVNPTDPAVTGPDIFAKLV 361
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...........eeee......eeee.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh.................hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----BRO1  PDB: A:8-361 UniProt: 8-394                                                                                                                                                                                                                                                                                                                                  PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rau A   4 VPRMPMIWLDLKEAGDFHFQPAVKKFVLKNYGENPEAYNEELKKLELLRQNAVRVPRDFEGCSVLRKYLGQLHYLQSRVPMGSGQEAAVPVTWTEIFSGKSVAHEDIKYEQACILYNLGALHSMLGAMDKRVSEEGMKVSCTHFQCAAGAFAYLREHFPQAYSVDMSRQILTLNVNLMLGQAQECLLEKSMLDNRKSFLVARISAQVVDYYKEACRALENPDTASLLGRIQKDWKKLVQMKIYYFAAVAHLHMGKQAEEQQKFGERVAYFQSALDKLNEAIKLAKGQPDTVQDALRFTMDVIGGKYNSAKKDNDFIYHEAVPALDTLQPVKGAPLVKPLPVNPTDPAVTGPDIFAKLV 361
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353        

Chain B from PDB  Type:PROTEIN  Length:357
 aligned with PTN23_HUMAN | Q9H3S7 from UniProtKB/Swiss-Prot  Length:1636

    Alignment length:357
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       
          PTN23_HUMAN     5 PRMPMIWLDLKEAGDFHFQPAVKKFVLKNYGENPEAYNEELKKLELLRQNAVRVPRDFEGCSVLRKYLGQLHYLQSRVPMGSGQEAAVPVTWTEIFSGKSVAHEDIKYEQACILYNLGALHSMLGAMDKRVSEEGMKVSCTHFQCAAGAFAYLREHFPQAYSVDMSRQILTLNVNLMLGQAQECLLEKSMLDNRKSFLVARISAQVVDYYKEACRALENPDTASLLGRIQKDWKKLVQMKIYYFAAVAHLHMGKQAEEQQKFGERVAYFQSALDKLNEAIKLAKGQPDTVQDALRFTMDVIGGKYNSAKKDNDFIYHEAVPALDTLQPVKGAPLVKPLPVNPTDPAVTGPDIFAKLV 361
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.............eeee......eeee.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh.................hhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---BRO1  PDB: B:8-361 UniProt: 8-394                                                                                                                                                                                                                                                                                                                                  PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rau B   5 PRMPMIWLDLKEAGDFHFQPAVKKFVLKNYGENPEAYNEELKKLELLRQNAVRVPRDFEGCSVLRKYLGQLHYLQSRVPMGSGQEAAVPVTWTEIFSGKSVAHEDIKYEQACILYNLGALHSMLGAMDKRVSEEGMKVSCTHFQCAAGAFAYLREHFPQAYSVDMSRQILTLNVNLMLGQAQECLLEKSMLDNRKSFLVARISAQVVDYYKEACRALENPDTASLLGRIQKDWKKLVQMKIYYFAAVAHLHMGKQAEEQQKFGERVAYFQSALDKLNEAIKLAKGQPDTVQDALRFTMDVIGGKYNSAKKDNDFIYHEAVPALDTLQPVKGAPLVKPLPVNPTDPAVTGPDIFAKLV 361
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       

   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 3RAU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PTN23_HUMAN | Q9H3S7)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    GO:0030030    cell projection organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0060271    cilium assembly    The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0010633    negative regulation of epithelial cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell migration.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:1903393    positive regulation of adherens junction organization    Any process that activates or increases the frequency, rate or extent of adherens junction organization.
    GO:2000643    positive regulation of early endosome to late endosome transport    Any process that activates or increases the frequency, rate or extent of early endosome to late endosome transport.
    GO:1903387    positive regulation of homophilic cell adhesion    Any process that activates or increases the frequency, rate or extent of homophilic cell adhesion.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from 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:0030334    regulation of cell migration    Any process that modulates the frequency, rate or extent of cell migration.
    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.
cellular component
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0036064    ciliary basal body    A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodelling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport.
    GO:0005929    cilium    A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PTN23_HUMAN | Q9H3S75cru 5crv 5lm1 5lm2

(-) Related Entries Specified in the PDB File

3r9m CRYSTAL STRUCTURE OF THE BROX BRO1 DOMAIN