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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE SECOND SH3 DOMAIN FROM PONSIN
 
Authors :  N. Pinotsis, M. Wilmanns, I. Margiolaki
Date :  30 Nov 06  (Deposition) - 23 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Sh3, Ponsin, Src Homology 3, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. Margiolaki, J. P. Wright, M. Wilmanns, A. N. Fitch, N. Pinotsis
Second Sh3 Domain Of Ponsin Solved From Powder Diffraction
J. Am. Chem. Soc. V. 129 11865 2007
PubMed-ID: 17784760  |  Reference-DOI: 10.1021/JA073846C
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PONSIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET151
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentSRC HOMOLOGY 3 (SH3) DOMAIN
    GeneSORBS1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:852 , ARG A:862 , PRO A:864 , GLY A:865 , THR A:866 , HOH A:991BINDING SITE FOR RESIDUE FMT A 901
2AC2SOFTWAREASN A:833 , SER A:867 , GLN A:869 , HOH A:915 , HOH A:918 , HOH A:923BINDING SITE FOR RESIDUE FMT A 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O31)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2O31)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O31)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.SRBS1_HUMAN793-852
867-928
1231-1292
  1-
A:824-882
-

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003712471bENSE00001402421chr10:97321135-9732107759SRBS1_HUMAN-00--
1.3aENST000003712473aENSE00001802906chr10:97250877-9725079286SRBS1_HUMAN-00--
1.5aENST000003712475aENSE00002181580chr10:97200937-9720088355SRBS1_HUMAN1-440--
1.6ENST000003712476ENSE00001198082chr10:97197312-9719724766SRBS1_HUMAN4-26230--
1.7ENST000003712477ENSE00000810934chr10:97194474-9719437996SRBS1_HUMAN26-58330--
1.8ENST000003712478ENSE00001122732chr10:97192333-97192205129SRBS1_HUMAN58-101440--
1.9ENST000003712479ENSE00001122727chr10:97181973-9718194727SRBS1_HUMAN101-110100--
1.10aENST0000037124710aENSE00001122718chr10:97181830-97181718113SRBS1_HUMAN110-147380--
1.13bENST0000037124713bENSE00001352339chr10:97174619-97174251369SRBS1_HUMAN148-2701230--
1.15ENST0000037124715ENSE00000810940chr10:97170534-97170390145SRBS1_HUMAN271-319490--
1.16ENST0000037124716ENSE00001021690chr10:97165904-9716587530SRBS1_HUMAN319-329110--
1.17ENST0000037124717ENSE00001021693chr10:97158946-97158774173SRBS1_HUMAN329-386580--
1.18ENST0000037124718ENSE00000810948chr10:97157040-9715697764SRBS1_HUMAN387-408220--
1.19ENST0000037124719ENSE00000716757chr10:97154832-9715475875SRBS1_HUMAN408-433260--
1.20ENST0000037124720ENSE00000987298chr10:97154430-9715436863SRBS1_HUMAN433-454220--
1.23ENST0000037124723ENSE00000810949chr10:97144042-9714399548SRBS1_HUMAN454-470170--
1.24bENST0000037124724bENSE00000810954chr10:97143871-97143742130SRBS1_HUMAN470-513440--
1.25bENST0000037124725bENSE00000987285chr10:97141556-97141442115SRBS1_HUMAN513-551390--
1.26ENST0000037124726ENSE00000987299chr10:97135813-9713573084SRBS1_HUMAN552-579280--
1.27ENST0000037124727ENSE00000987300chr10:97131806-9713174166SRBS1_HUMAN580-601220--
1.28ENST0000037124728ENSE00000987301chr10:97131184-97131083102SRBS1_HUMAN602-635340--
1.29ENST0000037124729ENSE00000987286chr10:97127456-9712740750SRBS1_HUMAN636-652170--
1.30ENST0000037124730ENSE00000987287chr10:97117560-97117388173SRBS1_HUMAN652-710590--
1.31ENST0000037124731ENSE00001214532chr10:97114724-9711463986SRBS1_HUMAN710-738290--
1.32ENST0000037124732ENSE00000987296chr10:97111133-97110966168SRBS1_HUMAN739-794560--
1.33ENST0000037124733ENSE00000987289chr10:97106209-9710616347SRBS1_HUMAN795-810160--
1.34ENST0000037124734ENSE00000987290chr10:97101435-97101321115SRBS1_HUMAN810-848391A:818-8214
1.35ENST0000037124735ENSE00000987291chr10:97101167-97101042126SRBS1_HUMAN849-890421A:822-844 (gaps)30
1.36aENST0000037124736aENSE00000987292chr10:97099084-97098890195SRBS1_HUMAN891-955651A:845-88440
1.37aENST0000037124737aENSE00001214682chr10:97097051-97096278774SRBS1_HUMAN956-12132580--
1.39ENST0000037124739ENSE00000987293chr10:97081778-9708172059SRBS1_HUMAN1214-1233200--
1.40ENST0000037124740ENSE00000987294chr10:97078189-97078077113SRBS1_HUMAN1233-1271390--
1.41cENST0000037124741cENSE00001383385chr10:97074883-970715313353SRBS1_HUMAN1271-1292220--

(-) 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:67
 aligned with SRBS1_HUMAN | Q9BX66 from UniProtKB/Swiss-Prot  Length:1292

    Alignment length:91
                                   849       859       869       879       889       899       909       919       929 
          SRBS1_HUMAN   840 GIFPRTYIELLPPAEKAQPKKLTPVQVLEYGEAIAKFNFNGDTQVEMSFRKGERITLLRQVDENWYEGRIPGTSRQGIFPITYVDVIKRPL 930
               SCOP domains d2o3                 1a       _ A: automated matches                                        SCOP domains
               CATH domains 2o31                 A0       0 A:818-884 SH3 Domains                                       CATH domains
               Pfam domains ---------------------------------SH3_1-2o31A01 A:827-874                         ---------- Pfam domains
         Sec.struct. author ....-----------------..-------eeeee..................eeeeeee....eeeee......eeeee...eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE SH3  PDB: -  --------------SH3  PDB: A:824-882 UniProt: 867-928                          -- PROSITE
               Transcript 1 Exon 1.34Exon 1.35  PDB: A:822-844 (gaps)          Exon 1.36a  PDB: A:845-884 [INCOMPLETE]  Transcript 1
                 2o31 A 818 GIDP-----------------FT-------GEAIAKFNFNGDTQVEMSFRKGERITLLRQVDENWYEGRIPGTSRQGIFPITYVDVIKRPL 884
                               |     -         - ||      -|      833       843       853       863       873       883 
                             821               822|     824                                                            
                                                823                                                                    

   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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: SH3 (175)

(-) Gene Ontology  (37, 37)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SRBS1_HUMAN | Q9BX66)
molecular function
    GO:0005070    SH3/SH2 adaptor activity    Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68).
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0008092    cytoskeletal protein binding    Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
    GO:0005158    insulin receptor binding    Interacting selectively and non-covalently with the insulin receptor.
    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:0007015    actin filament organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
    GO:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    GO:0032869    cellular response to insulin stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0048041    focal adhesion assembly    The aggregation and bonding together of a set of components to form a focal adhesion, a complex of intracellular signaling and structural proteins that provides a structural link between the internal actin cytoskeleton and the ECM, and also function as a locus of signal transduction activity.
    GO:0015758    glucose transport    The directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    GO:0006936    muscle contraction    A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
    GO:0090004    positive regulation of establishment of protein localization to plasma membrane    Any process that increases the frequency, rate or extent of the directed movement of a protein to a specific location in the plasma membrane.
    GO:0046326    positive regulation of glucose import    Any process that activates or increases the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle.
    GO:0045725    positive regulation of glycogen biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen.
    GO:0046889    positive regulation of lipid biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.
    GO:0009967    positive regulation of signal transduction    Any process that activates or increases the frequency, rate or extent of signal transduction.
    GO:0043149    stress fiber assembly    The aggregation, arrangement and bonding together of a set of components to form a stress fiber. A stress fiber is a contractile actin filament bundle that consists of short actin filaments with alternating polarity.
    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:0005912    adherens junction    A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0005913    cell-cell adherens junction    An adherens junction which connects a cell to another cell.
    GO:0005924    cell-substrate adherens junction    An adherens junction which connects a cell to the extracellular matrix.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0005899    insulin receptor complex    A disulfide-bonded, heterotetrameric receptor complex. The alpha chains are entirely extracellular, while each beta chain has one transmembrane domain. The ligand binds to the alpha subunit extracellular domain and the kinase is associated with the beta subunit intracellular domain.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    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.
    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.
    GO:0001725    stress fiber    A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber.
    GO:0005915    zonula adherens    A cell-cell adherens junction which forms a continuous belt near the apex of epithelial cells.

 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
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2o31)
 

(-) 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
  2o31
    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
  SRBS1_HUMAN | Q9BX66
    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
  SRBS1_HUMAN | Q9BX66
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SRBS1_HUMAN | Q9BX662dl3 2ecz 2lj0 2lj1 2mox 2o2w 2o9s 2o9v 4ln2 4lnp

(-) Related Entries Specified in the PDB File

2o2w POWDER DIFFRACTION STRUCTURE