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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SH3 DOMAIN FROM A S. CEREVISIAE HYPOTHETICAL 40.4 KDA PROTEIN IN COMPLEX WITH A PEPTIDE
 
Authors :  P. Kursula, I. Kursula, F. Lehmann, Y. -H. Song, M. Wilmanns
Date :  24 Mar 04  (Deposition) - 12 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sh3 Domain, Yeast, Structural Genomics, Protein-Peptide Complex, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Kursula, I. Kursula, F. Lehmann, Y. -H. Song, M. Wilmanns
Yeast Sh3 Domain Structural Genomics
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL 40.4 KDA PROTEIN IN PES4-HIS2 INTERGENIC REGION
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST17
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SH3 DOMAIN
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
 
Molecule 2 - 12-MER PEPTIDE FROM CYTOSKELETON ASSEMBLY CONTROL PROTEIN SLA1
    Chains: B
    Engineered: YES
    Other Details: SYNTHETIC 12-AA PEPTIDE FROM YEAST SLA1
    Synonym: 12-RESIDUE PEPTIDE FROM SLA1
    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 1SSH)

(-) Sites  (0, 0)

(no "Site" information available for 1SSH)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SSH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SSH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SSH)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.LSB3_YEAST400-459  1A:2-60

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YBL007C1YBL007C.1II:216369-2126353735SLA1_YEAST1-124412441B:2-1211
2.1YFR024C-A1YFR024C-A.1VI:203421-20337547LSB3_YEAST1-16160--
2.2YFR024C-A2YFR024C-A.2VI:203280-2019481333LSB3_YEAST16-4594441A:1-60 (gaps)70

(-) 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:60
 aligned with LSB3_YEAST | P43603 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:70
                                   399       409       419       429       439       449       459
           LSB3_YEAST   390 GRFTAPTSPSTSSPKAVALYSFAGEESGDLPFRKGDVITILKKSDSQNDWWTGRVNGREGIFPANYVELV 459
               SCOP domains d          1ssha_ A: automated matches                                 SCOP domains
               CATH domains 1          sshA00 A:1-60 SH3 Domains                                   CATH domains
               Pfam domains ----------------SH3_1-1sshA01 A:7-54                            ------ Pfam domains
         Sec.struct. author .----------...eeee..................eeeeee.......eeeeee..eeeeee...eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------SH3  PDB: A:2-60 UniProt: 400-459                            PROSITE
               Transcript 2 Exon 2.2  PDB: A:1-60 (gaps) UniProt: 16-459 [INCOMPLETE]              Transcript 2
                 1ssh A   1 G----------SSPKAVALYSFAGEESGDLPFRKGDVITILKKSDSQNDWWTGRVNGREGIFPANYVELV  60
                            |        - |      10        20        30        40        50        60
                            |          2                                                          
                            1                                                                     


Chain B from PDB  Type:PROTEIN  Length:11
 aligned with SLA1_YEAST | P32790 from UniProtKB/Swiss-Prot  Length:1244

    Alignment length:11
                                   201 
           SLA1_YEAST   192 GPPPAMPARPT 202
               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 1 Exon 1.1    Transcript 1
                 1ssh B   2 GPPPAMPARPT  12
                                    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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (25, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LSB3_YEAST | P43603)
molecular function
    GO:0051015    actin filament binding    Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    GO:0035091    phosphatidylinositol binding    Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    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:0051666    actin cortical patch localization    Any process in which actin cortical patches are transported to, or maintained in, a specific location. An actin cortical patch is a discrete actin-containing structure found just beneath the plasma membrane in fungal cells.
    GO:0051017    actin filament bundle assembly    The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness.
    GO:1900027    regulation of ruffle assembly    Any process that modulates the frequency, rate or extent of ruffle assembly.
cellular component
    GO:0030479    actin cortical patch    An endocytic patch that consists of an actin-containing structure found at the plasma membrane in cells; formed of networks of branched actin filaments that lie just beneath the plasma membrane and assemble, move, and disassemble rapidly. An example of this is the actin cortical patch found in Saccharomyces cerevisiae.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.

Chain B   (SLA1_YEAST | P32790)
molecular function
    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: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:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
    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.
biological process
    GO:0000147    actin cortical patch assembly    Assembly of an actin cortical patch, a discrete actin-containing structure found at the plasma membrane of fungal cells.
    GO:0030041    actin filament polymerization    Assembly of actin filaments by the addition of actin monomers to a filament.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
cellular component
    GO:0030479    actin cortical patch    An endocytic patch that consists of an actin-containing structure found at the plasma membrane in cells; formed of networks of branched actin filaments that lie just beneath the plasma membrane and assemble, move, and disassemble rapidly. An example of this is the actin cortical patch found in Saccharomyces cerevisiae.
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    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:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LSB3_YEAST | P43603: 1oot
        SLA1_YEAST | P32790: 1z9z 2hbp 2jt4 2v1q 3idw

(-) Related Entries Specified in the PDB File

1oot 1ruw 1va7