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(-) Description

Title :  ATOMIC-RESOLUTION STRUCTURE OF THE YEAST SLA1 SH3 DOMAIN 3
 
Authors :  I. Kursula, P. Kursula, P. Zou, F. Lehmann, Y. H. Song, M. Wilmanns
Date :  29 May 07  (Deposition) - 03 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Phosphorylation, Structural Protein, Yeast, Sh3 Domain, Cytoskeleton, Actin-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Kursula, I. Kursula, N. Pinotsis, F. Lehmann, P. Zou, Y. H. Song, M. Wilmanns
Structural Genomics Of Yeast Sh3 Domains
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CYTOSKELETON ASSEMBLY CONTROL PROTEIN SLA1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24D
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: SH3 DOMAIN 3, RESIDUES 357-413
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: SLA1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2NA1Ligand/IonSODIUM ION
3PT2Ligand/IonPLATINUM (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
3PT-1Ligand/IonPLATINUM (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
3PT-1Ligand/IonPLATINUM (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:32 , SER A:35 , LYS A:36 , TRP A:39 , HOH A:2050BINDING SITE FOR RESIDUE NA A1061
2AC2SOFTWAREPT B:1061 , HOH B:2002 , HOH B:2015BINDING SITE FOR RESIDUE CL B1062
3AC3SOFTWAREMET B:12 , CL B:1062BINDING SITE FOR RESIDUE PT B1061
4AC4SOFTWAREMET A:12BINDING SITE FOR RESIDUE PT A1062

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V1Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V1Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V1Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V1Q)

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YBL007C1YBL007C.1II:216369-2126353735SLA1_YEAST1-124412442A:1-60
B:3-60		60
58

(-) Sequences/Alignments

Asymmetric 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 SLA1_YEAST | P32790 from UniProtKB/Swiss-Prot  Length:1244

    Alignment length:60
                                   363       373       383       393       403       413
           SLA1_YEAST   354 SKKRGIVQYDFMAESQDELTIKSGDKVYILDDKKSKDWWMCQLVDSGKSGLVPAQFIEPV 413
               SCOP domains d2v1qa_ A: automated matches                                 SCOP domains
               CATH domains 2v1qA00 A:1-60 SH3 Domains                                   CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..................eeeeee......eeeeee.....eeeee...eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-60 UniProt: 1-1244 [INCOMPLETE]           Transcript 1
                 2v1q A   1 GMERGIVQYDFMAESQDELTIKSGDKVYILDDKKSKDWWMCQLVDSGKSGLVPAQFIEPV  60
                                    10        20        30        40        50        60


Chain B from PDB  Type:PROTEIN  Length:58
 aligned with SLA1_YEAST | P32790 from UniProtKB/Swiss-Prot  Length:1244

    Alignment length:58
                                   365       375       385       395       405        
           SLA1_YEAST   356 KRGIVQYDFMAESQDELTIKSGDKVYILDDKKSKDWWMCQLVDSGKSGLVPAQFIEPV 413
               SCOP domains d2v1qb_ B: automated matches                               SCOP domains
               CATH domains 2v1qB00 B:3-60 SH3 Domains                                 CATH domains
           Pfam domains (1) ---SH3_1-2v1qB01 B:6-54                             ------ Pfam domains (1)
           Pfam domains (2) ---SH3_1-2v1qB02 B:6-54                             ------ Pfam domains (2)
         Sec.struct. author .eeee..................eeeeee......eeeeee.....eeeee...eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-60 UniProt: 1-1244 [INCOMPLETE]         Transcript 1
                 2v1q B   3 ERGIVQYDFMAESQDELTIKSGDKVYILDDKKSKDWWMCQLVDSGKSGLVPAQFIEPV  60
                                    12        22        32        42        52
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: SH3 (175)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,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
        SLA1_YEAST | P32790: 1ssh 1z9z 2hbp 2jt4 3idw

(-) Related Entries Specified in the PDB File

1ssh CRYSTAL STRUCTURE OF THE SH3 DOMAIN FROM A S. CEREVISIAEHYPOTHETICAL 40.4 KDA PROTEIN IN COMPLEX WITH A PEPTIDE