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(-) Description

Title :  YEAST MYO3 SH3 DOMAIN, TRICLINIC CRYSTAL FORM
 
Authors :  P. Kursula, F. Lehmann, Y. H. Song, M. Wilmanns
Date :  12 Feb 04  (Deposition) - 14 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Structural Genomics, Sh3 Domain, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Kursula, F. Lehmann, Y. H. Song, M. Wilmanns
High-Throughput Structural Genomics Of Yeast Sh3 Domains
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MYOSIN-3 ISOFORM
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDEST17
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSH3 DOMAIN
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymMYO3

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU C:20BINDING SITE FOR RESIDUE GOL C 71

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VA7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VA7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VA7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VA7)

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YKL129C1YKL129C.1XI:200163-1963483816MYO3_YEAST1-127112714A:3-70
B:3-70
C:3-62
D:3-62
68
68
60
60

(-) 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:68
 aligned with MYO3_YEAST | P36006 from UniProtKB/Swiss-Prot  Length:1272

    Alignment length:68
                                  1131      1141      1151      1161      1171      1181        
          MYO3_YEAST   1122 DPKFEAAYDFPGSGSSSELPLKKGDIVFISRDEPSGWSLAKLLDGSKEGWVPTAYMTPYKDTRNTVPV 1189
               SCOP domains d1va7a_ A: automated matches                                         SCOP domains
               CATH domains 1va7A01 A:3-61 SH3 Domains                                 --------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...................eeeeeee....eeeeee.....eeeee...eee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-70 UniProt: 1-1271 [INCOMPLETE]                   Transcript 1
                1va7 A    3 DPKFEAAYDFPGSGSSSELPLKKGDIVFISRDEPSGWSLAKLLDGSKEGWVPTAYMTPYKDTRNTVPV   70
                                    12        22        32        42        52        62        

Chain B from PDB  Type:PROTEIN  Length:68
 aligned with MYO3_YEAST | P36006 from UniProtKB/Swiss-Prot  Length:1272

    Alignment length:68
                                  1131      1141      1151      1161      1171      1181        
          MYO3_YEAST   1122 DPKFEAAYDFPGSGSSSELPLKKGDIVFISRDEPSGWSLAKLLDGSKEGWVPTAYMTPYKDTRNTVPV 1189
               SCOP domains d1va7b_ B: automated matches                                         SCOP domains
               CATH domains 1va7B01 B:3-61 SH3 Domains                                 --------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...................eeeeeee....eeeeee.....eeeee...eee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-70 UniProt: 1-1271 [INCOMPLETE]                   Transcript 1
                1va7 B    3 DPKFEAAYDFPGSGSSSELPLKKGDIVFISRDEPSGWSLAKLLDGSKEGWVPTAYMTPYKDTRNTVPV   70
                                    12        22        32        42        52        62        

Chain C from PDB  Type:PROTEIN  Length:60
 aligned with MYO3_YEAST | P36006 from UniProtKB/Swiss-Prot  Length:1272

    Alignment length:60
                                  1131      1141      1151      1161      1171      1181
          MYO3_YEAST   1122 DPKFEAAYDFPGSGSSSELPLKKGDIVFISRDEPSGWSLAKLLDGSKEGWVPTAYMTPYK 1181
               SCOP domains d1va7c_ C: automated matches                                 SCOP domains
               CATH domains 1va7C01 C:3-61 SH3 Domains                                 - CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...................eeeeeee....eeeeee.....eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: C:3-62 UniProt: 1-1271 [INCOMPLETE]           Transcript 1
                1va7 C    3 DPKFEAAYDFPGSGSSSELPLKKGDIVFISRDEPSGWSLAKLLDGSKEGWVPTAYMTPYK   62
                                    12        22        32        42        52        62

Chain D from PDB  Type:PROTEIN  Length:60
 aligned with MYO3_YEAST | P36006 from UniProtKB/Swiss-Prot  Length:1272

    Alignment length:60
                                  1131      1141      1151      1161      1171      1181
          MYO3_YEAST   1122 DPKFEAAYDFPGSGSSSELPLKKGDIVFISRDEPSGWSLAKLLDGSKEGWVPTAYMTPYK 1181
               SCOP domains d1va7d_ D: automated matches                                 SCOP domains
               CATH domains 1va7D01 D:3-61 SH3 Domains                                 - CATH domains
           Pfam domains (1) ---SH3_1-1va7D01 D:6-54                             -------- Pfam domains (1)
           Pfam domains (2) ---SH3_1-1va7D02 D:6-54                             -------- Pfam domains (2)
           Pfam domains (3) ---SH3_1-1va7D03 D:6-54                             -------- Pfam domains (3)
           Pfam domains (4) ---SH3_1-1va7D04 D:6-54                             -------- Pfam domains (4)
         Sec.struct. author ..eeee...................eeeeeee....eeeeee.....eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: D:3-62 UniProt: 1-1271 [INCOMPLETE]           Transcript 1
                1va7 D    3 DPKFEAAYDFPGSGSSSELPLKKGDIVFISRDEPSGWSLAKLLDGSKEGWVPTAYMTPYK   62
                                    12        22        32        42        52        62

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: SH3 (175)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (MYO3_YEAST | P36006)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    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:0000146    microfilament motor activity    Catalysis of movement along a microfilament, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP).
    GO:0003774    motor activity    Catalysis of the generation of force resulting either in movement along a microfilament or microtubule, or in torque resulting in membrane scission, coupled to the hydrolysis of a nucleoside triphosphate.
    GO:0017022    myosin binding    Interacting selectively and non-covalently with any part of a myosin complex; myosins are any of a superfamily of molecular motor proteins that bind to actin and use the energy of ATP hydrolysis to generate force and movement along actin filaments.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0007121    bipolar cellular bud site selection    The process of defining subsequent sites of bud emergence such that budding takes place at alternating poles of a budding cell.
    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.
    GO:0006887    exocytosis    A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
    GO:0031505    fungal-type cell wall organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the fungal-type cell wall.
    GO:0006970    response to osmotic stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.
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: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:0016459    myosin complex    A protein complex, formed of one or more myosin heavy chains plus associated light chains and other proteins, that functions as a molecular motor; uses the energy of ATP hydrolysis to move actin filaments or to move vesicles or other cargo on fixed actin filaments; has magnesium-ATPase activity and binds actin. Myosin classes are distinguished based on sequence features of the motor, or head, domain, but also have distinct tail regions that are believed to bind specific cargoes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MYO3_YEAST | P360061ruw 2btt

(-) Related Entries Specified in the PDB File

1ruw SPACE GROUP I222