Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  YEAST BBC1 SH3 DOMAIN, TRICLINIC CRYSTAL FORM
 
Authors :  M. Wilmanns, L. Consani Textor, P. Kursula, I. Kursula, F. Lehmann, Y. H. Song
Date :  19 May 04  (Deposition) - 31 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
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 :  Sh3 Domain, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Wilmanns, L. Consani Textor, P. Kursula, I. Kursula, F. Lehmann, Y. H. Song
Crystal Structure Of Yeast Bbc1 Sh3 Domain, Triclinic Crystal Form
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MYOSIN TAIL REGION-INTERACTING PROTEIN MTI1
    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
    SynonymBBC1 PROTEIN

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1WDX)

(-) Sites  (0, 0)

(no "Site" information available for 1WDX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Val A:7 -Pro A:8
2Val B:7 -Pro B:8
3Val C:7 -Pro C:8
4Val D:7 -Pro D:8

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.BBC1_YEAST5-69
 
 
 
  4A:6-67
B:6-67
C:6-67
D:6-67
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.BBC1_YEAST5-69
 
 
 
  1A:6-67
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.BBC1_YEAST5-69
 
 
 
  1-
B:6-67
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.BBC1_YEAST5-69
 
 
 
  1-
-
C:6-67
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.BBC1_YEAST5-69
 
 
 
  1-
-
-
D:6-67

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YJL020C1YJL020C.1X:402404-3989313474BBC1_YEAST1-115711574A:5-67
B:5-67
C:5-67
D:5-67
63
63
63
63

(-) 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:63
 aligned with BBC1_YEAST | P47068 from UniProtKB/Swiss-Prot  Length:1157

    Alignment length:63
                                    13        23        33        43        53        63   
            BBC1_YEAST    4 PEVPFKVVAQFPYKSDYEDDLNFEKDQEIIVTSVEDAEWYFGEYQDSNGDVIEGIFPKSFVAV 66
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..................eeeeeee....eeeeeee.....eeeeeee...ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SH3  PDB: A:6-67 UniProt: 5-69                                 PROSITE
               Transcript 1 Exon 1.1  PDB: A:5-67 UniProt: 1-1157 [INCOMPLETE]              Transcript 1
                  1wdx A  5 PEVPFKVVAQFPYKSDYEDDLNFEKDQEIIVTSVEDAEWYFGEYQDSNGDVIEGIFPKSFVAV 67
                                    14        24        34        44        54        64   

Chain B from PDB  Type:PROTEIN  Length:63
 aligned with BBC1_YEAST | P47068 from UniProtKB/Swiss-Prot  Length:1157

    Alignment length:63
                                    13        23        33        43        53        63   
            BBC1_YEAST    4 PEVPFKVVAQFPYKSDYEDDLNFEKDQEIIVTSVEDAEWYFGEYQDSNGDVIEGIFPKSFVAV 66
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..................eeeeeee....eeeeeee.....eeeeeee...ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SH3  PDB: B:6-67 UniProt: 5-69                                 PROSITE
               Transcript 1 Exon 1.1  PDB: B:5-67 UniProt: 1-1157 [INCOMPLETE]              Transcript 1
                  1wdx B  5 PEVPFKVVAQFPYKSDYEDDLNFEKDQEIIVTSVEDAEWYFGEYQDSNGDVIEGIFPKSFVAV 67
                                    14        24        34        44        54        64   

Chain C from PDB  Type:PROTEIN  Length:63
 aligned with BBC1_YEAST | P47068 from UniProtKB/Swiss-Prot  Length:1157

    Alignment length:63
                                    13        23        33        43        53        63   
            BBC1_YEAST    4 PEVPFKVVAQFPYKSDYEDDLNFEKDQEIIVTSVEDAEWYFGEYQDSNGDVIEGIFPKSFVAV 66
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..................eeeeeee....eeeeeee.....eeeeeee...ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SH3  PDB: C:6-67 UniProt: 5-69                                 PROSITE
               Transcript 1 Exon 1.1  PDB: C:5-67 UniProt: 1-1157 [INCOMPLETE]              Transcript 1
                  1wdx C  5 PEVPFKVVAQFPYKSDYEDDLNFEKDQEIIVTSVEDAEWYFGEYQDSNGDVIEGIFPKSFVAV 67
                                    14        24        34        44        54        64   

Chain D from PDB  Type:PROTEIN  Length:63
 aligned with BBC1_YEAST | P47068 from UniProtKB/Swiss-Prot  Length:1157

    Alignment length:63
                                    13        23        33        43        53        63   
            BBC1_YEAST    4 PEVPFKVVAQFPYKSDYEDDLNFEKDQEIIVTSVEDAEWYFGEYQDSNGDVIEGIFPKSFVAV 66
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
           Pfam domains (1) -------SH3_1-1wdxD01 D:12-62                              ----- Pfam domains (1)
           Pfam domains (2) -------SH3_1-1wdxD02 D:12-62                              ----- Pfam domains (2)
           Pfam domains (3) -------SH3_1-1wdxD03 D:12-62                              ----- Pfam domains (3)
           Pfam domains (4) -------SH3_1-1wdxD04 D:12-62                              ----- Pfam domains (4)
         Sec.struct. author ....eeeee..................eeeeeee....eeeeeee.....eeeeeee...ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SH3  PDB: D:6-67 UniProt: 5-69                                 PROSITE
               Transcript 1 Exon 1.1  PDB: D:5-67 UniProt: 1-1157 [INCOMPLETE]              Transcript 1
                  1wdx D  5 PEVPFKVVAQFPYKSDYEDDLNFEKDQEIIVTSVEDAEWYFGEYQDSNGDVIEGIFPKSFVAV 67
                                    14        24        34        44        54        64   

   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 1WDX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WDX)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: SH3 (175)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (BBC1_YEAST | P47068)
molecular function
    GO:0017024    myosin I binding    Interacting selectively and non-covalently with a class I myosin; myosin I heavy chains are single-headed, possess tails of various lengths, and do not self-associate into bipolar filaments.
    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:0030036    actin cytoskeleton 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 and their associated proteins.
    GO:0007010    cytoskeleton 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.
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.

 Visualization

(-) Interactive Views

Asymmetric 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
(no "Ligands, Modified Residues, Ions" information available for 1wdx)
 
  Sites
(no "Sites" information available for 1wdx)
 
  Cis Peptide Bonds
    Val A:7 - Pro A:8   [ RasMol ]  
    Val B:7 - Pro B:8   [ RasMol ]  
    Val C:7 - Pro C:8   [ RasMol ]  
    Val D:7 - Pro D:8   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) 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
  1wdx
    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
  BBC1_YEAST | P47068
    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
  BBC1_YEAST | P47068
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        BBC1_YEAST | P470681tg0 1zuk 2dyf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1WDX)