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(-) Description

Title :  SUPRAFACIAL ORIENTATION OF THE SCFCDC4 DIMER ACCOMMODATES MULTIPLE GEOMETRIES FOR SUBSTRATE UBIQUITINATION
 
Authors :  S. Orlicky, D. Neculai, D. Ceccarelli
Date :  16 Mar 07  (Deposition) - 19 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.67
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Ubiquitination, Helix Bundle, Scf Complex, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Tang, S. Orlicky, Z. Lin, A. Willems, D. Neculai, D. Ceccarelli, F. Mercurio, B. H. Shilton, F. Sicheri, M. Tyers
Suprafacial Orientation Of The Scfcdc4 Dimer Accommodates Multiple Geometries For Substrate Ubiquitination.
Cell(Cambridge, Mass. ) V. 129 1165 2007
PubMed-ID: 17574027  |  Reference-DOI: 10.1016/J.CELL.2007.04.042

(-) Compounds

Molecule 1 - CELL DIVISION CONTROL PROTEIN 4
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentD DOMAIN
    GeneCDC4
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymF-BOX PROTEIN CDC4, E3 UBIQUITIN LIGASE COMPLEX SCF SUBUNIT CDC4

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)ABCD
Biological Unit 2 (1x)  CD
Biological Unit 3 (1x)AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2P63)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P63)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P63)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P63)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FBOXPS50181 F-box domain profile.CDC4_YEAST272-319
 
 
 
  4A:272-272
B:272-272
C:272-273
D:272-273
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FBOXPS50181 F-box domain profile.CDC4_YEAST272-319
 
 
 
  4A:272-272
B:272-272
C:272-273
D:272-273
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FBOXPS50181 F-box domain profile.CDC4_YEAST272-319
 
 
 
  2-
-
C:272-273
D:272-273
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FBOXPS50181 F-box domain profile.CDC4_YEAST272-319
 
 
 
  2A:272-272
B:272-272
-
-

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YFL009W1YFL009W.1VI:116139-1184782340CDC4_YEAST1-7797794A:221-272 (gaps)
B:222-272
C:221-273 (gaps)
D:223-273
81
51
82
51

(-) 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:52
 aligned with CDC4_YEAST | P07834 from UniProtKB/Swiss-Prot  Length:779

    Alignment length:81
                                   201       211       221       231       241       251       261       271 
           CDC4_YEAST   192 GTTTPLAKTTKTINNNNNIADLIESKDSIISPEYLSDEIFSAINNNLPHAYFKNLLFRLVANMDRSELSDLGTLIKDNLKR 272
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-----------------------------.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------F PROSITE
               Transcript 1 Exon 1.1  PDB: A:221-272 (gaps) UniProt: 1-779 [INCOMPLETE]                       Transcript 1
                 2p63 A 221 G-----------------------------SPEYLSDEIFSAINNNLPHAYFKNLLFRLVANmDRSELSDLGTLIKDNLKR 272
                            |        -         -         -|      231       241       251  |    261       271 
                            |                           222                             254-MSE              
                          221                                                                                

Chain B from PDB  Type:PROTEIN  Length:51
 aligned with CDC4_YEAST | P07834 from UniProtKB/Swiss-Prot  Length:779

    Alignment length:51
                                   231       241       251       261       271 
           CDC4_YEAST   222 SPEYLSDEIFSAINNNLPHAYFKNLLFRLVANMDRSELSDLGTLIKDNLKR 272
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------F PROSITE
               Transcript 1 Exon 1.1  PDB: B:222-272 UniProt: 1-779             Transcript 1
                 2p63 B 222 SPEYLSDEIFSAINNNLPHAYFKNLLFRLVANmDRSELSDLGTLIKDNLKR 272
                                   231       241       251  |    261       271 
                                                          254-MSE              

Chain C from PDB  Type:PROTEIN  Length:53
 aligned with CDC4_YEAST | P07834 from UniProtKB/Swiss-Prot  Length:779

    Alignment length:82
                                   201       211       221       231       241       251       261       271  
           CDC4_YEAST   192 GTTTPLAKTTKTINNNNNIADLIESKDSIISPEYLSDEIFSAINNNLPHAYFKNLLFRLVANMDRSELSDLGTLIKDNLKRD 273
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-----------------------------.....hhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------FB PROSITE
               Transcript 1 Exon 1.1  PDB: C:221-273 (gaps) UniProt: 1-779 [INCOMPLETE]                        Transcript 1
                 2p63 C 221 G-----------------------------SPEYLSDEIFSAINNNLPHAYFKNLLFRLVANmDRSELSDLGTLIKDNLKRD 273
                            |        -         -         -|      231       241       251  |    261       271  
                          221                           222                             254-MSE               

Chain D from PDB  Type:PROTEIN  Length:51
 aligned with CDC4_YEAST | P07834 from UniProtKB/Swiss-Prot  Length:779

    Alignment length:51
                                   232       242       252       262       272 
           CDC4_YEAST   223 PEYLSDEIFSAINNNLPHAYFKNLLFRLVANMDRSELSDLGTLIKDNLKRD 273
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------FB PROSITE
               Transcript 1 Exon 1.1  PDB: D:223-273 UniProt: 1-779             Transcript 1
                 2p63 D 223 PEYLSDEIFSAINNNLPHAYFKNLLFRLVANmDRSELSDLGTLIKDNLKRD 273
                                   232       242       252 |     262       272 
                                                         254-MSE               

   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 2P63)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2P63)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2P63)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (CDC4_YEAST | P07834)
molecular function
    GO:0050815    phosphoserine residue binding    Interacting selectively and non-covalently with a phosphorylated serine residue within a protein.
    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: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.
    GO:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
biological process
    GO:0000082    G1/S transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
    GO:0000086    G2/M transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
    GO:0031146    SCF-dependent proteasomal ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, with ubiquitin-protein ligation catalyzed by an SCF (Skp1/Cul1/F-box protein) complex, and mediated by the proteasome.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0042787    protein ubiquitination involved in ubiquitin-dependent protein catabolic process    The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
    GO:0019005    SCF ubiquitin ligase complex    A ubiquitin ligase complex in which a cullin from the Cul1 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a Skp1 adaptor and an F-box protein. SCF complexes are involved in targeting proteins for degradation by the proteasome. The best characterized complexes are those from yeast and mammals (with core subunits named Cdc53/Cul1, Rbx1/Hrt1/Roc1).
    GO:0043224    nuclear SCF ubiquitin ligase complex    A ubiquitin ligase complex, located in the nucleus, in which a cullin from the Cul1 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a Skp1 adaptor and an F-box protein. SCF complexes are involved in targeting proteins for degradation by the proteasome. The best characterized complexes are those from yeast and mammals (with core subunits named Cdc53/Cul1, Rbx1/Hrt1/Roc1).
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CDC4_YEAST | P078341nex 3mks 3v7d

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2P63)