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(-) Description

Title :  STRUCTURE OF THE CUL1-RBX1-SKP1-F BOXSKP2 SCF UBIQUITIN LIGASE COMPLEX
 
Authors :  N. Zheng, B. A. Schulman, L. Song, J. J. Miller, P. D. Jeffrey, P. Wang, C. Chu, D. M. Koepp, S. J. Elledge, M. Pagano, R. C. Conaway, J. W. Conaway, J. W. Harper, N. P. Pavletich
Date :  08 Apr 02  (Deposition) - 08 May 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ubiquitin, Ligase, Ubiquitination, Ring Finger, Winged-Helix (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Zheng, B. A. Schulman, L. Song, J. J. Miller, P. D. Jeffrey, P. Wang, C. Chu, D. M. Koepp, S. J. Elledge, M. Pagano, R. C. Conaway, J. W. Conaway, J. W. Harper, N. P. Pavletich
Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin Ligase Complex.
Nature V. 416 703 2002
PubMed-ID: 11961546  |  Reference-DOI: 10.1038/416703A
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANAPHASE PROMOTING COMPLEX
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX4T3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 773-846
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymAPC2WHB

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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

(-) Sites  (0, 0)

(no "Site" information available for 1LDD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 4)

Asymmetric/Biological Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLR127C1YLR127C.1XII:398320-3957592562APC2_YEAST1-8538534A:773-846
B:773-846
C:773-846
D:773-846
74
74
74
74

(-) 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:74
 aligned with APC2_YEAST | Q12440 from UniProtKB/Swiss-Prot  Length:853

    Alignment length:74
                                   782       792       802       812       822       832       842    
           APC2_YEAST   773 KYELTLQRSLPFIEGMLTNLGAMKLHKIHSFLKITVPKDWGYNRITLQQLEGYLNTLADEGRLKYIANGSYEIV 846
               SCOP domains d1ldda_ A: Anaphase promoting complex (APC)                                SCOP domains
               CATH domains 1lddA00 A:773-846 'winged helix' repressor DNA binding domain              CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..ee.....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:773-846 UniProt: 1-853 [INCOMPLETE]                       Transcript 1
                 1ldd A 773 KYELTLQRSLPFIEGMLTNLGAMKLHKIHSFLKITVPKDWGYNRITLQQLEGYLNTLADEGRLKYIANGSYEIV 846
                                   782       792       802       812       822       832       842    

Chain B from PDB  Type:PROTEIN  Length:74
 aligned with APC2_YEAST | Q12440 from UniProtKB/Swiss-Prot  Length:853

    Alignment length:74
                                   782       792       802       812       822       832       842    
           APC2_YEAST   773 KYELTLQRSLPFIEGMLTNLGAMKLHKIHSFLKITVPKDWGYNRITLQQLEGYLNTLADEGRLKYIANGSYEIV 846
               SCOP domains d1lddb_ B: Anaphase promoting complex (APC)                                SCOP domains
               CATH domains 1lddB00 B:773-846 'winged helix' repressor DNA binding domain              CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..ee.....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:773-846 UniProt: 1-853 [INCOMPLETE]                       Transcript 1
                 1ldd B 773 KYELTLQRSLPFIEGMLTNLGAMKLHKIHSFLKITVPKDWGYNRITLQQLEGYLNTLADEGRLKYIANGSYEIV 846
                                   782       792       802       812       822       832       842    

Chain C from PDB  Type:PROTEIN  Length:74
 aligned with APC2_YEAST | Q12440 from UniProtKB/Swiss-Prot  Length:853

    Alignment length:74
                                   782       792       802       812       822       832       842    
           APC2_YEAST   773 KYELTLQRSLPFIEGMLTNLGAMKLHKIHSFLKITVPKDWGYNRITLQQLEGYLNTLADEGRLKYIANGSYEIV 846
               SCOP domains d1lddc_ C: Anaphase promoting complex (APC)                                SCOP domains
               CATH domains 1lddC00 C:773-846 'winged helix' repressor DNA binding domain              CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..ee.....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:773-846 UniProt: 1-853 [INCOMPLETE]                       Transcript 1
                 1ldd C 773 KYELTLQRSLPFIEGMLTNLGAMKLHKIHSFLKITVPKDWGYNRITLQQLEGYLNTLADEGRLKYIANGSYEIV 846
                                   782       792       802       812       822       832       842    

Chain D from PDB  Type:PROTEIN  Length:74
 aligned with APC2_YEAST | Q12440 from UniProtKB/Swiss-Prot  Length:853

    Alignment length:74
                                   782       792       802       812       822       832       842    
           APC2_YEAST   773 KYELTLQRSLPFIEGMLTNLGAMKLHKIHSFLKITVPKDWGYNRITLQQLEGYLNTLADEGRLKYIANGSYEIV 846
               SCOP domains d1lddd_ D: Anaphase promoting complex (APC)                                SCOP domains
               CATH domains 1lddD00 D:773-846 'winged helix' repressor DNA binding domain              CATH domains
           Pfam domains (1) -----------APC2-1lddD01 D:784-845                                        - Pfam domains (1)
           Pfam domains (2) -----------APC2-1lddD02 D:784-845                                        - Pfam domains (2)
           Pfam domains (3) -----------APC2-1lddD03 D:784-845                                        - Pfam domains (3)
           Pfam domains (4) -----------APC2-1lddD04 D:784-845                                        - Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..ee.....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:773-846 UniProt: 1-853 [INCOMPLETE]                       Transcript 1
                 1ldd D 773 KYELTLQRSLPFIEGMLTNLGAMKLHKIHSFLKITVPKDWGYNRITLQQLEGYLNTLADEGRLKYIANGSYEIV 846
                                   782       792       802       812       822       832       842    

   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/Biological Unit

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (APC2_YEAST | Q12440)
molecular function
    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: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:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
    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:0031145    anaphase-promoting complex-dependent 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 the anaphase-promoting 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:0010458    exit from mitosis    The cell cycle transition where a cell leaves M phase and enters a new G1 phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place.
    GO:0007091    metaphase/anaphase transition of mitotic cell cycle    The cell cycle process in which a cell progresses from metaphase to anaphase during mitosis, triggered by the activation of the anaphase promoting complex by Cdc20/Sleepy homolog which results in the degradation of Securin.
    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:0006511    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 a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
    GO:0005680    anaphase-promoting complex    A ubiquitin ligase complex that degrades mitotic cyclins and anaphase inhibitory protein, thereby triggering sister chromatid separation and exit from mitosis. Substrate recognition by APC occurs through degradation signals, the most common of which is termed the Dbox degradation motif, originally discovered in cyclin B.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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 Specified in the PDB File

1ldj STRUCTURE OF THE CUL1-RBX1-SKP1-F BOXSKP2 SCF UBIQUITIN LIGASE COMPLEX
1ldk STRUCTURE OF THE CUL1-RBX1-SKP1-F BOXSKP2 SCF UBIQUITIN LIGASE COMPLEX