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(-) Description

Title :  A DUAL E3 MECHANISM FOR RUB1 LIGATION TO CDC53: DCN1(P)-CDC53(WHB)
 
Authors :  D. C. Scott, J. K Monda, C. R. R. Grace, D. M. Duda, R. W. Kriwacki, T. Kurz B. A. Schulman
Date :  22 Jul 10  (Deposition) - 15 Sep 10  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym. Unit :  A,E
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  E  (1x)
Keywords :  Ligase, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. C. Scott, J. K. Monda, C. R. Grace, D. M. Duda, R. W. Kriwacki, T. Kurz, B. A. Schulman
A Dual E3 Mechanism For Rub1 Ligation To Cdc53.
Mol. Cell V. 39 784 2010
PubMed-ID: 20832729  |  Reference-DOI: 10.1016/J.MOLCEL.2010.08.030

(-) Compounds

Molecule 1 - DEFECTIVE IN CULLIN NEDDYLATION PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentDCUN1 DOMAIN, RESIDUES 70-269
    GeneDCN1, YLR128W, L3111
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
 
Molecule 2 - CELL DIVISION CONTROL PROTEIN 53
    ChainsE
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 730-815
    GeneCDC53, YDL132W, D2190
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymCULLIN-A, E3 UBIQUITIN LIGASE COMPLEX SCF SUBUNIT CDC53

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AE
Biological Unit 1 (1x)AE
Biological Unit 2 (1x)A 
Biological Unit 3 (1x) E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:8 , ASP A:153 , HIS A:157 , GOL A:270 , HOH A:282 , HOH E:40 , GLU E:752 , ALA E:753 , LEU E:796 , LYS E:799BINDING SITE FOR RESIDUE GOL A 3968
2AC2SOFTWAREHOH A:2 , ASP A:106 , LEU A:107 , ALA A:108 , ASP A:153 , TYR A:199 , GOL A:3968 , LYS E:799BINDING SITE FOR RESIDUE GOL A 270
3AC3SOFTWAREALA A:253 , TRP A:254 , PRO A:255 , PHE A:256 , HIS E:767 , LYS E:790 , ILE E:793 , ASP E:794 , ARG E:804 , TYR E:811BINDING SITE FOR RESIDUE GOL E 3968

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O2P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O2P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O2P)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CULLIN_1PS01256 Cullin family signature.CDC53_YEAST789-815  1E:789-815
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CULLIN_1PS01256 Cullin family signature.CDC53_YEAST789-815  1E:789-815
Biological Unit 2 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CULLIN_1PS01256 Cullin family signature.CDC53_YEAST789-815  0-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CULLIN_1PS01256 Cullin family signature.CDC53_YEAST789-815  1E:789-815

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLR128W1YLR128W.1XII:398531-3985333DCN1_YEAST1-110--
1.2YLR128W2YLR128W.2XII:398628-399434807DCN1_YEAST2-2692681A:71-269199

(-) 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:199
 aligned with DCN1_YEAST | Q12395 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:199
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260         
           DCN1_YEAST    71 YPKELTQVFEHYINNNLFDIDSLVKFIEELGYNLEDLATLCLAHLLGYKKLEEPLKREDFLSTWFMQGCSTISDMQECIKTLDVKLHEDLQYFTQIYNYAFNLILDPNRKDIDTDEGIQYWKLFFQPEYPVRMEPDLLEAWFRFLRDEGKTTISKDTWRMLLLFFKRYPTIQKIISDYDETAAWPFIIDEFYECLQDQQ 269
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------------Cullin_binding-3o2pA01 A:142-266                                                                                             --- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhhhhhh.....hhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh........hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...hhhhhhh......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: A:71-269 UniProt: 2-269 [INCOMPLETE]                                                                                                                                                     Transcript 1
                 3o2p A  71 YPKELTQVFEHYINNNLFDIDSLVKFIEELGYNLEDLATLCLAHLLGYKKLEEPLKREDFLSTWFMQGCSTISDMQECIKTLDVKLHEDLQYFTQIYNYAFNLILDPNRKDIDTDEGIQYWKLFFQPEYPVRMEPDLLEAWFRFLRDEGKTTISKDTWRMLLLFFKRYPTIQKIISDYDETAAWPFIIDEFYECLQDQQ 269
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260         

Chain E from PDB  Type:PROTEIN  Length:86
 aligned with CDC53_YEAST | Q12018 from UniProtKB/Swiss-Prot  Length:815

    Alignment length:86
                                   739       749       759       769       779       789       799       809      
          CDC53_YEAST   730 NKRLTEDERIEKELNTERQIFLEACIVRIMKAKRNLPHTTLVNECIAQSHQRFNAKVSMVKRAIDSLIQKGYLQRGDDGESYAYLA 815
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------Cullin_Nedd8-3o2pE01 E:743-810                                      ----- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..eee.....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------CULLIN_1  PDB: E:789-815    PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 3o2p E 730 NKRLTEDERIEKELNTERQIFLEACIVRIMKAKRNLPHTTLVNECIAQSHQRFNAKVSMVKRAIDSLIQKGYLQRGDDGESYAYLA 815
                                   739       749       759       769       779       789       799       809      

   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 3O2P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O2P)

(-) Pfam Domains  (2, 2)

Asymmetric Unit

(-) Gene Ontology  (25, 27)

Asymmetric Unit(hide GO term definitions)
Chain A   (DCN1_YEAST | Q12395)
molecular function
    GO:0097602    cullin family protein binding    Interacting selectively and non-covalently with any member of the cullin family, hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3).
    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.
    GO:0031624    ubiquitin conjugating enzyme binding    Interacting selectively and non-covalently with a ubiquitin conjugating enzyme, any of the E2 proteins.
    GO:0032182    ubiquitin-like protein binding    Interacting selectively and non-covalently with a small conjugating protein such as ubiquitin or a ubiquitin-like protein.
biological process
    GO:0051443    positive regulation of ubiquitin-protein transferase activity    Any process that activates, maintains or increases the rate of ubiquitin transferase activity.
    GO:0045116    protein neddylation    Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0000151    ubiquitin ligase complex    A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

Chain E   (CDC53_YEAST | Q12018)
molecular function
    GO:0003688    DNA replication origin binding    Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
    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: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: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: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: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:0031461    cullin-RING ubiquitin ligase complex    Any ubiquitin ligase complex in which the catalytic core consists of a member of the cullin family and a RING domain protein; the core is associated with one or more additional proteins that confer substrate specificity.
    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

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

UniProtKB/Swiss-Prot
        CDC53_YEAST | Q120183o6b
        DCN1_YEAST | Q123952is9 2l4e 2l4f 3bq3 3o6b 3tdi

(-) Related Entries Specified in the PDB File

3o2u E2
3o6b E2 E3