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(-) Description

Title :  THE IDOL-UBE2D COMPLEX MEDIATES STEROL-DEPENDENT DEGRADATION OF THE LDL RECEPTOR
 
Authors :  L. Fairall, B. T. Goult, C. J. Millard, P. Tontonoz, J. W. R. Schwabe
Date :  04 May 11  (Deposition) - 29 Jun 11  (Release) - 29 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, E2 Ligase- E3 Ligase Complex, Ring Zinc-Finger, Ube2D1, Ubl Conjugation Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Zhang, L. Fairall, B. T. Goult, A. C. Calkin, C. Hong, C. J. Millard, P. Tontonoz, J. W. R. Schwabe
The Idol-Ube2D Complex Mediates Sterol-Dependent Degradation Of The Ldl Receptor.
Genes Dev. V. 25 1262 2011
PubMed-ID: 21685362  |  Reference-DOI: 10.1101/GAD.2056211

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE MYLIP
    ChainsA, B
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VariantROSETTA
    Expression System Vector TypePLASMID
    FragmentRING, RESIDUES 369-445
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymINDUCIBLE DEGRADER OF THE LDL-RECEPTOR, IDOL, MYOSIN REGULATORY LIGHT CHAIN INTERACTING PROTEIN, MIR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:387 , CYS A:390 , CYS A:408 , CYS A:411BINDING SITE FOR RESIDUE ZN A1001
2AC2SOFTWARECYS A:402 , HIS A:404 , CYS A:418 , CYS A:421BINDING SITE FOR RESIDUE ZN A1002
3AC3SOFTWARECYS B:387 , CYS B:390 , GLU B:393 , CYS B:408 , CYS B:411BINDING SITE FOR RESIDUE ZN B1001
4AC4SOFTWARECYS B:402 , HIS B:404 , CYS B:418 , CYS B:421BINDING SITE FOR RESIDUE ZN B1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Cys A:400 -Pro A:401
2Cys B:400 -Pro B:401

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_RING_2PS50089 Zinc finger RING-type profile.MYLIP_HUMAN387-422
 
  2A:387-422
B:387-422

(-) Exons   (0, 0)

(no "Exon" information available for 2YHN)

(-) 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:64
 aligned with MYLIP_HUMAN | Q8WY64 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:64
                                   382       392       402       412       422       432    
          MYLIP_HUMAN   373 VLQEKLRKLKEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVEHVQHVYLPTH 436
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh............eeee.......hhhhhh.............eeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------ZF_RING_2  PDB: A:387-422           -------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 2yhn A 373 VLQEKLRKLKEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVEHVQHVYLPTH 436
                                   382       392       402       412       422       432    

Chain B from PDB  Type:PROTEIN  Length:64
 aligned with MYLIP_HUMAN | Q8WY64 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:64
                                   382       392       402       412       422       432    
          MYLIP_HUMAN   373 VLQEKLRKLKEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVEHVQHVYLPTH 436
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------zf-C3HC4_3-2yhnB01 B:383-428                  -------- Pfam domains (1)
           Pfam domains (2) ----------zf-C3HC4_3-2yhnB02 B:383-428                  -------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhh...........eeee.......hhhhhhhh...........eeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------ZF_RING_2  PDB: B:387-422           -------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 2yhn B 373 VLQEKLRKLKEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVEHVQHVYLPTH 436
                                   382       392       402       412       422       432    

   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 2YHN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: RING (39)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MYLIP_HUMAN | Q8WY64)
molecular function
    GO:0008092    cytoskeletal protein binding    Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0042632    cholesterol homeostasis    Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell.
    GO:0006928    movement of cell or subcellular component    The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
    GO:0010989    negative regulation of low-density lipoprotein particle clearance    Any process that decreases the rate, frequency or extent of low-density lipoprotein particle clearance. Low-density lipoprotein particle clearance is the process in which a low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0045732    positive regulation of protein catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0031648    protein destabilization    Any process that decreases the stability of a protein, making it more vulnerable to degradative processes or aggregation.
    GO:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    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:0032803    regulation of low-density lipoprotein particle receptor catabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of low-density lipoprotein particle receptors.
cellular component
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

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        MYLIP_HUMAN | Q8WY642yho

(-) Related Entries Specified in the PDB File

2yho THE IDOL-UBE2D COMPLEX MEDIATES STEROL-DEPENDENT DEGRADATION OF THE LDL RECEPTOR