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(-) Description

Title :  STRUCTURAL INSIGHTS INTO NEDD8 ACTIVATION OF CULLIN-RING LIGASES: CONFORMATIONAL CONTROL OF CONJUGATION.
 
Authors :  D. M. Duda, B. A. Schulman
Date :  08 Jul 08  (Deposition) - 30 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  C,R
Keywords :  Ubiquitin, Nedd8, Cullin, Host-Virus Interaction, Receptor, Ubl Conjugation, Ubl Conjugation Pathway, Acetylation, Cytoplasm, Dna Damage, Dna Repair, Metal-Binding, Nucleus, Zinc, Zinc-Finger, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. M. Duda, L. A. Borg, D. C. Scott, H. W. Hunt, M. Hammel, B. A. Schulman
Structural Insights Into Nedd8 Activation Of Cullin-Ring Ligases: Conformational Control Of Conjugation.
Cell(Cambridge, Mass. ) V. 134 995 2008
PubMed-ID: 18805092  |  Reference-DOI: 10.1016/J.CELL.2008.07.022
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CULLIN-5
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX4T1
    Expression System StrainBL21(DE3)GOLD
    FragmentRESIDUES 401-780
    GeneCUL5, VACM1
    MutationYES
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCUL-5, VASOPRESSIN-ACTIVATED CALCIUM-MOBILIZING RECEPTOR, VACM-1
 
Molecule 2 - RING-BOX PROTEIN 1
    ChainsR
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRSF-DUET
    Expression System StrainBL21(DE3)GOLD
    GeneRBX1, RNF75, ROC1
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRBX1, REGULATOR OF CULLIN-1, RING FINGER PROTEIN 75, PROTEIN ZYP

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit CR

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS R:42 , CYS R:45 , HIS R:80 , CYS R:83BINDING SITE FOR RESIDUE ZN R 201
2AC2SOFTWARECYS R:75 , HIS R:77 , CYS R:94 , ASP R:97BINDING SITE FOR RESIDUE ZN R 202
3AC3SOFTWARECYS R:53 , CYS R:56 , CYS R:68 , HIS R:82BINDING SITE FOR RESIDUE ZN R 203

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1R:42 -R:45
2R:45 -R:83
3R:53 -R:68
4R:56 -R:68

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_RING_2PS50089 Zinc finger RING-type profile.RBX1_HUMAN53-98  1R:53-98
2CULLIN_2PS50069 Cullin family profile.CUL5_HUMAN403-638  1C:403-638
3CULLIN_1PS01256 Cullin family signature.CUL5_HUMAN753-780  1C:753-780

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002162251bENSE00000880432chr22:41347363-41347480118RBX1_HUMAN1-26261R:19-268
1.2ENST000002162252ENSE00000654972chr22:41349559-4134963779RBX1_HUMAN27-53271R:27-5327
1.3aENST000002162253aENSE00000654975chr22:41360051-4136012171RBX1_HUMAN53-76241R:53-76 (gaps)24
1.4bENST000002162254bENSE00000654978chr22:41363803-4136388886RBX1_HUMAN77-105291R:77-10529
1.5bENST000002162255bENSE00001814441chr22:41368480-41369313834RBX1_HUMAN105-10841R:105-1084

(-) 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 C from PDB  Type:PROTEIN  Length:378
 aligned with CUL5_HUMAN | Q93034 from UniProtKB/Swiss-Prot  Length:780

    Alignment length:380
                                   410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780
           CUL5_HUMAN   401 ESKCPELLANYCDMLLRKTPLSKKLTSEEIEAKLKEVLLVLKYVQNKDVFMRYHKAHLTRRLILDISADSEIEENMVEWLREVGMPADYVNKLARMFQDIKVSEDLNQAFKEMHKNNKLALPADSVNIKILNAGAWSRSSEKVFVSLPTELEDLIPEVEEFYKKNHSGRKLHWHHLMSNGIITFKNEVGQYDLEVTTFQLAVLFAWNQRPREKISFENLKLATELPDAELRRTLWSLVAFPKLKRQVLLYEPQVNSPKDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMREEENEGIVQLRILRTQEAIIQIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYIRRDESDINTFIYMA 780
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...--..hhh.eeeeeeehhhhh..........hhhhhhhhhhhhhhhhh....eeeee.hhh.eeeeeee....eeeeeeehhhhhhhhhhh......eehhhhhhhhh.hhhhhhhhhhhhhh........eee.....hhhhh....eeee.....ee....ee.eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --CULLIN_2  PDB: C:403-638 UniProt: 403-638                                                                                                                                                                                                   ------------------------------------------------------------------------------------------------------------------CULLIN_1  PDB: C:753-780     PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dpl C 401 ESKCPEELANYCDMLLRKTPLSKKLTSEEIEAKLKEVLKKLKYVQNKDVFMRYHKAHLTRRLILDISADSEIEENMVEWLREVGMPADYVNKLARMFQDIKVSEDLNQAFKEMHKNN--ALPADSVNIKILNAGAWSRSSEKVFVSLPTELEDLIPEVEEFYKKNHSGRKLHWHHLMSNGIITFKNEVGQYDLEVTTFQLAVLFAWNQRPREKISFENLKLATELPDAELRRTLWSLVAFPKLKRQVLLYEPQVNSPKDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMREEENEGIVQLRILRTQEAIIQIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYIRRDESDINTFIYMA 780
                                   410       420       430       440       450       460       470       480       490       500       510      |520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780
                                                                                                                                              517  |                                                                                                                                                                                                                                                                    
                                                                                                                                                 520                                                                                                                                                                                                                                                                    

Chain R from PDB  Type:PROTEIN  Length:87
 aligned with RBX1_HUMAN | P62877 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:90
                                    28        38        48        58        68        78        88        98       108
           RBX1_HUMAN    19 KKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH 108
               SCOP domains d3dplr_ R: RIGG-box protein 1 (RBX1) of SCF u   biquitin ligase complex                    SCOP domains
               CATH domains 3dplR00 R:19-108 Zinc/RING finger domain, C3H   C4 (zinc finger)                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeee...................hhhhhh...---...eeee....eeehhhhhhhhh.............eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------ZF_RING_2  PDB: R:53-98 UniProt: 53-98        ---------- PROSITE
           Transcript 1 (1) 1.1b    Exon 1.2  PDB: R:27-53     -----------------------Exon 1.4b  PDB: R:77-105     --- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.3a UniProt: 53-76----------------------------1.5b Transcript 1 (2)
                 3dpl R  19 KKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASA---ECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH 108
                                    28        38        48        58    |   68        78        88        98       108
                                                                       63  67                                         

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DPL)

(-) Gene Ontology  (60, 70)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C   (CUL5_HUMAN | Q93034)
molecular function
    GO:0005262    calcium channel activity    Enables the facilitated diffusion of a calcium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
    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:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    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:0038128    ERBB2 signaling pathway    A series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptors on the surface of a cell, where the signal is transmitted by ERBB2. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB2 receptors are themselves unable to bind to ligands, but act as a signal-amplifying tyrosine kinase within a heterodimeric pair.
    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:0070588    calcium ion transmembrane transport    A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0097193    intrinsic apoptotic signaling pathway    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway starts with reception of an intracellular signal (e.g. DNA damage, endoplasmic reticulum stress, oxidative stress etc.), and ends when the execution phase of apoptosis is triggered. The intrinsic apoptotic signaling pathway is crucially regulated by permeabilization of the mitochondrial outer membrane (MOMP).
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    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.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0031466    Cul5-RING ubiquitin ligase complex    A ubiquitin ligase complex in which a cullin from the Cul5 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by an elongin-BC adaptor and a SOCS/BC box protein.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain R   (RBX1_HUMAN | P62877)
molecular function
    GO:0019788    NEDD8 transferase activity    Catalysis of the transfer of NEDD8 from one protein to another via the reaction X-NEDD8 + Y --> Y-NEDD8 + X, where both X-NEDD8 and Y-NEDD8 are covalent linkages.
    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: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:0032403    protein complex binding    Interacting selectively and non-covalently with any 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.
    GO:0034450    ubiquitin-ubiquitin ligase activity    Isoenergetic transfer of ubiquitin from one protein to an existing ubiquitin chain via the reaction X-ubiquitin + Y-ubiquitin -> Y-ubiquitin-ubiquitin + X, where both the X-ubiquitin and Y-ubiquitin-ubiquitin linkages are thioester bonds between the C-terminal glycine of ubiquitin and a sulfhydryl side group of a cysteine residue.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0042769    DNA damage response, detection of DNA damage    The series of events required to receive a stimulus indicating DNA damage has occurred and convert it to a molecular signal.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    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:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0070911    global genome nucleotide-excision repair    The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
    GO:0090090    negative regulation of canonical Wnt signaling pathway    Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0000715    nucleotide-excision repair, DNA damage recognition    The identification of lesions in DNA, such as pyrimidine-dimers, intrastrand cross-links, and bulky adducts. The wide range of substrate specificity suggests the repair complex recognizes distortions in the DNA helix.
    GO:0000717    nucleotide-excision repair, DNA duplex unwinding    The unwinding, or local denaturation, of the DNA duplex to create a bubble around the site of the DNA damage.
    GO:0033683    nucleotide-excision repair, DNA incision    A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound.
    GO:0006295    nucleotide-excision repair, DNA incision, 3'-to lesion    The endonucleolytic cleavage of the damaged strand of DNA 3' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision precedes the incision formed 5' to the site of damage.
    GO:0006296    nucleotide-excision repair, DNA incision, 5'-to lesion    The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage.
    GO:0006294    nucleotide-excision repair, preincision complex assembly    The aggregation, arrangement and bonding together of proteins on DNA to form the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage. This assembly occurs before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
    GO:0006293    nucleotide-excision repair, preincision complex stabilization    The stabilization of the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage as well as the unwound DNA. The stabilization of the protein-DNA complex ensures proper positioning of the preincision complex before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
    GO:0043161    proteasome-mediated 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, and mediated by the proteasome.
    GO:0030163    protein catabolic process    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:0006513    protein monoubiquitination    Addition of a single ubiquitin group to a protein.
    GO:0045116    protein neddylation    Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
    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:0061418    regulation of transcription from RNA polymerase II promoter in response to hypoxia    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
    GO:0006283    transcription-coupled nucleotide-excision repair    The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0031462    Cul2-RING ubiquitin ligase complex    A ubiquitin ligase complex in which a cullin from the Cul2 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by an elongin-BC adaptor and a SOCS/BC box protein.
    GO:0031463    Cul3-RING ubiquitin ligase complex    A ubiquitin ligase complex in which a cullin from the Cul3 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a BTB-domain-containing protein.
    GO:0031464    Cul4A-RING E3 ubiquitin ligase complex    A ubiquitin ligase complex in which a cullin from the Cul4A subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by an adaptor protein.
    GO:0031465    Cul4B-RING E3 ubiquitin ligase complex    A ubiquitin ligase complex in which a cullin from the Cul4B subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by unknown subunits.
    GO:0031466    Cul5-RING ubiquitin ligase complex    A ubiquitin ligase complex in which a cullin from the Cul5 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by an elongin-BC adaptor and a SOCS/BC box protein.
    GO:0031467    Cul7-RING ubiquitin ligase complex    A ubiquitin ligase complex in which a cullin from the Cul7 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a Skp1 linker and an F-box protein.
    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:0030891    VCB complex    A protein complex that possesses ubiquitin ligase activity; the complex is usually pentameric; for example, in mammals the subunits are pVHL, elongin B, elongin C, cullin-2 (Cul2), and Rbx1.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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        CUL5_HUMAN | Q930343dqv 4jgh 4n9f
        RBX1_HUMAN | P628771ldj 1ldk 1u6g 2hye 2lgv 3dqv 3rtr 4f52 4p5o 5n4w

(-) Related Entries Specified in the PDB File

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