3OLM - JenaLib

Asymmetric/Biological Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:412
 aligned with RSP5_YEAST | P39940 from UniProtKB/Swiss-Prot  Length:809

    Alignment length:420
                                   394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804
           RSP5_YEAST   385 QLGPLPSGWEMRLTNTARVYFVDHNTKTTTWDDPRLPSSLDQNVPQYKRDFRRKVIYFRSQPALRILPGQCHIKVRRKNIFEDAYQEIMRQTPEDLKKRLMIKFDGEEGLDYGGVSREFFFLLSHEMFNPFYCLFEYSAYDNYTIQINPNSGINPEHLNYFKFIGRVVGLGVFHRRFLDAFFVGALYKMMLRKKVVLQDMEGVDAEVYNSLNWMLENSIDGVLDLTFSADDERFGEVVTVDLKPDGRNIEVTDGNKKEYVELYTQWRIVDRVQEQFKAFMDGFNELIPEDLVTVFDERELELLIGGIAEIDIEDWKKHTDYRGYQESDEVIQWFWKCVSEWDNEQRARLLQFTTGTSRIPVNGFKDLQGSDGPRRFTIEKAGEVQQLPKSHTCFNRVDLPQYVDYDSMKQKLTLAVEETI 804
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----WW-3olmA02 A:389-418          --------------------------------------------------------------------------------------HECT-3olmA01 A:505-804                                                                                                                                                                                                                                                                                       Pfam domains
         Sec.struct. author ....................eee....eee..............hhhhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhhhhhh..eeeeee...--------hhhhhhhhhhhhhhhhh.eee.......eee.hhhhhh.hhhhhhhhhhhhhhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhhhhhhhh............eeeeee..eeeeee...hhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhh.....hhhhhhhheeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhh.ee..ee..eeee.........eeehhh.eee.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) --------WW_DOMAIN_1  PDB: A:393-41-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (4)
                PROSITE (1) --WW_DOMAIN_2  PDB: A:387-420       -------------------------------------------------------HECT  PDB: A:476-804 UniProt: 476-809                                                                                                                                                                                                                                                                                                     PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3olm A 385 QLGPLPSGWEMRLTNTARVYFVDHNTKTTTWDDPRLPSSLDQNVPQYKRDFRRKVIYFRSQPALRILPGQCHIKVRRKNIFEDAYQEIMRQTPEDLKKRLMIKFDGEE--------REFFFLLSHEMFNPFYCLFEYSAYDNYTIQINPNSGINPEHLNYFKFIGRVVGLGVFHRRFLDAFFVGALYKMMLRKKVVLQDMEGVDAEVYNSLNWMLENSIDGVLDLTFSADDERFGEVVTVDLKPDGRNIEVTDGNKKEYVELYTQWRIVDRVQEQFKAFMDGFNELIPEDLVTVFDERELELLIGGIAEIDIEDWKKHTDYRGYQESDEVIQWFWKCVSEWDNEQRARLLQFTTGTSRIPVNGFKDLQGSDGPRRFTIEKAGEVQQLPKSHTCFNRVDLPQYVDYDSMKQKLTLAVEETI 804
                                   394       404       414       424       434       444       454       464       474       484       | -      |504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804
                                                                                                                                     492      501

Chain D from PDB  Type:PROTEIN  Length:74
 aligned with UBI4P_YEAST | P0CG63 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:74
                                   314       324       334       344       354       364       374    
          UBI4P_YEAST   305 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 378
               SCOP domains d3olmd_ D: automated matches                                               SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.....eeee.....................eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: D:1-74 UniProt: 305-380                                  PROSITE (1)
                PROSITE (2) --------------------------UBIQUITIN_1  PDB: D:27-52 ---------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: D:1-74 UniProt: 1-381 [INCOMPLETE]                          Transcript 1
                 3olm D   1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR  74
                                    10        20        30        40        50        60        70

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 '\|'

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RSP5_YEAST | P39940)

molecular function
	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:0035091	phosphatidylinositol binding	Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
	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:0034644	cellular response to UV	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 an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
	GO:0006333	chromatin assembly or disassembly	The formation or destruction of chromatin structures.
	GO:0032511	late endosome to vacuole transport via multivesicular body sorting pathway	The directed movement of substances from endosomes to vacuoles by a pathway in which molecules are sorted into multivesicular bodies, which then fuse with the vacuole.
	GO:0007005	mitochondrion organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
	GO:0045807	positive regulation of endocytosis	Any process that activates or increases the frequency, rate or extent of endocytosis.
	GO:0045723	positive regulation of fatty acid biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids.
	GO:0032436	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	Any process that activates or increases the frequency, rate or extent of 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:0048260	positive regulation of receptor-mediated endocytosis	Any process that activates or increases the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	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:0051865	protein autoubiquitination	The ubiquitination by a protein of one or more of its own amino acid residues, or residues on an identical protein. Ubiquitination occurs on the lysine residue by formation of an isopeptide crosslink.
	GO:0006513	protein monoubiquitination	Addition of a single ubiquitin group to a 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:0032956	regulation of actin cytoskeleton organization	Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
	GO:0010794	regulation of dolichol biosynthetic process	Any process that modulates the frequency, rate or extent of dolichol biosynthesis. Dolichol biosynthesis consists of the chemical reactions and pathways resulting in the formation of dolichols, any 2,3-dihydropolyprenol derived from four or more linked isoprene units.
	GO:0032443	regulation of ergosterol biosynthetic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of ergosterol.
	GO:0031384	regulation of initiation of mating projection growth	Any process that modulates the frequency, rate, or extent of the start of mating projection formation by unicellular fungi.
	GO:0010793	regulation of mRNA export from nucleus	Any process that modulates the frequency, rate or extent of the directed movement of mRNA from the nucleus to the cytoplasm.
	GO:0010796	regulation of multivesicular body size	Any process that modulates the volume of a multivesicular body, a type of late endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles.
	GO:0006808	regulation of nitrogen utilization	Any process that modulates the frequency, rate or extent of nitrogen utilization.
	GO:0019220	regulation of phosphate metabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
	GO:0032880	regulation of protein localization	Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
	GO:2000232	regulation of rRNA processing	Any process that modulates the frequency, rate or extent of rRNA processing.
	GO:2000203	regulation of ribosomal large subunit export from nucleus	Any process that modulates the frequency, rate or extent of ribosomal large subunit export from nucleus.
	GO:2000238	regulation of tRNA export from nucleus	Any process that modulates the frequency, rate or extent of tRNA export from nucleus.
	GO:2000235	regulation of tRNA processing	Any process that modulates the frequency, rate or extent of tRNA processing.
	GO:0010795	regulation of ubiquinone biosynthetic process	Any process that modulates the frequency, rate or extent of ubiquinone biosynthesis. Ubiquinone biosynthesis consists of the chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.
	GO:0042493	response to drug	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0034517	ribophagy	The process in which cells degrade mature ribosomes under conditions of starvation.
	GO:0070086	ubiquitin-dependent endocytosis	Endocytosis of a protein that requires the substrate to be modified by ubiquitination. Several plasma membrane proteins, including cell surface permeases and some receptors, are targeted for internalization by endocytosis, and are thereafter delivered to the vacuole or lysosome, where they are degraded.
	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:0043162	ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	The chemical reactions and pathways resulting in the breakdown of a protein or peptide covalently tagged with ubiquitin, via the multivesicular body (MVB) sorting pathway; ubiquitin-tagged proteins are sorted into MVBs, and delivered to a lysosome/vacuole for degradation.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0030479	actin cortical patch	An endocytic patch that consists of an actin-containing structure found at the plasma membrane in cells; formed of networks of branched actin filaments that lie just beneath the plasma membrane and assemble, move, and disassemble rapidly. An example of this is the actin cortical patch found in Saccharomyces cerevisiae.
	GO:0005934	cellular bud tip	The end of a cellular bud distal to the site of attachment to the mother cell.
	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:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	GO:0031234	extrinsic component of cytoplasmic side of plasma membrane	The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
	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.
	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 D (UBI4P_YEAST | P0CG63)

molecular function
	GO:0043008	ATP-dependent 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) using energy from the hydrolysis of ATP.
	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:0031386	protein tag	A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
biological process
	GO:0030437	ascospore formation	The process in which cells that are products of meiosis acquire the specialized features of ascospores. Ascospores are generally found in clusters of four or eight spores within a single mother cell, the ascus, and are characteristic of the ascomycete fungi (phylum Ascomycota).
	GO:0016579	protein deubiquitination	The removal of one or more ubiquitin groups from a protein.
	GO:0006513	protein monoubiquitination	Addition of a single ubiquitin group to a 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.
cellular component
	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.
	GO:1990429	peroxisomal importomer complex	A protein complex responsible for transporting proteins into the peroxisomal matrix. An example of this complex is Pex14 found in S. cerevisae which has 9 core components and 12 transient interaction partners.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (5, 5)

Exons (1, 1)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (2, 2)

Gene Ontology (54, 60)

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