2PM9 - JenaLib

Asymmetric/Biological Unit

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	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
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Chain A from PDB  Type:PROTEIN  Length:384
 aligned with SEC31_YEAST | P38968 from UniProtKB/Swiss-Prot  Length:1273

    Alignment length:406
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404      
          SEC31_YEAST     5 AEFSRTATFAWSHDKIPLLVSGTVSGTVDANFSTDSSLELWSLLAADSEKPIASLQVDSKFNDLDWSHNNKIIAGALDNGSLELYSTNEANNAINSMARFSNHSSSVKTVKFNAKQDNVLASGGNNGEIFIWDMNKCTESPSNYTPLTPGQSMSSVDEVISLAWNQSLAHVFASAGSSNFASIWDLKAKKEVIHLSYTSPNSGIKQQLSVVEWHPKNSTRVATATGSDNDPSILIWDLRNANTPLQTLNQGHQKGILSLDWCHQDEHLLLSSGRDNTVLLWNPESAEQLSQFPARGNWCFKTKFAPEAPDLFACASFDNKIEVQTLQNLTNTLDEQETETKQQESETDFWNNVSREESKEKPTVFHLQAPTWYGEPSPAAHWAFGGKLVQITPDGKGVSITNPKIS 410
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-2pm9A01 A:246-286                   ---------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-2pm9A02 A:246-286                   ---------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeee............eeee.................eeee..hhhhh...........eeeeee......eeeee....eeee..........eeee.........eeee.......eeee.....ee..............................eeee......eeeee.....eeeee....eeeeee............eeeeee......eeeeee.........eee..................eeeeee.......eeeee...eeeee......eeeeee........eee......eeee.....eeeeee..........----------------------.......................eee...eee................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------WD_REPEATS_1   -----------------------------------------------------------------------------------------WD_REPEATS_1   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:5-410 (gaps) UniProt: 1-1273 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                             Transcript 1
                 2pm9 A   5 AEFSRTATFAWSHDKIPLLVSGTVSGTVDANFSTDSSLELWSLLAADSEKPIASLQVDSKFNDLDWSHNNKIIAGALDNGSLELYSTNEANNAINSMARFSNHSSSVKTVKFNAKQDNVLASGGNNGEIFIWDMNKCTESPSNYTPLTPGQSMSSVDEVISLAWNQSLAHVFASAGSSNFASIWDLKAKKEVIHLSYTSPNSGIKQQLSVVEWHPKNSTRVATATGSDNDPSILIWDLRNANTPLQTLNQGHQKGILSLDWCHQDEHLLLSSGRDNTVLLWNPESAEQLSQFPARGNWCFKTKFAPEAPDLFACASFDNKIEVQTLQNLTNTLDE----------------------SKEKPSVFHLQAPTWYGEPSPAAHWAFGGKLVQITPDGKGVSITNPKIS 410
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334    |    -         -       364       374       384       394       404      
                                                                                                                                                                                                                                                                                                                                                                        339                    362

Chain B from PDB  Type:PROTEIN  Length:280
 aligned with SEC13_YEAST | Q04491 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:291
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291 
          SEC13_YEAST     2 VVIANAHNELIHDAVLDYYGKRLATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVDWAHPKFGTILASCSYDGKVLIWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPLLLVASSDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPATIEEDGEHNGTKESRKFVTGGADNLVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYLASVSQDRTCIIWTQDNEQGPWKKTLLKEEKFPDVLWRASWSLSGNVLALSGGDNKVTLWKENLEGKWEPA 292
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-2pm9B01 B:195-235                   --------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-2pm9B02 B:195-235                   --------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-2pm9B03 B:195-235                   --------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-2pm9B04 B:195-235                   --------------------------------------------------------- Pfam domains (4)
           Pfam domains (5) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-2pm9B05 B:195-235                   --------------------------------------------------------- Pfam domains (5)
         Sec.struct. author ..........eeee.........eeee...eeeeeeee..eeeeeeeee.....eeeeee.hhhhh.eeeeee....eeeee.hhhh.eeeeee......eeeeee.......eeeeee...eeeeee.........eeee.....eee.......-----------...eeeeee....eeeee........ee............eeee.......eeeeeee...ee..eee......................eeee......eeee.....eeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: B:2-292 (gaps) UniProt: 1-297 [INCOMPLETE]                                                                                                                                                                                                                                           Transcript 2
                 2pm9 B   2 VVIANAHNEMIHDAVMDYYGKRMATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVDWAHPKFGTILASCSYDGKVMIWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPMLLVASSDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPAT-----------ESRKFVTGGADNLVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYMASVSQDRTCIIWTQDNEQGPWKKTLLKEEKFPDVLWRASWSLSGNVLALSGGDNKVTLWKENLEGKWEPA 292
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     |   -       171       181       191       201       211       221       231       241       251       261       271       281       291 
                                                                                                                                                                                     157         169

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 (SEC31_YEAST | P38968)

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:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
	GO:0090114	COPII-coated vesicle budding	The evagination of an endoplasmic reticulum membrane, resulting in formation of a COPII-coated vesicle.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
	GO:0016192	vesicle-mediated transport	A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
	GO:0030127	COPII vesicle coat	One of two multimeric complexes that forms a membrane vesicle coat. COPII is best characterized in S. cerevisiae, where the subunits are called Sar1p, Sec13p, Sec31p, Sec23p, and Sec24p. Vesicles with COPII coats are found associated with endoplasmic reticulum (ER) membranes at steady state.
	GO:0012507	ER to Golgi transport vesicle membrane	The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi.
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B (SEC13_YEAST | Q04491)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
	GO:0090114	COPII-coated vesicle budding	The evagination of an endoplasmic reticulum membrane, resulting in formation of a COPII-coated vesicle.
	GO:0051028	mRNA transport	The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0031081	nuclear pore distribution	Any process that establishes the spatial arrangement of nuclear pores within the nuclear envelope.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:1904263	positive regulation of TORC1 signaling	Any process that activates or increases the frequency, rate or extent of TORC1 signaling.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
	GO:0030433	ubiquitin-dependent ERAD pathway	The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
	GO:0016192	vesicle-mediated transport	A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
	GO:0030127	COPII vesicle coat	One of two multimeric complexes that forms a membrane vesicle coat. COPII is best characterized in S. cerevisiae, where the subunits are called Sar1p, Sec13p, Sec31p, Sec23p, and Sec24p. Vesicles with COPII coats are found associated with endoplasmic reticulum (ER) membranes at steady state.
	GO:0012507	ER to Golgi transport vesicle membrane	The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi.
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0035859	Seh1-associated complex	A protein complex that associates dynamically with the vacuolar membrane, and is proposed to have a role in membrane-associated trafficking or regulatory processes. In S. cerevisiae the complex contains Seh1p, Sec13p, Npr2p, Npr3p, Iml1p, Mtc5p, Rtc1p, and Sea4p.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005643	nuclear pore	Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
	GO:0031080	nuclear pore outer ring	A subcomplex of the nuclear pore complex (NPC) that forms the outer rings of the core scaffold, a lattice-like structure that gives the NPC its shape and strength. In S. cerevisiae, the two outer rings each contain multiple copies of the following proteins: Nup133p, Nup120p, Nup145Cp, Nup85p, Nup84p, Seh1p, and Sec13p. In vertebrates, the two outer rings each contain multiple copies of the following proteins: Nup133, Nup160, Nup96, Nup75, Nup107, Seh1, Sec13, Nup43, Nup37, and ALADIN. Components are arranged in 8-fold symmetrical 'spokes' around the central transport channel. A single 'spoke', can be isolated and is sometimes referred to as the Nup84 complex (S. cerevisiae) or the Nup107-160 complex (vertebrates).
	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:0005774	vacuolar membrane	The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.
	GO:0005773	vacuole	A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

Description

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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 (1, 2)

Exons (2, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 7)

Gene Ontology (26, 39)

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