1GK6 - 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:55
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:174
                                                                                                                                                                                                      281 
                                                                                                                                                                                                    279 | 
                                                                                                                                                                                                  278 | | 
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269        |-| | 
           GCN4_YEAST   110 YENLEDNSKEWTSLFDNDIPVTTDDVSLADKAIESTEEVSLVPSNLEVSTTSFLPTPVLEDAKLTQTRKVKKPNSVVKKSHHVGKDDESRLDHLGVVAYNRKQRSIPLSPIVPESSDPAALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLV-GER-   -
               SCOP domains d1gk6a_ A: Vi                                                                 mentin                                           coil                                            SCOP domains
               CATH domains 1gk6A00 A:355                                                                 -409  [                                          code            =1.20.5.170, no name defined]   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh-----------------------------------------------------------------hhhhhhh------------------------------------------hhhh------------hhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------BZIP_BASIC     -------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------BZIP  PDB: A:375-402 UniProt: 231-276         ------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gk6 A 355 MKQLEDKVEELLS-----------------------------------------------------------------KNYHLEN------------------------------------------EVAR------------LKKLVGDLLNVKMALDIEIATYRKLLEGEES 409
                                   364  |      -         -         -         -         -         -       369    |    -         -         -         -       377|        -   |   385       395       405    
                                      367                                                               368   374                                        375  |          379                              
                                                                                                                                                            378

Chain A from PDB  Type:PROTEIN  Length:55
 aligned with VIME_HUMAN | P08670 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:176
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403      
           VIME_HUMAN   234 LKKLHEEEIQELQAQIQEQHVQIDVDVSKPDLTAALRDVRQQYESVAAKNLQEAEEWYKSKFADLSEAANRNNDALRQAKQESTEYRRQVQSLTCEVDALKGTNESLERQMREMEENFAVEAANYQDTIGRLQDEIQNMKEEMARHLREYQDLLNVKMALDIEIATYRKLLEGEES 409
               SCOP domains d1gk 6a_ A:               Vim                                                                                              ent     in coil                                       SCOP domains
               CATH domains 1gk6 A00 A:3              55-                                                                                              409       [code=1.20.       5.170, no name defined]   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh-hhhhhhh--------------hhh----------------------------------------------------------------------------------------------hhh-----hhhhhhhhhhhhh-------hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------IF       ---- PROSITE
               Transcript 1 1.5b   Exon 1.6  PDB: A:361-368 (gaps) UniProt: 241-294      Exon 1.7a  PDB: - UniProt: 295-336        Exon 1.8a  PDB: A:369-409 (gaps) UniProt: 337-410 [INCOMPLETE]            Transcript 1
                 1gk6 A 355 MKQL-EDKVEEL--------------LSK----------------------------------------------------------------------------------------------NYH-----LENEVARLKKLVG-------DLLNVKMALDIEIATYRKLLEGEES 409
                               | | 363 |       -      | |-         -         -         -         -         -         -         -         -         -   | |   - |     380   |     - |     393       403      
                             358 |   365            366 |                                                                                            369 |   372         384     385                        
                               359                    368                                                                                              371

Chain B from PDB  Type:PROTEIN  Length:52
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:171
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279 
           GCN4_YEAST   110 YENLEDNSKEWTSLFDNDIPVTTDDVSLADKAIESTEEVSLVPSNLEVSTTSFLPTPVLEDAKLTQTRKVKKPNSVVKKSHHVGKDDESRLDHLGVVAYNRKQRSIPLSPIVPESSDPAALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVGE 280
               SCOP domains d1gk6b_ B: Vi                                                                 mentin                                           coil                                         SCOP domains
               CATH domains 1gk6B00 B:355                                                                 -406                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh-----------------------------------------------------------------hhhhhhh------------------------------------------hhhh---------hhhh---hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------BZIP_BASIC     ----------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------BZIP  PDB: B:375-402 UniProt: 231-276         ---- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gk6 B 355 MKQLEDKVEELLS-----------------------------------------------------------------KNYHLEN------------------------------------------EVAR---------LKKL---VGDLLNVKMALDIEIATYRKLLEG 406
                                   364  |      -         -         -         -         -         -       369    |    -         -         -         -       377|        -|  |   385       395       405 
                                      367                                                               368   374                                        375  |       379  | 383                       
                                                                                                                                                            378          382

Chain B from PDB  Type:PROTEIN  Length:52
 aligned with VIME_HUMAN | P08670 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:173
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403   
           VIME_HUMAN   234 LKKLHEEEIQELQAQIQEQHVQIDVDVSKPDLTAALRDVRQQYESVAAKNLQEAEEWYKSKFADLSEAANRNNDALRQAKQESTEYRRQVQSLTCEVDALKGTNESLERQMREMEENFAVEAANYQDTIGRLQDEIQNMKEEMARHLREYQDLLNVKMALDIEIATYRKLLEG 406
               SCOP domains d1gk 6b_ B:               Vim                                                                                              ent     in coil                                    SCOP domains
               CATH domains 1gk6 B00 B:3              55-                                                                                              406                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh-hhhhhhh--------------hhh----------------------------------------------------------------------------------------------hhh-----hhhhhhhhhhhhh-------hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------IF       - PROSITE
               Transcript 1 1.5b   Exon 1.6  PDB: B:361-368 (gaps) UniProt: 241-294      Exon 1.7a  PDB: - UniProt: 295-336        Exon 1.8a  PDB: B:369-406 (gaps) UniProt: 337-410 [INCOMPLETE]         Transcript 1
                 1gk6 B 355 MKQL-EDKVEEL--------------LSK----------------------------------------------------------------------------------------------NYH-----LENEVARLKKLVG-------DLLNVKMALDIEIATYRKLLEG 406
                               | | 363 |       -      | |-         -         -         -         -         -         -         -         -         -   | |   - |     380   |     - |     393       403   
                             358 |   365            366 |                                                                                            369 |   372         384     385                     
                               359                    368                                                                                              371

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,B (GCN4_YEAST | P03069)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
	GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	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:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	GO:0001135	transcription factor activity, RNA polymerase II transcription factor recruiting	The function of binding to an RNA polymerase II (RNAP II) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP II.
	GO:0001084	transcription factor activity, TFIID-class binding	Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0001190	transcriptional activator activity, RNA polymerase II transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
	GO:0001191	transcriptional repressor activity, RNA polymerase II transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
biological process
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0010691	negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to nutrient levels	Any process that decreases the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes by RNA polymerase II, originating at an RNA polymerase II promoter, as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0001080	nitrogen catabolite activation of transcription from RNA polymerase II promoter	A transcription regulation process in which the presence of one nitrogen source leads to an increase in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources.
	GO:0045899	positive regulation of RNA polymerase II transcriptional preinitiation complex assembly	Any process that activates or increases the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.
	GO:1903833	positive regulation of cellular response to amino acid starvation	Any process that activates or increases the frequency, rate or extent of cellular response to amino acid starvation.
	GO:0060261	positive regulation of transcription initiation from RNA polymerase II promoter	Any process that increases the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	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:0005667	transcription factor complex	A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Chain A,B (VIME_HUMAN | P08670)

molecular function
	GO:0003725	double-stranded RNA binding	Interacting selectively and non-covalently with double-stranded RNA.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:1990254	keratin filament binding	Interacting selectively and non-covalently with a keratin filament, an intermediate filament composed of acidic and basic keratins (types I and II), typically expressed in epithelial cells.
	GO:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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:0097110	scaffold protein binding	Interacting selectively and non-covalently with a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes.
	GO:0005200	structural constituent of cytoskeleton	The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
	GO:0005212	structural constituent of eye lens	The action of a molecule that contributes to the structural integrity of the lens of an eye.
	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:0060020	Bergmann glial cell differentiation	The process in which neuroepithelial cells of the neural tube give rise to Brgmann glial cells, specialized bipotential progenitors cells of the cerebellum. Differentiation includes the processes involved in commitment of a cell to a specific fate.
	GO:0060395	SMAD protein signal transduction	The cascade of processes by which a signal interacts with a receptor, causing a change in the activity of a SMAD protein, and ultimately effecting a change in the functioning of the cell.
	GO:0014002	astrocyte development	The process aimed at the progression of an astrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. An astrocyte is the most abundant type of glial cell. Astrocytes provide support for neurons and regulate the environment in which they function.
	GO:0045109	intermediate filament organization	Control of the spatial distribution of intermediate filaments; includes organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
	GO:0045103	intermediate filament-based process	Any cellular process that depends upon or alters the intermediate filament cytoskeleton, that part of the cytoskeleton comprising intermediate filaments and their associated proteins.
	GO:0070307	lens fiber cell development	The process whose specific outcome is the progression of a lens fiber cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a lens fiber cell fate. A lens fiber cell is any of the elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye.
	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:0030049	muscle filament sliding	The sliding of actin thin filaments and myosin thick filaments past each other in muscle contraction. This involves a process of interaction of myosin located on a thick filament with actin located on a thin filament. During this process ATP is split and forces are generated.
	GO:0010977	negative regulation of neuron projection development	Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	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:0031252	cell leading edge	The area of a motile cell closest to the direction of movement.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0005882	intermediate filament	A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins.
	GO:0045111	intermediate filament cytoskeleton	Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the cell.
	GO:0043005	neuron projection	A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	GO:0005777	peroxisome	A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.
	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.

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 (3, 6)

Exons (3, 6)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (55, 57)

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