3EQH - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   X-RAY STRUCTURE OF THE HUMAN MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1 (MEK1) IN A TERNARY COMPLEX WITH U0126, ADP AND MG2P

Authors :   T. O. Fischmann

Date :   30 Sep 08 (Deposition) - 24 Feb 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)

Keywords :   Mek1 Kinase, Atp-Binding, Disease Mutation, Kinase, Nucleotide- Binding, Phosphoprotein, Serine/Threonine-Protein Kinase, Transferase, Tyrosine-Protein Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. O. Fischmann, C. K. Smith, T. W. Mayhood, J. E. Myers, P. Reichert, A. Mannarino, D. Carr, H. Zhu, J. Wong, R. S. Yang, H. V. Le, V. S. Madison
Crystal Structures Of Mek1 Binary And Ternary Complexes Wit Nucleotides And Inhibitors.
Biochemistry V. 48 2661 2009
PubMed-ID: 19161339 | Reference-DOI: 10.1021/BI801898E

Molecule 1 - DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1
	Chains	:	A
	EC Number	:	2.7.12.2
	Engineered	:	YES
	Fragment	:	PROTEIN KINASE DOMAIN, UNP RESIDUES 35-393
	Gene	:	MAP2K1, MEK1, PRKMK1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MAP KINASE KINASE 1, MAPKK 1, ERK ACTIVATOR KINASE 1, MAPK/ERK KINASE 1, MEK1

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 5)

No.	Name	Count	Type	Full Name
1	5BM	1	Ligand/Ion	(2Z)-BIS{AMINO[(2-AMINOPHENYL)SULFANYL]METHYLIDENE}BUTANEDINITRILE
2	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	CA	1	Ligand/Ion	CALCIUM ION
4	MG	1	Ligand/Ion	MAGNESIUM ION
5	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	5BM	1	Ligand/Ion	(2Z)-BIS{AMINO[(2-AMINOPHENYL)SULFANYL]METHYLIDENE}BUTANEDINITRILE
2	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	CA	-1	Ligand/Ion	CALCIUM ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	5BM	2	Ligand/Ion	(2Z)-BIS{AMINO[(2-AMINOPHENYL)SULFANYL]METHYLIDENE}BUTANEDINITRILE
2	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	CA	-1	Ligand/Ion	CALCIUM ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:97 , ILE A:99 , LEU A:118 , VAL A:127 , ILE A:141 , MET A:143 , ASP A:190 , ASP A:208 , PHE A:209 , GLY A:210 , VAL A:211 , SER A:212 , ILE A:216	BINDING SITE FOR RESIDUE 5BM A 1
2	AC2	SOFTWARE	MG A:3 , ALA A:76 , GLY A:77 , GLY A:80 , VAL A:82 , ALA A:95 , LYS A:97 , GLU A:144 , MET A:146 , SER A:150 , GLN A:153 , LYS A:192 , SER A:194 , ASN A:195 , LEU A:197 , ASP A:208 , HOH A:504 , HOH A:511 , HOH A:523 , HOH A:531 , HOH A:532	BINDING SITE FOR RESIDUE ADP A 2
3	AC3	SOFTWARE	ADP A:2 , ASN A:195 , ASP A:208 , HOH A:531 , HOH A:532	BINDING SITE FOR RESIDUE MG A 3
4	AC4	SOFTWARE	ASP A:65 , ASP A:66 , HOH A:526	BINDING SITE FOR RESIDUE CA A 5
5	AC5	SOFTWARE	ASP A:65 , ASP A:66 , HOH A:479 , HOH A:527	BINDING SITE FOR RESIDUE NA A 6

(no "SS Bond" information available for 3EQH)

Asymmetric Unit

No.	Residues
1	Ile A:263	-	Pro A:264

Asymmetric Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_035093	F	53	S	MP2K1_HUMAN	Disease (CFC3)	121908594	A	F	53	S
2	UniProt	VAR_069780	G	128	V	MP2K1_HUMAN	Disease (CFC3)	730880508	A	G	128	V
3	UniProt	VAR_035094	Y	130	C	MP2K1_HUMAN	Disease (CFC3)	121908595	A	Y	130	C

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_035093	F	53	S	MP2K1_HUMAN	Disease (CFC3)	121908594	A	F	53	S
2	UniProt	VAR_069780	G	128	V	MP2K1_HUMAN	Disease (CFC3)	730880508	A	G	128	V
3	UniProt	VAR_035094	Y	130	C	MP2K1_HUMAN	Disease (CFC3)	121908595	A	Y	130	C

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_035093	F	53	S	MP2K1_HUMAN	Disease (CFC3)	121908594	A	F	53	S
2	UniProt	VAR_069780	G	128	V	MP2K1_HUMAN	Disease (CFC3)	730880508	A	G	128	V
3	UniProt	VAR_035094	Y	130	C	MP2K1_HUMAN	Disease (CFC3)	121908595	A	Y	130	C

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	MP2K1_HUMAN	74-97	1	A:74-97
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	MP2K1_HUMAN	186-198	1	A:186-198

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	MP2K1_HUMAN	74-97	1	A:74-97
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	MP2K1_HUMAN	186-198	1	A:186-198

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	MP2K1_HUMAN	74-97	2	A:74-97
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	MP2K1_HUMAN	186-198	2	A:186-198

Asymmetric Unit (10, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000307102	1	ENSE00001257104	chr15:66679155-66679765	611	MP2K1_HUMAN	1-27	27	0	-	-
1.2a	ENST00000307102	2a	ENSE00001199409	chr15:66727365-66727575	211	MP2K1_HUMAN	27-97	71	1	A:39-97	59
1.3	ENST00000307102	3	ENSE00001675310	chr15:66729084-66729230	147	MP2K1_HUMAN	98-146	49	1	A:98-146	49
1.4	ENST00000307102	4	ENSE00001134060	chr15:66735618-66735695	78	MP2K1_HUMAN	147-172	26	1	A:147-172	26
1.5	ENST00000307102	5	ENSE00001134055	chr15:66736994-66737045	52	MP2K1_HUMAN	173-190	18	1	A:173-190	18
1.6	ENST00000307102	6	ENSE00001199390	chr15:66774093-66774217	125	MP2K1_HUMAN	190-231	42	1	A:190-231	42
1.7b	ENST00000307102	7b	ENSE00001257056	chr15:66777328-66777529	202	MP2K1_HUMAN	232-299	68	1	A:232-277	46
1.8	ENST00000307102	8	ENSE00001199379	chr15:66779566-66779630	65	MP2K1_HUMAN	299-320	22	1	A:307-320	14
1.9	ENST00000307102	9	ENSE00001199374	chr15:66781553-66781614	62	MP2K1_HUMAN	321-341	21	1	A:321-341	21
1.10	ENST00000307102	10	ENSE00001199370	chr15:66782056-66782101	46	MP2K1_HUMAN	341-356	16	1	A:341-356	16
1.11	ENST00000307102	11	ENSE00001199414	chr15:66782840-66783882	1043	MP2K1_HUMAN	357-393	37	1	A:357-381	25

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:314
 aligned with MP2K1_HUMAN | Q02750 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:343
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378   
          MP2K1_HUMAN    39 ELELDEQQRKRLEAFLTQKQKVGELKDDDFEKISELGAGNGGVVFKVSHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSDGEISICMEHMDGGSLDQVLKKAGRIPEQILGKVSIAVIKGLTYLREKHKIMHRDVKPSNILVNSRGEIKLCDFGVSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWSMGLSLVEMAVGRYPIPPPDAKELELMFGCQVEGDAAETPPRPRTPGRPLSSYGMDSRPPMAIFELLDYIVNEPPPKLPSGVFSLEFQDFVNKCLIKNPAERADLKQLMVHAFIKRSDAEEVDFAGWLCSTIGL 381
               SCOP domains d3eqha_ A: Dual specificity mitogen-activated protein kinase kinase 1, Mek1                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh....hhh.eeeeeeeee....eeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhh.......eeeeee....eeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh......hhh.eee.....eee.....hhhhhhhhh..........hhhhhhh...hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.-----------------------------..hhhhhhhhhhhh..........hhhhhhhhhhhh........hhhhhhhhhhhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------S--------------------------------------------------------------------------V-C----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------PROTEIN_KINASE_ATP      ----------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:39-97 UniProt: 27-97 [INCOMPLETE]        Exon 1.3  PDB: A:98-146 UniProt: 98-146          Exon 1.4  PDB: A:147-172  Exon 1.5          -----------------------------------------Exon 1.7b  PDB: A:232-277 UniProt: 232-299 [INCOMPLETE]             -----------------------------------------Exon 1.10       Exon 1.11  PDB: A:357-381 Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:190-231 UniProt: 190-231 -------------------------------------------------------------------Exon 1.8 [INCOMPLETE] Exon 1.9             ---------------------------------------- Transcript 1 (2)
                 3eqh A  39 ELELDEQQRKRLEAFLTQKQKVGELKDDDFEKISELGAGNGGVVFKVSHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSDGEISICMEHMDGGSLDQVLKKAGRIPEQILGKVSIAVIKGLTYLREKHKIMHRDVKPSNILVNSRGEIKLCDFGVSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWSMGLSLVEMAVGRYPIPPPDAKELELMFGC-----------------------------PMAIFELLDYIVNEPPPKLPSGVFSLEFQDFVNKCLIKNPAERADLKQLMVHAFIKRSDAEEVDFAGWLCSTIGL 381
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268        |-         -         -       308       318       328       338       348       358       368       378   
                                                                                                                                                                                                                                                                        277                           307

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Protein kinase-like (PK-like) (2589)

Superfamily: Protein kinase-like (PK-like) (2589)

Family: Protein kinases, catalytic subunit (1977)

Protein domain: Dual specificity mitogen-activated protein kinase kinase 1, Mek1 (16)

Human (Homo sapiens) [TaxId: 9606] (16)

d3eqha_

(no "CATH Domain" information available for 3EQH)

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

Asymmetric Unit(hide GO term definitions)

Chain A (MP2K1_HUMAN | Q02750)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004708	MAP kinase kinase activity	Catalysis of the concomitant phosphorylation of threonine (T) and tyrosine (Y) residues in a Thr-Glu-Tyr (TEY) thiolester sequence in a MAP kinase (MAPK) substrate.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0047485	protein N-terminus binding	Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) 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:0004672	protein kinase activity	Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
	GO:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0043539	protein serine/threonine kinase activator activity	Binds to and increases the activity of a protein serine/threonine kinase.
	GO:0004674	protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
	GO:0004712	protein serine/threonine/tyrosine kinase activity	Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; ATP + a protein threonine = ADP + protein threonine phosphate; and ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
	GO:0004713	protein tyrosine kinase activity	Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
	GO:0004728	signal transducer, downstream of receptor, with protein tyrosine phosphatase activity	Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
	GO:0004702	signal transducer, downstream of receptor, with serine/threonine kinase activity	Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: ATP protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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:0070371	ERK1 and ERK2 cascade	An intracellular protein kinase cascade containing at least ERK1 or ERK2 (MAPKs), a MEK (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: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:0000187	activation of MAPK activity	The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
	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:0048870	cell motility	Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
	GO:0090398	cellular senescence	A cell aging process stimulated in response to cellular stress, whereby normal cells lose the ability to divide through irreversible cell cycle arrest.
	GO:0021697	cerebellar cortex formation	The process that gives rise to the cerebellar cortex. This process pertains to the initial formation of a structure from unspecified parts. The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function.
	GO:0006935	chemotaxis	The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0060502	epithelial cell proliferation involved in lung morphogenesis	The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population that contributes to the shaping of the lung.
	GO:0060324	face development	The biological process whose specific outcome is the progression of a face from an initial condition to its mature state. The face is the ventral division of the head.
	GO:0007507	heart development	The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
	GO:0030216	keratinocyte differentiation	The process in which a relatively unspecialized cell acquires specialized features of a keratinocyte.
	GO:0060711	labyrinthine layer development	The process in which the labyrinthine layer of the placenta progresses, from its formation to its mature state.
	GO:0060425	lung morphogenesis	The process in which the anatomical structures of the lung are generated and organized.
	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:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0010629	negative regulation of gene expression	Any process that decreases 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:0030182	neuron differentiation	The process in which a relatively unspecialized cell acquires specialized features of a neuron.
	GO:0018108	peptidyl-tyrosine phosphorylation	The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0060674	placenta blood vessel development	The process whose specific outcome is the progression of a blood vessel of the placenta over time, from its formation to the mature structure.
	GO:0070374	positive regulation of ERK1 and ERK2 cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0050772	positive regulation of axonogenesis	Any process that activates or increases the frequency, rate or extent of axonogenesis.
	GO:0045597	positive regulation of cell differentiation	Any process that activates or increases the frequency, rate or extent of cell differentiation.
	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:0098779	positive regulation of macromitophagy in response to mitochondrial depolarization	The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
	GO:1903800	positive regulation of production of miRNAs involved in gene silencing by miRNA	Any process that activates or increases the frequency, rate or extent of production of miRNAs involved in gene silencing by miRNA.
	GO:0071902	positive regulation of protein serine/threonine kinase activity	Any process that increases the rate, frequency, or extent of protein serine/threonine kinase activity.
	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:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0035897	proteolysis in other organism	The chemical reactions and pathways performed by an organism resulting in the hydrolysis of proteins in another organism by cleavage of their peptide bonds.
	GO:0090170	regulation of Golgi inheritance	Any process that modulates the rate, frequency or extent of Golgi inheritance. Golgi inheritance is the partitioning of Golgi apparatus between daughter cells at cell division.
	GO:0048679	regulation of axon regeneration	Any process that modulates the frequency, rate or extent of axon regeneration.
	GO:2000641	regulation of early endosome to late endosome transport	Any process that modulates the frequency, rate or extent of early endosome to late endosome transport.
	GO:0001932	regulation of protein phosphorylation	Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein.
	GO:0032872	regulation of stress-activated MAPK cascade	Any process that modulates the frequency, rate or extent of signal transduction mediated by the stress-activated MAPK cascade.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0048538	thymus development	The process whose specific outcome is the progression of the thymus over time, from its formation to the mature structure. The thymus is a symmetric bi-lobed organ involved primarily in the differentiation of immature to mature T cells, with unique vascular, nervous, epithelial, and lymphoid cell components.
	GO:0030878	thyroid gland development	The process whose specific outcome is the progression of the thyroid gland over time, from its formation to the mature structure. The thyroid gland is an endoderm-derived gland that produces thyroid hormone.
	GO:0060440	trachea formation	The process pertaining to the initial formation of a trachea from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the trachea is recognizable. The trachea is the portion of the airway that attaches to the bronchi as it branches.
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: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:0005769	early endosome	A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
	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: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:0005770	late endosome	A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005815	microtubule organizing center	An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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Description

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