4A69 - 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 :   STRUCTURE OF HDAC3 BOUND TO COREPRESSOR AND INOSITOL TETRAPHOSPHATE

Authors :   P. J. Watson, L. Fairall, G. M. Santos, J. W. R. Schwabe

Date :   01 Nov 11 (Deposition) - 11 Jan 12 (Release) - 25 Jan 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.06

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)

Keywords :   Transcription, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. J. Watson, L. Fairall, G. M. Santos, J. W. R. Schwabe
Structure Of Hdac3 Bound To Co-Repressor And Inositol Tetraphosphate.
Nature V. 481 335 2012
PubMed-ID: 22230954 | Reference-DOI: 10.1038/NATURE10728

Molecule 1 - HISTONE DEACETYLASE 3,
	Chains	:	A, B
	EC Number	:	3.5.1.98
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293F
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PCDNA3
	Expression System Taxid	:	9606
	Fragment	:	RESIDUES 1-376
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HD3, RPD3-2, SMAP45, HDAC3

Molecule 2 - NUCLEAR RECEPTOR COREPRESSOR 2
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293F
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PCDNA3
	Expression System Taxid	:	9606
	Fragment	:	RESIDUES 389-480
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	N-COR2, CTG REPEAT PROTEIN 26, SMAP270, SILENCING MEDIATOR OF RETINOIC ACID AND THYROID HORMONE RECEPTOR, SMRT, T3 RECEPTOR-ASSOCIATING FACTOR, TRAC, THYROID-,RETINOIC-ACID-RECEPTOR-ASSOCIATED COREPRESSOR

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 14)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	I0P	2	Ligand/Ion	D-MYO INOSITOL 1,4,5,6 TETRAKISPHOSPHATE
4	K	4	Ligand/Ion	POTASSIUM ION
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	I0P	1	Ligand/Ion	D-MYO INOSITOL 1,4,5,6 TETRAKISPHOSPHATE
4	K	-1	Ligand/Ion	POTASSIUM ION
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	I0P	1	Ligand/Ion	D-MYO INOSITOL 1,4,5,6 TETRAKISPHOSPHATE
4	K	-1	Ligand/Ion	POTASSIUM ION
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:170 , HIS A:172 , ASP A:259 , ACT A:501	BINDING SITE FOR RESIDUE ZN A 500
02	AC2	SOFTWARE	HIS A:134 , HIS A:135 , GLY A:143 , ASP A:170 , HIS A:172 , ASP A:259 , GLY A:296 , TYR A:298 , ZN A:500	BINDING SITE FOR RESIDUE ACT A 501
03	AC3	SOFTWARE	ASP A:168 , ASP A:170 , HIS A:172 , SER A:191 , PHE A:192	BINDING SITE FOR RESIDUE K A 503
04	AC4	SOFTWARE	PHE A:181 , THR A:184 , VAL A:187 , TYR A:217 , HOH A:2087 , HOH A:2090	BINDING SITE FOR RESIDUE K A 504
05	AC5	SOFTWARE	GLN A:113 , THR A:116 , HOH A:2070 , ARG B:265 , I0P D:501 , HOH D:2011	BINDING SITE FOR RESIDUE GOL A 505
06	AC6	SOFTWARE	THR A:116 , ASN A:119 , ASN A:120 , GLU A:156 , TYR A:160 , LYS D:449 , I0P D:501	BINDING SITE FOR RESIDUE GOL A 506
07	AC7	SOFTWARE	ASP B:170 , HIS B:172 , ASP B:259 , ACT B:501	BINDING SITE FOR RESIDUE ZN B 500
08	AC8	SOFTWARE	HIS B:134 , HIS B:135 , ASP B:170 , HIS B:172 , ASP B:259 , GLY B:296 , TYR B:298 , ZN B:500 , MET C:412	BINDING SITE FOR RESIDUE ACT B 501
09	AC9	SOFTWARE	ASP B:168 , ASP B:170 , HIS B:172 , SER B:191 , PHE B:192	BINDING SITE FOR RESIDUE K B 503
10	BC1	SOFTWARE	PHE B:181 , THR B:184 , VAL B:187 , TYR B:217 , HOH B:2071 , HOH B:2075	BINDING SITE FOR RESIDUE K B 504
11	BC2	SOFTWARE	ARG A:265 , HOH A:2130 , TYR B:51 , GLN B:113 , THR B:116 , I0P C:501	BINDING SITE FOR RESIDUE GOL B 505
12	BC3	SOFTWARE	ASN B:119 , ASN B:120 , GLU B:156 , TYR B:160 , LYS C:449 , TYR C:470 , I0P C:501	BINDING SITE FOR RESIDUE GOL B 506
13	BC4	SOFTWARE	HIS A:17 , GLY A:21 , LYS A:25 , ARG A:265 , VAL A:300 , ARG A:301 , TYR A:331 , HOH A:2139 , HOH A:2140 , HOH A:2143 , ASN B:120 , GOL B:505 , GOL B:506 , HOH B:2062 , LYS C:449 , TYR C:470 , TYR C:471 , LYS C:474 , HOH C:2021 , HOH C:2022 , HOH C:2023	BINDING SITE FOR RESIDUE I0P C 501
14	BC5	SOFTWARE	THR A:116 , ASN A:120 , GOL A:505 , GOL A:506 , HIS B:17 , GLY B:21 , HIS B:22 , LYS B:25 , ARG B:265 , VAL B:300 , TYR B:331 , HOH B:2120 , HOH B:2121 , LYS D:449 , TYR D:470 , TYR D:471 , LYS D:474 , HOH D:2009 , HOH D:2010 , HOH D:2011	BINDING SITE FOR RESIDUE I0P D 501

(no "SS Bond" information available for 4A69)

Asymmetric Unit

No.	Residues
1	Phe A:200	-	Pro A:201
2	Ala A:333	-	Pro A:334
3	Phe B:200	-	Pro B:201
4	Ala B:333	-	Pro B:334

(no "SAP(SNP)/Variant" information available for 4A69)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SANT	PS51293	SANT domain profile.	NCOR2_HUMAN	427-478 610-661	2	C:427-476 D:427-475 -

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SANT	PS51293	SANT domain profile.	NCOR2_HUMAN	427-478 610-661	1	C:427-476 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SANT	PS51293	SANT domain profile.	NCOR2_HUMAN	427-478 610-661	1	- D:427-475 -

(no "Exon" information available for 4A69)

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:369
 aligned with HDAC3_HUMAN | O15379 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:369
                                    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       301       311       321       331       341       351       361         
          HDAC3_HUMAN     2 AKTVAYFYDPDVGNFHYGAGHPMKPHRLALTHSLVLHYGLYKKMIVFKPYQASQHDMCRFHSEDYIDFLQRVSPTNMQGFTKSLNAFNVGDDCPVFPGLFEFCSRYTGASLQGATQLNNKICDIAINWAGGLHHAKKFEASGFCYVNDIVIGILELLKYHPRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKYGNYFFPGTGDMYEVGAESGRYYCLNVPLRDGIDDQSYKHLFQPVINQVVDFYQPTCIVLQCGADSLGCDRLGCFNLSIRGHGECVEYVKSFNIPLLVLGGGGYTVRNVARCWTYETSLLVEEAISEELPYSEYFEYFAPDFTLHPDVSTRIENQNSRQYLDQIRQTIFENLKMLN 370
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.................hhhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhh...........hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh............hhhhhh.................hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a69 A   2 AKTVAYFYDPDVGNFHYGAGHPMKPHRLALTHSLVLHYGLYKKMIVFKPYQASQHDMCRFHSEDYIDFLQRVSPTNMQGFTKSLNAFNVGDDCPVFPGLFEFCSRYTGASLQGATQLNNKICDIAINWAGGLHHAKKFEASGFCYVNDIVIGILELLKYHPRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKYGNYFFPGTGDMYEVGAESGRYYCLNVPLRDGIDDQSYKHLFQPVINQVVDFYQPTCIVLQCGADSLGCDRLGCFNLSIRGHGECVEYVKSFNIPLLVLGGGGYTVRNVARCWTYETSLLVEEAISEELPYSEYFEYFAPDFTLHPDVSTRIENQNSRQYLDQIRQTIFENLKMLN 370
                                    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       301       311       321       331       341       351       361

Chain B from PDB  Type:PROTEIN  Length:369
 aligned with HDAC3_HUMAN | O15379 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:369
                                    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       301       311       321       331       341       351       361         
          HDAC3_HUMAN     2 AKTVAYFYDPDVGNFHYGAGHPMKPHRLALTHSLVLHYGLYKKMIVFKPYQASQHDMCRFHSEDYIDFLQRVSPTNMQGFTKSLNAFNVGDDCPVFPGLFEFCSRYTGASLQGATQLNNKICDIAINWAGGLHHAKKFEASGFCYVNDIVIGILELLKYHPRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKYGNYFFPGTGDMYEVGAESGRYYCLNVPLRDGIDDQSYKHLFQPVINQVVDFYQPTCIVLQCGADSLGCDRLGCFNLSIRGHGECVEYVKSFNIPLLVLGGGGYTVRNVARCWTYETSLLVEEAISEELPYSEYFEYFAPDFTLHPDVSTRIENQNSRQYLDQIRQTIFENLKMLN 370
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..................hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhh...........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhh............hhhhhh.................hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a69 B   2 AKTVAYFYDPDVGNFHYGAGHPMKPHRLALTHSLVLHYGLYKKMIVFKPYQASQHDMCRFHSEDYIDFLQRVSPTNMQGFTKSLNAFNVGDDCPVFPGLFEFCSRYTGASLQGATQLNNKICDIAINWAGGLHHAKKFEASGFCYVNDIVIGILELLKYHPRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKYGNYFFPGTGDMYEVGAESGRYYCLNVPLRDGIDDQSYKHLFQPVINQVVDFYQPTCIVLQCGADSLGCDRLGCFNLSIRGHGECVEYVKSFNIPLLVLGGGGYTVRNVARCWTYETSLLVEEAISEELPYSEYFEYFAPDFTLHPDVSTRIENQNSRQYLDQIRQTIFENLKMLN 370
                                    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       301       311       321       331       341       351       361

Chain C from PDB  Type:PROTEIN  Length:69
 aligned with NCOR2_HUMAN | Q9Y618 from UniProtKB/Swiss-Prot  Length:2525

    Alignment length:69
                                   417       427       437       447       457       467         
          NCOR2_HUMAN   408 KFINMNGLMADPMKVYKDRQVMNMWSEQEKETFREKFMQHPKNFGLIASFLERKTVAECVLYYYLTKKN 476
               SCOP domains d4a69c_ C: automated matches                                          SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhh....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------SANT  PDB: C:427-476 UniProt: 427-478              PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 4a69 C 408 KFINMNGLMADPMKVYKDRQVMNMWSEQEKETFREKFMQHPKNFGLIASFLERKTVAECVLYYYLTKKN 476
                                   417       427       437       447       457       467

Chain D from PDB  Type:PROTEIN  Length:68
 aligned with NCOR2_HUMAN | Q9Y618 from UniProtKB/Swiss-Prot  Length:2525

    Alignment length:68
                                   417       427       437       447       457       467        
          NCOR2_HUMAN   408 KFINMNGLMADPMKVYKDRQVMNMWSEQEKETFREKFMQHPKNFGLIASFLERKTVAECVLYYYLTKK 475
               SCOP domains d4a69d_ D: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------SANT  PDB: D:427-475 UniProt: 427-478             PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 4a69 D 408 KFINMNGLMADPMKVYKDRQVMNMWSEQEKETFREKFMQHPKNFGLIASFLERKTVAECVLYYYLTKK 475
                                   417       427       437       447       457       467

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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Homeodomain-like (373)

Family: Myb/SANT domain (34)

Protein domain: automated matches (1)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d4a69c_	C:
1b	d4a69d_	D:

(no "CATH Domain" information available for 4A69)

(no "Pfam Domain" information available for 4A69)

Asymmetric Unit(hide GO term definitions)

Chain A,B (HDAC3_HUMAN | O15379)

molecular function
	GO:0032041	NAD-dependent histone deacetylase activity (H3-K14 specific)	Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 14) + H2O = histone H3 L-lysine (position 14) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 14 of the histone H3 protein.
	GO:0051059	NF-kappaB binding	Interacting selectively and non-covalently with NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters.
	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:0030332	cyclin binding	Interacting selectively and non-covalently with cyclins, proteins whose levels in a cell varies markedly during the cell cycle, rising steadily until mitosis, then falling abruptly to zero. As cyclins reach a threshold level, they are thought to drive cells into G2 phase and thus to mitosis.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0004407	histone deacetylase activity	Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.
	GO:0042826	histone deacetylase binding	Interacting selectively and non-covalently with the enzyme histone deacetylase.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	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:0033558	protein deacetylase activity	Catalysis of the hydrolysis of an acetyl group or groups from a protein substrate.
	GO:0003714	transcription corepressor activity	Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
	GO:0044255	cellular lipid metabolic process	The chemical reactions and pathways involving lipids, as carried out by individual cells.
	GO:0071498	cellular response to fluid shear stress	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fluid shear stress stimulus. Fluid shear stress is the force acting on an object in a system where the fluid is moving across a solid surface.
	GO:0007623	circadian rhythm	Any biological process in an organism that recurs with a regularity of approximately 24 hours.
	GO:0070932	histone H3 deacetylation	The modification of histone H3 by the removal of one or more acetyl groups.
	GO:0016575	histone deacetylation	The modification of histones by removal of acetyl groups.
	GO:0046329	negative regulation of JNK cascade	Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the JNK cascade.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0010832	negative regulation of myotube differentiation	Any process that decreases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
	GO:1903507	negative regulation of nucleic acid-templated transcription	Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription.
	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:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0032008	positive regulation of TOR signaling	Any process that activates or increases the frequency, rate or extent of TOR signaling.
	GO:0001934	positive regulation of protein phosphorylation	Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
	GO:0042993	positive regulation of transcription factor import into nucleus	Any process that activates or increases the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus.
	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:0006476	protein deacetylation	The removal of an acetyl group from a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
	GO:0031647	regulation of protein stability	Any process that affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0051225	spindle assembly	The aggregation, arrangement and bonding together of a set of components to form the spindle, the array of microtubules and associated molecules that serves to move duplicated chromosomes apart.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0000118	histone deacetylase complex	A protein complex that possesses histone deacetylase activity.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	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.
	GO:0005876	spindle microtubule	Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole.
	GO:0017053	transcriptional repressor complex	A protein complex that possesses activity that prevents or downregulates transcription.

Chain C,D (NCOR2_HUMAN | Q9Y618)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0005112	Notch binding	Interacting selectively and non-covalently with the Notch (N) protein, a surface receptor.
	GO:0042826	histone deacetylase binding	Interacting selectively and non-covalently with the enzyme histone deacetylase.
	GO:0016922	ligand-dependent nuclear receptor binding	Interacting selectively and non-covalently, in a ligand dependent manner, with a nuclear receptor protein.
	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:0003714	transcription corepressor activity	Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
	GO:0044255	cellular lipid metabolic process	The chemical reactions and pathways involving lipids, as carried out by individual cells.
	GO:1903799	negative regulation of production of miRNAs involved in gene silencing by miRNA	Any process that stops, prevents or reduces the frequency, rate or extent of production of miRNAs involved in gene silencing by miRNA.
	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:0072365	regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of a cellular ketone metabolic process by stopping, preventing, or reducing the frequency, rate or extent of 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:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0000118	histone deacetylase complex	A protein complex that possesses histone deacetylase activity.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0016604	nuclear body	Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	GO:0016363	nuclear matrix	The dense fibrillar network lying on the inner side of the nuclear membrane.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0017053	transcriptional repressor complex	A protein complex that possesses activity that prevents or downregulates transcription.

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	NCOR2_HUMAN \| Q9Y618	:	1kkq 1r2b 1xc5 2gpv 2l5g 2ltp 2odd 2rt5 3r29 3r2a 4oar 5x8q 5x8x

1kkq	CRYSTAL STRUCTURE OF THE HUMAN PPAR-ALPHA LIGAND- BINDINGDOMAIN IN COMPLEX WITH AN ANTAGONIST GW6471 AND A SMRTCOREPRESSOR MOTIF
1r2b	CRYSTAL STRUCTURE OF THE BCL6 BTB DOMAIN COMPLEXED WITH ASMRT CO-REPRESSOR PEPTIDE
1xc5	SOLUTION STRUCTURE OF THE SMRT DEACETYLASE ACTIVATION DOMAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (51, 63)

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