2RT5 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   STRUCTURAL INSIGHTS INTO THE RECRUITMENT OF SMRT BY THE CO-REPRESSOR SHARP UNDER PHOSPHORYLATIVE REGULATION

Authors :   S. Mikami, T. Kanaba, M. Mishima

Date :   22 Apr 13 (Deposition) - 04 Dec 13 (Release) - 04 Dec 13 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)
NMR Structure *: A,B  (1x)

Keywords :   Sharp, Spoc Domain, Smrt, Phosphorylation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Mikami, T. Kanaba, N. Takizawa, A. Kobayashi, R. Maesaki, T. Fujiwara, Y. Ito, M. Mishima
Structural Insights Into The Recruitment Of Smrt By The Corepressor Sharp Under Phosphorylative Regulation
Structure 2013
PubMed-ID: 24268649 | Reference-DOI: 10.1016/J.STR.2013.10.007

Molecule 1 - MSX2-INTERACTING PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PGEX6P-3
	Expression System Vector Type	:	VECTOR
	Fragment	:	SPOC DOMAIN, RESIDUES 3496-3664
	Gene	:	SHARP
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SMART/HDAC1-ASSOCIATED REPRESSOR PROTEIN, SPEN HOMOLOG

Molecule 2 - PEPTIDE FROM SILENCING MEDIATOR OF RETINOIC ACID AND THYROID HORMONE RECEPTOR
	Chains	:	B
	Engineered	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

		1	2
NMR Structure (20x)	:	A	B
NMR Structure * (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 2)

No.	Name	Count	Type	Full Name
1	SEP	2	Mod. Amino Acid	PHOSPHOSERINE

NMR Structure * (1, 2)

No.	Name	Count	Type	Full Name
1	SEP	2	Mod. Amino Acid	PHOSPHOSERINE

(no "Site" information available for 2RT5)

(no "SS Bond" information available for 2RT5)

(no "Cis Peptide Bond" information available for 2RT5)

(no "SAP(SNP)/Variant" information available for 2RT5)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SPOC	PS50917	SPOC domain profile.	MINT_HUMAN	3498-3664	1	A:3498-3664

NMR Structure * (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SPOC	PS50917	SPOC domain profile.	MINT_HUMAN	3498-3664	1	A:3498-3664

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000375759	1	ENSE00001468313	chr1:16174359-16174645	287	MINT_HUMAN	1-28	28	0	-	-
1.2	ENST00000375759	2	ENSE00001065383	chr1:16199311-16199631	321	MINT_HUMAN	28-135	108	0	-	-
1.4a	ENST00000375759	4a	ENSE00000955468	chr1:16202697-16203173	477	MINT_HUMAN	135-294	160	0	-	-
1.5a	ENST00000375759	5a	ENSE00000827972	chr1:16235816-16235976	161	MINT_HUMAN	294-348	55	0	-	-
1.6	ENST00000375759	6	ENSE00002153898	chr1:16237596-16237796	201	MINT_HUMAN	348-415	68	0	-	-
1.7	ENST00000375759	7	ENSE00001734774	chr1:16242623-16242774	152	MINT_HUMAN	415-465	51	0	-	-
1.8	ENST00000375759	8	ENSE00001633894	chr1:16245421-16245546	126	MINT_HUMAN	466-507	42	0	-	-
1.9	ENST00000375759	9	ENSE00001776313	chr1:16245899-16246012	114	MINT_HUMAN	508-545	38	0	-	-
1.10b	ENST00000375759	10b	ENSE00001771430	chr1:16247365-16247478	114	MINT_HUMAN	546-583	38	0	-	-
1.11	ENST00000375759	11	ENSE00001597480	chr1:16248744-16248844	101	MINT_HUMAN	584-617	34	0	-	-
1.12b	ENST00000375759	12b	ENSE00000827978	chr1:16254586-16262761	8176	MINT_HUMAN	617-3342	2726	0	-	-
1.13	ENST00000375759	13	ENSE00000751295	chr1:16263658-16264140	483	MINT_HUMAN	3343-3503	161	1	A:3496-3503	8
1.14	ENST00000375759	14	ENSE00000827979	chr1:16264307-16264501	195	MINT_HUMAN	3504-3568	65	1	A:3504-3568	65
1.15b	ENST00000375759	15b	ENSE00000827980	chr1:16265213-16265371	159	MINT_HUMAN	3569-3621	53	1	A:3569-3621	53
1.16b	ENST00000375759	16b	ENSE00001468270	chr1:16265791-16266955	1165	MINT_HUMAN	3622-3664	43	1	A:3622-3664	43

NMR Structure

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:169
 aligned with MINT_HUMAN | Q96T58 from UniProtKB/Swiss-Prot  Length:3664

    Alignment length:169
                                  3505      3515      3525      3535      3545      3555      3565      3575      3585      3595      3605      3615      3625      3635      3645      3655         
          MINT_HUMAN   3496 VDMVQLLKKYPIVWQGLLALKNDTAAVQLHFVSGNNVLAHRSLPLSEGGPPLRIAQRMRLEATQLEGVARRMTVETDYCLLLALPCGRDQEDVVSQTESLKAAFITYLQAKQAAGIINVPNPGSNQPAYVLQIFPPCEFSESHLSRLAPDLLASISNISPHLMIVIASV 3664
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh....eeeeeeeee..eeeeeeeeeeeehhhhhhhhh........ee..ee...hhhhhhhhhhhhh....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh..eeeee.........eeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --SPOC  PDB: A:3498-3664 UniProt: 3498-3664                                                                                                                               PROSITE
               Transcript 1 1.13    Exon 1.14  PDB: A:3504-3568 UniProt: 3504-3568                   Exon 1.15b  PDB: A:3569-3621 UniProt: 3569-3621      Exon 1.16b  PDB: A:3622-3664                Transcript 1
                2rt5 A 3496 VDMVQLLKKYPIVWQGLLALKNDTAAVQLHFVSGNNVLAHRSLPLSEGGPPLRIAQRMRLEATQLEGVARRMTVETDYCLLLALPCGRDQEDVVSQTESLKAAFITYLQAKQAAGIINVPNPGSNQPAYVLQIFPPCEFSESHLSRLAPDLLASISNISPHLMIVIASV 3664
                                  3505      3515      3525      3535      3545      3555      3565      3575      3585      3595      3605      3615      3625      3635      3645      3655

Chain B from PDB  Type:PROTEIN  Length:8
 aligned with NCOR2_HUMAN | Q9Y618 from UniProtKB/Swiss-Prot  Length:2525

    Alignment length:8
         NCOR2_HUMAN   2518 YETLSDSE 2525
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                2rt5 B 2518 YETLsDsE 2525
                                | | 
                             2522-SEP
                               2524-SEP

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 '\|'

(no "SCOP Domain" information available for 2RT5)

(no "CATH Domain" information available for 2RT5)

(no "Pfam Domain" information available for 2RT5)

NMR Structure(hide GO term definitions)

Chain A (MINT_HUMAN | Q96T58)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0001085	RNA polymerase II transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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: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: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:0007219	Notch signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0000398	mRNA splicing, via spliceosome	The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
	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:0050769	positive regulation of neurogenesis	Any process that activates or increases the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
	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.
	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: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: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.

Chain B (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.

NMR Structure
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(no "Related Entries Specified in the PDB File" available for 2RT5)

Description

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Ligands, Modified Residues, Ions (1, 2)

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