2LKM - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   STRUCTURAL BASIS FOR MOLECULAR INTERACTIONS INVOLVING MRG DOMAINS: IMPLICATIONS IN CHROMATIN BIOLOGY

Authors :   T. Xie, I. Radhakrishnan

Date :   16 Oct 11 (Deposition) - 18 Jan 12 (Release) - 21 Mar 12 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

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

Keywords :   Protein-Protein Complex, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Xie, R. Graveline, G. S. Kumar, Y. Zhang, A. Krishnan, G. David, I. Radhakrishnan
Structural Basis For Molecular Interactions Involving Mrg Domains: Implications In Chromatin Biology.
Structure V. 20 151 2012
PubMed-ID: 22244764 | Reference-DOI: 10.1016/J.STR.2011.10.019

Molecule 1 - PHD FINGER PROTEIN 12
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector	:	PMCSG7
	Fragment	:	UNP RESIDUES 200-241
	Gene	:	PHF12, KIAA1523
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PHD FACTOR 1, PF1

Molecule 2 - MORTALITY FACTOR 4-LIKE PROTEIN 1
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector	:	PMCSG7
	Fragment	:	UNP RESIDUES 194-362
	Gene	:	MORF4L1, MRG15, FWP006, HSPC008, HSPC061, PP368
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MORF-RELATED GENE 15 PROTEIN, PROTEIN MSL3-1, TRANSCRIPTION FACTOR-LIKE PROTEIN MRG15

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2LKM)

(no "Site" information available for 2LKM)

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

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

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MRG	PS51640	MRG domain profile.	MO4L1_HUMAN	191-362	1	B:155-323

NMR Structure * (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MRG	PS51640	MRG domain profile.	MO4L1_HUMAN	191-362	1	B:155-323

NMR Structure (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000331268	2b	ENSE00001829419	chr15:79165211-79165399	189	MO4L1_HUMAN	1-14	14	0	-	-
1.3	ENST00000331268	3	ENSE00001335587	chr15:79170555-79170601	47	MO4L1_HUMAN	14-29	16	0	-	-
1.4	ENST00000331268	4	ENSE00001335586	chr15:79172854-79172921	68	MO4L1_HUMAN	30-52	23	0	-	-
1.5	ENST00000331268	5	ENSE00001335584	chr15:79177309-79177425	117	MO4L1_HUMAN	52-91	40	0	-	-
1.6	ENST00000331268	6	ENSE00001335511	chr15:79178483-79178569	87	MO4L1_HUMAN	91-120	30	0	-	-
1.7	ENST00000331268	7	ENSE00001335510	chr15:79179611-79179691	81	MO4L1_HUMAN	120-147	28	0	-	-
1.8	ENST00000331268	8	ENSE00001335509	chr15:79183331-79183356	26	MO4L1_HUMAN	147-156	10	0	-	-
1.9	ENST00000331268	9	ENSE00001335507	chr15:79183826-79183914	89	MO4L1_HUMAN	156-185	30	0	-	-
1.10	ENST00000331268	10	ENSE00001335505	chr15:79184554-79184655	102	MO4L1_HUMAN	186-219	34	1	B:152-180	29
1.11	ENST00000331268	11	ENSE00001335503	chr15:79185881-79185969	89	MO4L1_HUMAN	220-249	30	1	B:181-210	30
1.12	ENST00000331268	12	ENSE00001335501	chr15:79186400-79186572	173	MO4L1_HUMAN	249-307	59	1	B:210-268	59
1.13	ENST00000331268	13	ENSE00001335499	chr15:79187162-79187246	85	MO4L1_HUMAN	307-335	29	1	B:268-296	29
1.14b	ENST00000331268	14b	ENSE00001899262	chr15:79189325-79190475	1151	MO4L1_HUMAN	335-362	28	1	B:296-323	28

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:42
 aligned with PHF12_HUMAN | Q96QT6 from UniProtKB/Swiss-Prot  Length:1004

    Alignment length:42
                                   209       219       229       239  
          PHF12_HUMAN   200 DYVQPQLRRPFELLIAAAMERNPTQFQLPNELTCTTALPGSS 241
               SCOP domains ------------------------------------------ SCOP domains
               CATH domains ------------------------------------------ CATH domains
               Pfam domains ------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------ PROSITE
                 Transcript ------------------------------------------ Transcript
                 2lkm A 200 DYVQPQLRRPFELLIAAAMERNPTQFQLPNELTCTTALPGSS 241
                                   209       219       229       239

Chain B from PDB  Type:PROTEIN  Length:172
 aligned with MO4L1_HUMAN | Q9UBU8 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:172
                                   200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360  
          MO4L1_HUMAN   191 NRVEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYKKSRGNTDNKEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPEYHRKAV 362
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhh...eee.......hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh..........hhhhhhhhhh.....hhhh..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.hhhh.....eee...hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE MRG  PDB: B:155-323 UniProt: 191-362                                                                                                                                         PROSITE
           Transcript 1 (1) Exon 1.10  PDB: B:152-180    Exon 1.11  PDB: B:181-210     ---------------------------------------------------------Exon 1.13  PDB: B:268-296    --------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.12  PDB: B:210-268 UniProt: 249-307                 ---------------------------Exon 1.14b  PDB: B:296-323   Transcript 1 (2)
                 2lkm B 152 SNAEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYRKSRGNTDNKEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPEYHRKAV 323
                                   161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321

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 2LKM)

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

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

NMR Structure(hide GO term definitions)

Chain A (PHF12_HUMAN | Q96QT6)

molecular function
	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
	GO:0001106	RNA polymerase II transcription corepressor activity	Interacting selectively and non-covalently with an RNA polymerase II repressing transcription factor and also with the RNA polymerase II basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
	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:0042393	histone binding	Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0035091	phosphatidylinositol binding	Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
	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:0001222	transcription corepressor binding	Interacting selectively and non-covalently with a transcription corepressor, any protein involved in negative regulation of transcription via protein-protein interactions with transcription factors and other proteins that negatively regulate transcription. Transcription corepressors do not bind DNA directly, but rather mediate protein-protein interactions between repressing transcription factors and the basal transcription machinery.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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: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:0016580	Sin3 complex	A multiprotein complex that functions broadly in eukaryotic organisms as a transcriptional repressor of protein-coding genes, through the gene-specific deacetylation of histones. Amongst its subunits, the Sin3 complex contains Sin3-like proteins, and a number of core proteins that are shared with the NuRD complex (including histone deacetylases and histone binding proteins). The Sin3 complex does not directly bind DNA itself, but is targeted to specific genes through protein-protein interactions with DNA-binding proteins.
	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 (MO4L1_HUMAN | Q9UBU8)

molecular function
	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: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).
biological process
	GO:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0006974	cellular response to DNA damage stimulus	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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0006338	chromatin remodeling	Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
	GO:0006342	chromatin silencing	Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.
	GO:0000724	double-strand break repair via homologous recombination	The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.
	GO:0043968	histone H2A acetylation	The modification of histone H2A by the addition of an acetyl group.
	GO:0043967	histone H4 acetylation	The modification of histone H4 by the addition of an acetyl group.
	GO:0016575	histone deacetylation	The modification of histones by removal of acetyl groups.
	GO:0040008	regulation of growth	Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.
	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:0035267	NuA4 histone acetyltransferase complex	A complex having histone acetylase activity on chromatin, as well as ATPase, DNA helicase and structural DNA binding activities. The complex is thought to be involved in double-strand DNA break repair. Subunits of the human complex include HTATIP/TIP60, TRRAP, RUVBL1, BUVBL2, beta-actin and BAF53/ACTL6A. In yeast, the complex has 13 subunits, including the catalytic subunit Esa1 (homologous to human Tip60).
	GO:0016580	Sin3 complex	A multiprotein complex that functions broadly in eukaryotic organisms as a transcriptional repressor of protein-coding genes, through the gene-specific deacetylation of histones. Amongst its subunits, the Sin3 complex contains Sin3-like proteins, and a number of core proteins that are shared with the NuRD complex (including histone deacetylases and histone binding proteins). The Sin3 complex does not directly bind DNA itself, but is targeted to specific genes through protein-protein interactions with DNA-binding proteins.
	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.

NMR Structure
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	MO4L1_HUMAN \| Q9UBU8	:	2aql 2efi 2f5j 2f5k 2n1d
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