3M54 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   SET7/9 Y305F IN COMPLEX WITH TAF10 PEPTIDE AND ADOHCY

Authors :   P. A. Del Rizzo, J. -F. Couture, M. S. Roiko, B. S. Strunk, J. S. Brunzell L. M. Dirk, R. L. Houtz, R. C. Trievel

Date :   12 Mar 10 (Deposition) - 28 Jul 10 (Release) - 14 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A,B

Keywords :   Ternary Complex, Set Domain, Methyltransferase, S-Adenosyl-L- Homocysteine, Taf10 Peptide, Chromatin Regulator, Chromosomal Protein, Nucleus, S-Adenosyl-L-Methionine, Transcription, Transcription Regulation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. A. Del Rizzo, J. F. Couture, L. M. Dirk, B. S. Strunk, M. S. Roiko, J. S. Brunzelle, R. L. Houtz, R. C. Trievel
Set7/9 Catalytic Mutants Reveal The Role Of Active Site Water Molecules In Lysine Multiple Methylation.
J. Biol. Chem. V. 285 31849 2010
PubMed-ID: 20675860 | Reference-DOI: 10.1074/JBC.M110.114587

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE SETD7
	Chains	:	A
	EC Number	:	2.1.1.43
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHIS2
	Expression System Strain	:	BL21(DE3)ROSETTA2
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 110-366
	Gene	:	KIAA1717, KMT7, SET7, SET9, SETD7
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Strain	:	9606
	Synonym	:	HISTONE H3-K4 METHYLTRANSFERASE SETD7, H3-K4-HMTASE SETD7, SET DOMAIN-CONTAINING PROTEIN 7, SET7/9, LYSINE N-METHYLTRANSFERASE 7

Molecule 2 - TAF10 PEPTIDE
	Chains	:	B
	Engineered	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:44 , HOH A:66 , HOH A:90 , ALA A:226 , GLU A:228 , GLY A:264 , ASN A:265 , HIS A:293 , LYS A:294 , ASN A:296 , HIS A:297 , TYR A:335 , TRP A:352 , GLU A:356 , HOH A:379 , HOH A:463 , HOH A:475 , HOH A:480	BINDING SITE FOR RESIDUE SAH A 800

(no "SS Bond" information available for 3M54)

Asymmetric/Biological Unit

No.	Residues
1	Glu A:279	-	Pro A:280

(no "SAP(SNP)/Variant" information available for 3M54)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SET	PS50280	SET domain profile.	SETD7_HUMAN	214-336	1	A:214-336

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000274031	1a	ENSE00001831410	chr4:140477928-140477252	677	SETD7_HUMAN	1-14	14	0	-	-
1.3	ENST00000274031	3	ENSE00001613109	chr4:140468203-140468074	130	SETD7_HUMAN	14-57	44	0	-	-
1.4a	ENST00000274031	4a	ENSE00001643989	chr4:140454520-140454319	202	SETD7_HUMAN	57-124	68	1	A:116-124	9
1.5	ENST00000274031	5	ENSE00001671090	chr4:140450374-140450185	190	SETD7_HUMAN	125-188	64	1	A:125-188	64
1.6	ENST00000274031	6	ENSE00001802218	chr4:140444589-140444508	82	SETD7_HUMAN	188-215	28	1	A:188-215	28
1.7b	ENST00000274031	7b	ENSE00001663487	chr4:140441548-140441431	118	SETD7_HUMAN	215-254	40	1	A:215-254	40
1.8	ENST00000274031	8	ENSE00001734092	chr4:140439196-140439039	158	SETD7_HUMAN	255-307	53	1	A:255-307	53
1.9	ENST00000274031	9	ENSE00001192306	chr4:140432997-140427190	5808	SETD7_HUMAN	307-366	60	1	A:307-365 (gaps)	59

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:245
 aligned with SETD7_HUMAN | Q8WTS6 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:250
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365
          SETD7_HUMAN   116 HGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSPPGKSGPEAPEWYQVELKAFQATQQ 365
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains MORN-3m54A01 --------------------------------------------------------------------------------------------------SET-3m54A02 A:227-336                                                                                         ----------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeee.........eeeeeee.....eeeeeeee..eeeeeeeeeeeeee..eeeeee.....ee.................hhhhhhheeeee.......eeeee........eeeee..eeehhhhhhh.hhhhh...ee.....eee..............hhhhhee.....eeeeeeee...eeeeeeee........eeee........-----...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------SET  PDB: A:214-336 UniProt: 214-336                                                                                       ----------------------------- PROSITE
           Transcript 1 (1) Exon 1.4aExon 1.5  PDB: A:125-188 UniProt: 125-188                       --------------------------Exon 1.7b  PDB: A:215-254               Exon 1.8  PDB: A:255-307 UniProt: 255-307            ---------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------Exon 1.6  PDB: A:188-215    -------------------------------------------------------------------------------------------Exon 1.9  PDB: A:307-365 (gaps) UniProt: 307-366            Transcript 1 (2)
                 3m54 A 116 HGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIFDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSP-----PEAPEWYQVELKAFQATQQ 365
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335     |   - |     355       365
                                                                                                                                                                                                                                                           341   347

Chain B from PDB  Type:PROTEIN  Length:9
 aligned with TAF10_HUMAN | Q12962 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:9
          TAF10_HUMAN   185 RSKSKDRKY 193
               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
                 3m54 B 185 xSKSKDRKY 193
                            |        
                          185-ACE

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 3M54)

(no "CATH Domain" information available for 3M54)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: MORN (14)

Family: MORN (14)

Homo sapiens (Human) (14)

MORN-3m54A01

A:116-128

Clan: no clan defined [family: SET] (46)

Family: SET (46)

Homo sapiens (Human) (34)

SET-3m54A02

A:227-336

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SETD7_HUMAN | Q8WTS6)

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:0018024	histone-lysine N-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0002039	p53 binding	Interacting selectively and non-covalently with one of the p53 family of proteins.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0016279	protein-lysine N-methyltransferase activity	Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the epsilon-amino group of a lysine residue in a protein substrate.
	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: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:0070828	heterochromatin organization	Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic heterochromatin, a compact and highly condensed form of chromatin.
	GO:0034968	histone lysine methylation	The modification of a histone by addition of one or more methyl groups to a lysine residue.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0018027	peptidyl-lysine dimethylation	The methylation of peptidyl-lysine to form peptidyl-N6,N6-dimethyl-L-lysine.
	GO:0018022	peptidyl-lysine methylation	The methylation of peptidyl-lysine to form either the mono-, di- or trimethylated derivative.
	GO:0018026	peptidyl-lysine monomethylation	The methylation of peptidyl-lysine to form peptidyl-N6-methyl-L-lysine.
	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:0051570	regulation of histone H3-K9 methylation	Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 9 of histone H3.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0045471	response to ethanol	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	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.

Chain B (TAF10_HUMAN | Q12962)

molecular function
	GO:0070063	RNA polymerase binding	Interacting selectively and non-covalently with an RNA polymerase molecule or complex.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0030331	estrogen receptor binding	Interacting selectively and non-covalently with an estrogen receptor.
	GO:0004402	histone acetyltransferase activity	Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
	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:0003713	transcription coactivator activity	Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0006352	DNA-templated transcription, initiation	Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
	GO:0043966	histone H3 acetylation	The modification of histone H3 by the addition of an acetyl group.
	GO:0016578	histone deubiquitination	The modification of histones by removal of ubiquitin groups.
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:1901796	regulation of signal transduction by p53 class mediator	Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006368	transcription elongation from RNA polymerase II promoter	The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006367	transcription initiation from RNA polymerase II promoter	Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0000125	PCAF complex	A large multiprotein complex that possesses histone acetyltransferase activity and is involved in regulation of transcription. The composition is similar to that of the SAGA complex, but includes fewer Spt and Ada proteins, and more TAFs.
	GO:0030914	STAGA complex	A large multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. The composition is similar to that of the SAGA complex; for example, the human complex contains the transcription-transformation cofactor TRRAP, hGCN5L acetylase, novel human ADA-like and SPT-like cofactors, and a subset of TAFs.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	GO:0005669	transcription factor TFIID complex	A complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters.
	GO:0033276	transcription factor TFTC complex	A protein complex that does not contain either a TATA-binding protein (TBP) or a TBP-like factor, but is composed of several TAFIIs and other proteins, including a histone acetyltransferase. This complex is able to nucleate transcription initiation by RNA polymerase II, can mediate transcriptional activation, and has histone acetyltransferase activity.

Asymmetric/Biological Unit
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	3m54
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2f69	TERNARY COMPLEX OF SET7/9 BOUND TO ADOHCY AND A TAF10 PEPTIDE
3m53
3m55
3m56
3m57
3m58
3m59
3m5a

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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Exons (6, 6)

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