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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURAL BASIS FOR THE PRODUCT SPECIFICITY OF HISTONE LYSINE METHYLTRANSFERASES

Authors :   X. Zhang, Z. Yang, S. I. Khan, J. R. Horton, H. Tamaru, E. U. Selker, X. Cheng

Date :   21 May 03 (Deposition) - 05 Aug 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.59

Chains :   Asym. Unit : A,B,P,Q
Biol. Unit 1: A,P  (1x)
Biol. Unit 2: B,Q  (1x)

Keywords :   Ternary Structure Of Dim-5, A Suv39-Type Histone-H3 Lys-9 Methyltransferase, Set Domain Protein Forms A Knot-Like Substructure, Pre-Set Triangular Zn3Cys9 Zinc Cluster, Post- Set Zinc-Binding Site, A Hybrid Beta Sheet Formed By Dim-5 And H3 Tail (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Zhang, Z. Yang, S. I. Khan, J. R. Horton, H. Tamaru, E. U. Selker, X. Cheng
Structural Basis For The Product Specificity Of Histone Lysine Methyltransferases
Mol. Cell V. 12 177 2003
PubMed-ID: 12887903 | Reference-DOI: 10.1016/S1097-2765(03)00224-7
(for further references see the PDB file header)

Molecule 1 - HISTONE H3 METHYLTRANSFERASE DIM-5
	Chains	:	A, B
	EC Number	:	2.1.1.43
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PXC379
	Expression System Strain	:	BL21(DE3) CODON PLUS RIL (STRATAGENE)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PGEX2T
	Fragment	:	RESIDUES 17-318
	Organism Scientific	:	NEUROSPORA CRASSA
	Organism Taxid	:	5141

Molecule 2 - HISTONE H3
	Chains	:	P, Q
	Engineered	:	YES
	Fragment	:	RESIDUES 1-15
	Other Details	:	THE HISTONE H3 PEPTIDE (N-TERMINAL RESIDUES 1-15) IS SYNTHESIZED.
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	P	Q
Biological Unit 1 (1x)	:	A		P
Biological Unit 2 (1x)	:		B		Q

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:66 , CYS A:81 , CYS A:128 , CYS A:132	BINDING SITE FOR RESIDUE ZN A 1
02	AC2	SOFTWARE	CYS A:74 , CYS A:128 , CYS A:134 , CYS A:138	BINDING SITE FOR RESIDUE ZN A 2
03	AC3	SOFTWARE	CYS A:66 , CYS A:68 , CYS A:74 , CYS A:79	BINDING SITE FOR RESIDUE ZN A 3
04	AC4	SOFTWARE	CYS A:244 , CYS A:306 , CYS A:308 , CYS A:313	BINDING SITE FOR RESIDUE ZN A 4
05	AC5	SOFTWARE	ZN B:6 , CYS B:132	BINDING SITE FOR RESIDUE ZN B 5
06	AC6	SOFTWARE	ZN B:5 , ZN B:7 , CYS B:134 , CYS B:138	BINDING SITE FOR RESIDUE ZN B 6
07	AC7	SOFTWARE	ZN B:6	BINDING SITE FOR RESIDUE ZN B 7
08	AC8	SOFTWARE	CYS B:244 , CYS B:306 , CYS B:308 , CYS B:313	BINDING SITE FOR RESIDUE ZN B 8
09	AC9	SOFTWARE	ARG A:159 , TRP A:161 , ASP A:202 , VAL A:203 , TYR A:204 , ARG A:238 , ASN A:241 , HIS A:242 , TYR A:283 , CYS A:306 , LEU A:307 , LEU A:317	BINDING SITE FOR RESIDUE SAH A 319
10	BC1	SOFTWARE	ARG B:159 , TRP B:161 , LYS B:201 , ASP B:202 , VAL B:203 , TYR B:204 , ARG B:238 , ASN B:241 , HIS B:242 , TYR B:283 , LYS B:305 , CYS B:306 , LEU B:307 , LEU B:317 , LYS Q:9	BINDING SITE FOR RESIDUE SAH B 2

(no "SS Bond" information available for 1PEG)

(no "Cis Peptide Bond" information available for 1PEG)

(no "SAP(SNP)/Variant" information available for 1PEG)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PRE_SET	PS50867	Pre-SET domain profile.	DIM5_NEUCR	77-159	2	A:64-146 B:64-146
2	SET	PS50280	SET domain profile.	DIM5_NEUCR	162-297	2	A:149-284 B:149-284
3	POST_SET	PS50868	Post-SET domain profile.	DIM5_NEUCR	315-331	2	A:306-318 B:304-318

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PRE_SET	PS50867	Pre-SET domain profile.	DIM5_NEUCR	77-159	1	A:64-146 -
2	SET	PS50280	SET domain profile.	DIM5_NEUCR	162-297	1	A:149-284 -
3	POST_SET	PS50868	Post-SET domain profile.	DIM5_NEUCR	315-331	1	A:306-318 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PRE_SET	PS50867	Pre-SET domain profile.	DIM5_NEUCR	77-159	1	- B:64-146
2	SET	PS50280	SET domain profile.	DIM5_NEUCR	162-297	1	- B:149-284
3	POST_SET	PS50868	Post-SET domain profile.	DIM5_NEUCR	315-331	1	- B:304-318

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YNL031C	1	YNL031C.1	XIV:576052-575642	411	H3_YEAST	1-136	136	2	P:7-13 Q:7-11	7 5

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:266
 aligned with DIM5_NEUCR | Q8X225 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:293
                                    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   
           DIM5_NEUCR    39 LPISIVNREDDAFLNPNFRFIDHSIIGKNVPVADQSFRVGCSCASDEECMYSTCQCLDEMAPDSDEEADPYTRKKRFAYYSQGAKKGLLRDRVLQSQEPIYECHQGCACSKDCPNRVVERGRTVPLQIFRTKDRGWGVKCPVNIKRGQFVDRYLGEIITSEEADRRRAESTIARRKDVYLFALDKFSDPDSLDPLLAGQPLEVDGEYMSGPTRFINHSCDPNMAIFARVGDHADKHIHDLALFAIKDIPKGTELTFDYVNGLTGLESDAHDPSKISEMTKCLCGTAKCRGYLW 331
               SCOP domains d1pega_ A: Dim-5                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1pegA00 A:26-318 SET domain                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee............ee....ee...........................hhhhh....------.....................hhhhhhhh..ee..............hhhhhh....eeeee.....eeee.........eeee...eeehhhhhhhhhhhhhhhh.....eee................-..eee...eehhhhhhee.....eeeeeee.........eeeeee........eeee....--------------------............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------PRE_SET  PDB: A:64-146 UniProt: 77-159                                             --SET  PDB: A:149-284 UniProt: 162-297                                                                                                    -----------------POST_SET          PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1peg A  26 LPISIVNREDDAFLNPNFRFIDHSIIGKNVPVADQSFRVGCSCASDEECMYSTCQCLDEMAP------DPYTRKKRFAYYSQGAKKGLLRDRVLQSQEPIYECHQGCACSKDCPNRVVERGRTVPLQIFRTKDRGWGVKCPVNIKRGQFVDRYLGEIITSEEADRRRAESTIARRKDVYLFALDKFSDPDSLDPLLAG-PLEVDGEYMSGPTRFINHSCDPNMAIFARVGDHADKHIHDLALFAIKDIPKGTELTFDYVN--------------------CLCGTAKCRGYLW 318
                                    35        45        55        65        75        85 |      95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285         -         -|      315   
                                                                                        87     94                                                                                                                              223 |                                                         285                  306            
                                                                                                                                                                                                                                 225

Chain B from PDB  Type:PROTEIN  Length:256
 aligned with DIM5_NEUCR | Q8X225 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:293
                                    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   
           DIM5_NEUCR    39 LPISIVNREDDAFLNPNFRFIDHSIIGKNVPVADQSFRVGCSCASDEECMYSTCQCLDEMAPDSDEEADPYTRKKRFAYYSQGAKKGLLRDRVLQSQEPIYECHQGCACSKDCPNRVVERGRTVPLQIFRTKDRGWGVKCPVNIKRGQFVDRYLGEIITSEEADRRRAESTIARRKDVYLFALDKFSDPDSLDPLLAGQPLEVDGEYMSGPTRFINHSCDPNMAIFARVGDHADKHIHDLALFAIKDIPKGTELTFDYVNGLTGLESDAHDPSKISEMTKCLCGTAKCRGYLW 331
               SCOP domains d1pegb_ B: Dim-5                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1pegB00 B:26-318 SET domain                                                                                                                                                                                                                                                                           CATH domains
           Pfam domains (1) Pre-SET-1pegB01 B:26-141                                                                                            ------------------SET-1pegB03 B:160-284                                                                                                        --                 --------------- Pfam domains (1)
           Pfam domains (2) Pre-SET-1pegB02 B:26-141                                                                                            ------------------SET-1pegB04 B:160-284                                                                                                        --                 --------------- Pfam domains (2)
         Sec.struct. author ..eeee............ee....ee....................................------------...............hhhhhhhh..ee..............hhhhhh....eeeee.....eeee.........eeeee..eeehhhhhhhhhhhhhh.......eee..........--------.eee...eehhhhhhee.....eeeeeee.........eeeeee........eeee.....-----------------............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------PRE_SET  PDB: B:64-146 UniProt: 77-159                                             --SET  PDB: B:149-284 UniProt: 162-297                                                                                                    -----------------POST_SET          PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1peg B  26 LPISIVNREDDAFLNPNFRFIDHSIIGKNVPVADQSFRVGCSCASDEECMYSTCQCLDEMAP------------KRFAYYSQGAKKGLLRDRVLQSQEPIYECHQGCACSKDCPNRVVERGRTVPLQIFRTKDRGWGVKCPVNIKRGQFVDRYLGEIITSEEADRRRAESTIARRKDVYLFALDKFSDPDSL--------LEVDGEYMSGPTRFINHSCDPNMAIFARVGDHADKHIHDLALFAIKDIPKGTELTFDYVNG-----------------TKCLCGTAKCRGYLW 318
                                    35        45        55        65        75        85 |       -    |  105       115       125       135       145       155       165       175       185       195       205       215 |       -|      235       245       255       265       275       285|        -       305       315   
                                                                                        87          100                                                                                                                  217      226                                                         286               304

Chain P from PDB  Type:PROTEIN  Length:7
 aligned with H3_KLULA | P61831 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:7
             H3_KLULA     8 ARKSTGG  14
               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
                 1peg P   7 ARKSTGG  13

Chain P from PDB  Type:PROTEIN  Length:7
 aligned with H3_YEAST | P61830 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:7
             H3_YEAST     8 ARKSTGG  14
               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 1 1.1     Transcript 1
                 1peg P   7 ARKSTGG  13

Chain Q from PDB  Type:PROTEIN  Length:5
 aligned with H3_KLULA | P61831 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:5
             H3_KLULA     8 ARKST  12
               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
                 1peg Q   7 ARKST  11

Chain Q from PDB  Type:PROTEIN  Length:5
 aligned with H3_YEAST | P61830 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:5
             H3_YEAST     8 ARKST  12
               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 1 1.1   Transcript 1
                 1peg Q   7 ARKST  11

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: beta-clip (280)

Superfamily: SET domain (44)

Family: Histone lysine methyltransferases (21)

Protein domain: Dim-5 (2)

Fungus (Neurospora crassa) [TaxId: 5141] (2)

1a	d1pega_	A:
1b	d1pegb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Complex (381)

Topology: Beta-clip-like (18)

Homologous Superfamily: SET domain (18)

Neurospora crassa. Organism_taxid: 5141. (2)

1a	1pegB00	B:26-318
1b	1pegA00	A:26-318

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Pre-SET] (11)

Family: Pre-SET (11)

Neurospora crassa (2)

1a	Pre-SET-1pegB01	B:26-141
1b	Pre-SET-1pegB02	B:26-141

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

Family: SET (46)

Neurospora crassa (2)

2a	SET-1pegB03	B:160-284
2b	SET-1pegB04	B:160-284

Asymmetric Unit(hide GO term definitions)

Chain A,B (DIM5_NEUCR | Q8X225)

molecular function
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	GO:0042054	histone methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + histone = S-adenosyl-L-homocysteine + methyl-histone. Histone methylation generally occurs on either an arginine or lysine residue.
	GO:0046974	histone methyltransferase activity (H3-K9 specific)	Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 9) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 9). This reaction is the addition of a methyl group onto lysine at position 9 of the histone H3 protein.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0035064	methylated histone binding	Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	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:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
	GO:0003727	single-stranded RNA binding	Interacting selectively and non-covalently with single-stranded RNA.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0051315	attachment of mitotic spindle microtubules to kinetochore	The cell cycle process in which spindle microtubules become physically associated with the proteins making up the kinetochore complex as part of mitotic metaphase plate congression.
	GO:0034613	cellular protein localization	Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
	GO:0030702	chromatin silencing at centromere	Repression of transcription of centromeric DNA by altering the structure of chromatin.
	GO:1990141	chromatin silencing at centromere outer repeat region	Repression of transcription of DNA at the outer repeat region of a regional centromere by altering the structure of chromatin.
	GO:0000183	chromatin silencing at rDNA	Repression of transcription of ribosomal DNA by altering the structure of chromatin.
	GO:0030466	chromatin silencing at silent mating-type cassette	Repression of transcription at silent mating-type loci by alteration of the structure of chromatin.
	GO:0031048	chromatin silencing by small RNA	Repression of transcription by conversion of large regions of DNA into heterochromatin, directed by small RNAs sharing sequence identity to the repressed region.
	GO:0007535	donor selection	The process that determines which donor locus a cell uses, in preference to another, in mating type switching.
	GO:1902368	heterochromatin maintenance involved in chromatin silencing at centromere outer repeat region	Any heterochromatin maintenance that is involved in chromatin silencing at centromere outer repeat region.
	GO:0051567	histone H3-K9 methylation	The modification of histone H3 by addition of one or more methyl groups to lysine at position 9 of the histone.
	GO:0034968	histone lysine methylation	The modification of a histone by addition of one or more methyl groups to a lysine residue.
	GO:0045141	meiotic telomere clustering	The cell cycle process in which the dynamic reorganization of telomeres occurs in early meiotic prophase, during which meiotic chromosome ends are gathered in a bouquet arrangement at the inner surface of the nuclear envelope proximal to the spindle pole body. This plays an important role in progression through meiosis and precedes synapsis.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	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:0090065	regulation of production of siRNA involved in RNA interference	Any process that modulates the frequency, rate or extent of the production of siRNA, the cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of RNA interference.
cellular component
	GO:0043494	CLRC ubiquitin ligase complex	An cullin-dependent E3 ubiquitin ligase/histone H3-K9 methyltransferase complex essential for heterochromatin assembly by RNAi.
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0034507	chromosome, centromeric outer repeat region	The portion of the centromeric region of a chromosome that flanks the core region, encompassing repeated regions of a chromosome centromere and the proteins that bind to it.
	GO:0000775	chromosome, centromeric region	The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	GO:0044732	mitotic spindle pole body	The microtubule organizing center that forms as part of the mitotic cell cycle; functionally homologous to the animal cell centrosome.
	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 P,Q (H3_KLULA | P61831)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
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:0000786	nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
	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 P,Q (H3_YEAST | P61830)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0006333	chromatin assembly or disassembly	The formation or destruction of chromatin structures.
	GO:0070911	global genome nucleotide-excision repair	The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
	GO:0009303	rRNA transcription	The synthesis of ribosomal RNA (rRNA), any RNA that forms part of the ribosomal structure, from a DNA template.
	GO:0043935	sexual sporulation resulting in formation of a cellular spore	The formation of spores derived from the products of meiosis. A cellular spore is a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
	GO:0043505	CENP-A containing nucleosome	A form of nucleosome located only at the centromere, in which the histone H3 is replaced by the variant form CENP-A (sometimes known as CenH3).
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000788	nuclear nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures.
	GO:0000786	nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
	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:0031298	replication fork protection complex	A protein complex conserved in eukaryotes and associated with the replication fork; the complex stabilizes stalled replication forks and is thought to be involved in coordinating leading- and lagging-strand synthesis and in replication checkpoint signaling.

Asymmetric Unit
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	H3_KLULA \| P61831
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	2.1.1.43
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UniProtKB/Swiss-Prot
	DIM5_NEUCR \| Q8X225	:	1ml9
	H3_KLULA \| P61831	:	1m1d 1pu9 1pua
	H3_YEAST \| P61830	:	1id3 1m1d 1pu9 1pua 1qsn 2cnx 2h2g 2idc 2jmj 2rnw 2rnx 2rsn 3mp1 3mp6 3q33 4jjn 4kud 4psx 5d7e 5iok

1ml9	STRUCTURE OF THE NEUROSPOSA SET DOMAIN PROTEIN DIM-5, A HISTONE H3 LYSINE METHYLTRASFERASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (1, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (2, 4)

Gene Ontology (43, 51)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File