3OXF - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   HUMAN LYSINE METHYLTRANSFERASE SMYD3 IN COMPLEX WITH ADOHCY (FORM I)

Authors :   S. Xu, J. Wu, B. Sun, C. Zhong, J. Ding

Date :   21 Sep 10 (Deposition) - 23 Feb 11 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.82

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

Keywords :   Smyd Proteins, Mynd, Set Domain, Histone Lysine Methyltransferase, Histone Methylation, H3K4, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Xu, J. Wu, B. Sun, C. Zhong, J. Ding
Structural And Biochemical Studies Of Human Lysine Methyltransferase Smyd3 Reveal The Important Functional Roles Of Its Post-Set And Tpr Domains And The Regulation Of Its Activity By Dna Binding.
Nucleic Acids Res. V. 39 4438 2011
PubMed-ID: 21266482 | Reference-DOI: 10.1093/NAR/GKR019

Molecule 1 - SET AND MYND DOMAIN-CONTAINING PROTEIN 3
	Chains	:	A, B
	EC Number	:	2.1.1.43
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3) CODON PLUS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SMYD3, ZMYND1, ZNFN3A1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ZINC FINGER MYND DOMAIN-CONTAINING PROTEIN 1

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	ZN	6	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 (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:14 , GLY A:15 , ASN A:16 , TYR A:124 , GLU A:130 , ASN A:132 , ASN A:181 , SER A:202 , ASN A:205 , HIS A:206 , TYR A:239 , TYR A:257 , PHE A:259 , HOH A:450	BINDING SITE FOR RESIDUE SAH A 437
2	AC2	SOFTWARE	CYS A:49 , CYS A:52 , CYS A:71 , CYS A:75	BINDING SITE FOR RESIDUE ZN A 438
3	AC3	SOFTWARE	CYS A:62 , CYS A:65 , HIS A:83 , CYS A:87	BINDING SITE FOR RESIDUE ZN A 439
4	AC4	SOFTWARE	CYS A:208 , CYS A:261 , CYS A:263 , CYS A:266	BINDING SITE FOR RESIDUE ZN A 440
5	AC5	SOFTWARE	ARG B:14 , GLY B:15 , ASN B:16 , TYR B:124 , ASN B:132 , SER B:202 , LEU B:204 , ASN B:205 , HIS B:206 , TYR B:239 , TYR B:257 , PHE B:259	BINDING SITE FOR RESIDUE SAH B 437
6	AC6	SOFTWARE	CYS B:49 , CYS B:52 , CYS B:71 , CYS B:75	BINDING SITE FOR RESIDUE ZN B 438
7	AC7	SOFTWARE	CYS B:62 , CYS B:65 , HIS B:83 , CYS B:87	BINDING SITE FOR RESIDUE ZN B 439
8	AC8	SOFTWARE	CYS B:208 , CYS B:261 , CYS B:263 , CYS B:266	BINDING SITE FOR RESIDUE ZN B 440

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

Asymmetric Unit

No.	Residues
1	Lys A:94	-	Pro A:95
2	Lys B:94	-	Pro B:95

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

Asymmetric Unit (3, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SET	PS50280	SET domain profile.	SMYD3_HUMAN	4-240	2	A:4-240 B:4-240
2	ZF_MYND_1	PS01360	Zinc finger MYND-type signature.	SMYD3_HUMAN	49-87	2	A:49-87 B:49-87
3	ZF_MYND_2	PS50865	Zinc finger MYND-type profile.	SMYD3_HUMAN	49-87	2	A:49-87 B:49-87

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SET	PS50280	SET domain profile.	SMYD3_HUMAN	4-240	1	A:4-240 -
2	ZF_MYND_1	PS01360	Zinc finger MYND-type signature.	SMYD3_HUMAN	49-87	1	A:49-87 -
3	ZF_MYND_2	PS50865	Zinc finger MYND-type profile.	SMYD3_HUMAN	49-87	1	A:49-87 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SET	PS50280	SET domain profile.	SMYD3_HUMAN	4-240	1	- B:4-240
2	ZF_MYND_1	PS01360	Zinc finger MYND-type signature.	SMYD3_HUMAN	49-87	1	- B:49-87
3	ZF_MYND_2	PS50865	Zinc finger MYND-type profile.	SMYD3_HUMAN	49-87	1	- B:49-87

(no "Exon" information available for 3OXF)

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:426
 aligned with SMYD3_HUMAN | Q9H7B4 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:426
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422      
          SMYD3_HUMAN     3 PLKVEKFATAKRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDKKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIRAS 428
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee.....eeeee........eeeee...eeee.hhhh..............ee.......ee.hhhhhhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhh.....hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh....hhhhhhhhhhhhheeee.....eeeeee..hhhhhee.....eeeeee..eeeeee..........ee.......hhhhhhhhhhhhhh....hhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -SET  PDB: A:4-240 UniProt: 4-240                                                                                                                                                                                                             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------ZF_MYND_2  PDB: A:49-87 UniProt: 49-87 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----------------------------------------------ZF_MYND_1  PDB: A:49-87 UniProt: 49-87 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oxf A   3 PLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDRKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIRAS 428
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422

Chain B from PDB  Type:PROTEIN  Length:425
 aligned with SMYD3_HUMAN | Q9H7B4 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:425
                                    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       371       381       391       401       411       421     
          SMYD3_HUMAN     2 EPLKVEKFATAKRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDKKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIR 426
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------zf-MYND-3oxfB01 B:49-87                --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------zf-MYND-3oxfB02 B:49-87                --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -------------SET-3oxfB03 B:15-240                                                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (3)
           Pfam domains (4) -------------SET-3oxfB04 B:15-240                                                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (4)
         Sec.struct. author ....eeeee.....eeeee........eeeee...eeee...................ee.......ee.hhhhhhhhhhhhh.hhhhhhh......hhhhhhhhhhhhhh.....hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh....hhhhhhhhhhhhheeee.....eeeeee..hhhhhee.....eeeeee..eeeeee........eeee.......hhhhhhhhhhhh......hhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --SET  PDB: B:4-240 UniProt: 4-240                                                                                                                                                                                                             ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) -----------------------------------------------ZF_MYND_2  PDB: B:49-87 UniProt: 49-87 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------ZF_MYND_1  PDB: B:49-87 UniProt: 49-87 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oxf B   2 EPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDRKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIR 426
                                    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       371       381       391       401       411       421

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 3OXF)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TRASH (61)

Family: zf-MYND (11)

Homo sapiens (Human) (9)

1a	zf-MYND-3oxfB01	B:49-87
1b	zf-MYND-3oxfB02	B:49-87

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

Family: SET (46)

Homo sapiens (Human) (34)

2a	SET-3oxfB03	B:15-240
2b	SET-3oxfB04	B:15-240

Asymmetric Unit(hide GO term definitions)

Chain A,B (SMYD3_HUMAN | Q9H7B4)

molecular function
	GO:0000993	RNA polymerase II core binding	Interacting selectively and non-covalently with RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits.
	GO:0000979	RNA polymerase II core promoter sequence-specific DNA binding	Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery.
	GO:0001162	RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding	Interacting selectively and non-covalently with an RNA polymerase II intronic DNA sequence that regulates the transcription of the transcript it is contained within.
	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:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	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:0071549	cellular response to dexamethasone 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 dexamethasone stimulus.
	GO:0045184	establishment of protein localization	The directed movement of a protein to a specific location.
	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:0014904	myotube cell development	The process aimed at the progression of a myotube cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
	GO:0006469	negative regulation of protein kinase activity	Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
	GO:0006334	nucleosome assembly	The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
	GO:0033138	positive regulation of peptidyl-serine phosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
	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.
cellular component
	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.

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	3oxf
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	SMYD3_HUMAN \| Q9H7B4	:	3mek 3oxg 3oxl 3pdn 3qwp 3ru0 5ccl 5ccm 5ex0 5ex3 5hi7 5hq8

Description

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Ligands, Modified Residues, Ions (2, 8)

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SS Bonds (0, 0)

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