3H6Z - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE FOUR MBT REPEATS OF DROSOPHILA MELANOGASTER SFMBT IN COMPLEX WITH PEPTIDE RHR (ME)K VLR

Authors :   C. Grimm, C. W. Mueller

Date :   24 Apr 09 (Deposition) - 16 Jun 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Mbt, Mbr Repeat, Aromatic Cage, Chromatin Regulator, Dna-Binding, Metal-Binding, Nucleus, Repressor, Transcription, Transcription Regulation, Zinc-Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Grimm, R. Matos, N. Ly-Hartig, U. Steuerwald, D. Lindner, V. Rybin, J. Muller, C. W. Muller
Molecular Recognition Of Histone Lysine Methylation By The Polycomb Group Repressor Dsfmbt
Embo J. V. 28 1965 2009
PubMed-ID: 19494831 | Reference-DOI: 10.1038/EMBOJ.2009.147

Molecule 1 - POLYCOMB PROTEIN SFMBT
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM11
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 535-977
	Gene	:	SFMBT
	Mutation	:	YES
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Synonym	:	SCM-LIKE WITH FOUR MBT DOMAIN-CONTAINING PROTEIN 1, DSFMBT

Molecule 2 - 'HR(MLZ)VLR
	Chains	:	L, M
	Engineered	:	YES
	Other Details	:	PEPTIDE SYNTHESIS
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	L	M
Biological Unit 1 (1x)	:	A		L
Biological Unit 2 (1x)	:		B		M

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	MLZ	2	Mod. Amino Acid	N-METHYL-LYSINE
2	SUC	4	Ligand/Ion	SUCROSE

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	MLZ	1	Mod. Amino Acid	N-METHYL-LYSINE
2	SUC	2	Ligand/Ion	SUCROSE

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	MLZ	1	Mod. Amino Acid	N-METHYL-LYSINE
2	SUC	2	Ligand/Ion	SUCROSE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:698 , ILE A:701 , PHE A:728 , PRO A:809 , LEU A:810 , LEU A:918 , MET A:919 , PRO A:921	BINDING SITE FOR RESIDUE SUC A 1
2	AC2	SOFTWARE	HIS A:557 , ARG A:686 , ASP A:733 , LYS A:781	BINDING SITE FOR RESIDUE SUC A 2
3	AC3	SOFTWARE	LYS B:698 , ILE B:701 , PHE B:728 , TRP B:729 , PRO B:809 , LEU B:918 , MET B:919 , PRO B:921	BINDING SITE FOR RESIDUE SUC B 1
4	AC4	SOFTWARE	HIS B:557 , ARG B:686 , ASP B:733	BINDING SITE FOR RESIDUE SUC B 2

(no "SS Bond" information available for 3H6Z)

(no "Cis Peptide Bond" information available for 3H6Z)

(no "SAP(SNP)/Variant" information available for 3H6Z)

Asymmetric Unit (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MBT	PS51079	MBT repeat profile.	SMBT_DROME	536-647 655-753 761-871 879-975	8	A:536-647 B:536-647 A:655-753 B:655-753 A:761-871 B:761-871 A:879-975 B:879-975

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MBT	PS51079	MBT repeat profile.	SMBT_DROME	536-647 655-753 761-871 879-975	4	A:536-647 - A:655-753 - A:761-871 - A:879-975 -

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MBT	PS51079	MBT repeat profile.	SMBT_DROME	536-647 655-753 761-871 879-975	4	- B:536-647 - B:655-753 - B:761-871 - B:879-975

(no "Exon" information available for 3H6Z)

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:431
 aligned with SMBT_DROME | Q9VK33 from UniProtKB/Swiss-Prot  Length:1220

    Alignment length:518
                                   469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969        
           SMBT_DROME   460 GAVGDATAPGSTEEGASTPNSYLSAAPTPKALRLFKDIYPQDDLPQIPKYERLPVPCPQMEKIISIRRRMYDPTHSYDWLPRLSKENFNAAPVTCFPHAPGCEVWDNLGVGMKVEVENTDCDSIEVIQPGQTPTSFWVATILEIKGYKALMSYEGFDTDSHDFWVNLCNAEVHSVGWCATRGKPLIPPRTIEHKYKDWKDFLVGRLSGARTLPSNFYNKINDSLQSRFRLGLNLECVDKDRISQVRLATVTKIVGKRLFLRYFDSDDGFWCHEDSPIIHPVGWATTVGHNLAAPQDYLERMLAGREAMIEVHEDDATIELFKMNFTFDEYYSDGKTNSFVEGMKLEAVDPLNLSSICPATVMAVLKFGYMMIRIDSYQPDASGSDWFCYHEKSPCIFPAGFCSVNNISVTPPNGYDSRTFTWEGYLRDTGAVAAGQHLFHRIIPDHGFEVGMSLECADLMDPRLVCVATVARVVGRLLKVHFDGWTDEYDQWLDCESADIYPVGWCVLVNHKLEGPPR 977
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....-----------------------------------------------------------------------...hhhhhh.......hhhhh....hhhhhh......eeee.----------------...eeeeeeeee..eeeeee....hhhhheeee.........hhhhhhh.....hhhhhhhh..hhhhhhhhhh.......hhhhhhhhhh........eeeee......eeeeeeeeeee..eeeeee.....eeeee.....ee..hhhhhhh.eee.hhhhhhhhhh.............hhhhh.....hhhhhh...........eeeeee..eeeeeeeeeeeee....eeeeee............eeee.....ee..hhhhhh...............hhhhhhhhhh....hhhhh.............eeeee.......eeeeeeeeee..eeeee....hhhhheeee.....ee..hhhhhhh..ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------MBT  PDB: A:536-647 UniProt: 536-647                                                                            -------MBT  PDB: A:655-753 UniProt: 655-753                                                               -------MBT  PDB: A:761-871 UniProt: 761-871                                                                           -------MBT  PDB: A:879-975 UniProt: 879-975                                                             -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h6z A 531 GAMG-----------------------------------------------------------------------SYDWLPRLSKENFNAAPVTCFPHAPGCEVWDNLGVGMKVEVE----------------TSFWVATILEIKGYKALMSYEGFDTDSHDFWVNLCNAEVHSVGWCATRGKPLIPPRTIEHKYKDWKDFLVGRLSGARTLPSNFYNKINDSLQSRFRLGLNLECVDKDRISQVRLATVTKIVGDRLFLRYFDSDDGFWCHEDSPIIHPVGWATTVGHNLAAPQDYLERMLAGREAMIEVHEDDATIELFKMNFTFDEYYSDGKTNSFVEGMKLEAVDPLNLSSICPATVMAVLKFGYMMIRIDSYQPDASGSDWFCYHEKSPCIFPAGFCSVNNISVTPPNGYDSRTFTWEGYLSDTGAVAAGQHLFHDIIPDHGFEVGMSLECADLMDPRLVCVATVARVVGRLLKVHFDGWTDEYDQWLDCESADIYPVGWCVLVNHKLEGPPR 977
                               |     -         -         -         -         -         -         -     | 539       549       559       569      |  -         -   |   599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969        
                             534                                                                     535                                      576              593

Chain B from PDB  Type:PROTEIN  Length:431
 aligned with SMBT_DROME | Q9VK33 from UniProtKB/Swiss-Prot  Length:1220

    Alignment length:518
                                   469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969        
           SMBT_DROME   460 GAVGDATAPGSTEEGASTPNSYLSAAPTPKALRLFKDIYPQDDLPQIPKYERLPVPCPQMEKIISIRRRMYDPTHSYDWLPRLSKENFNAAPVTCFPHAPGCEVWDNLGVGMKVEVENTDCDSIEVIQPGQTPTSFWVATILEIKGYKALMSYEGFDTDSHDFWVNLCNAEVHSVGWCATRGKPLIPPRTIEHKYKDWKDFLVGRLSGARTLPSNFYNKINDSLQSRFRLGLNLECVDKDRISQVRLATVTKIVGKRLFLRYFDSDDGFWCHEDSPIIHPVGWATTVGHNLAAPQDYLERMLAGREAMIEVHEDDATIELFKMNFTFDEYYSDGKTNSFVEGMKLEAVDPLNLSSICPATVMAVLKFGYMMIRIDSYQPDASGSDWFCYHEKSPCIFPAGFCSVNNISVTPPNGYDSRTFTWEGYLRDTGAVAAGQHLFHRIIPDHGFEVGMSLECADLMDPRLVCVATVARVVGRLLKVHFDGWTDEYDQWLDCESADIYPVGWCVLVNHKLEGPPR 977
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....-----------------------------------------------------------------------...hhhhhh.......hhhhh....hhhhhh......eeee.----------------...eeeeeeeee..eeeeee....hhhhheeee......ee.hhhhhhh.....hhhhhhhh..hhhhhhhhhh.......hhhhhhhhhh........eeeeee..eeeeeeeeeeeeee..eeeeee.....eeeee.....ee..hhhhhhh.eee.hhhhhhhhhh.............hhhhh.....hhhhhh..........eeeeeee..eeeeeeeeeeeee....eeeeee............eeee.....ee..hhhhhh...............hhhhhhhhhh.ee.hhhhh.............eeeee.......eeeeeeeeee..eeeeee...hhhhheeee.....ee..hhhhhhh..ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------MBT  PDB: B:536-647 UniProt: 536-647                                                                            -------MBT  PDB: B:655-753 UniProt: 655-753                                                               -------MBT  PDB: B:761-871 UniProt: 761-871                                                                           -------MBT  PDB: B:879-975 UniProt: 879-975                                                             -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h6z B 531 GAMG-----------------------------------------------------------------------SYDWLPRLSKENFNAAPVTCFPHAPGCEVWDNLGVGMKVEVE----------------TSFWVATILEIKGYKALMSYEGFDTDSHDFWVNLCNAEVHSVGWCATRGKPLIPPRTIEHKYKDWKDFLVGRLSGARTLPSNFYNKINDSLQSRFRLGLNLECVDKDRISQVRLATVTKIVGDRLFLRYFDSDDGFWCHEDSPIIHPVGWATTVGHNLAAPQDYLERMLAGREAMIEVHEDDATIELFKMNFTFDEYYSDGKTNSFVEGMKLEAVDPLNLSSICPATVMAVLKFGYMMIRIDSYQPDASGSDWFCYHEKSPCIFPAGFCSVNNISVTPPNGYDSRTFTWEGYLSDTGAVAAGQHLFHDIIPDHGFEVGMSLECADLMDPRLVCVATVARVVGRLLKVHFDGWTDEYDQWLDCESADIYPVGWCVLVNHKLEGPPR 977
                               |     -         -         -         -         -         -         -     | 539       549       559       569      |  -         -   |   599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969        
                             534                                                                     535                                      576              593

Chain L from PDB  Type:PROTEIN  Length:6
                                      
               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
                 3h6z L  18 HRkVLR  23
                              |   
                             20-MLZ

Chain M from PDB  Type:PROTEIN  Length:6
                                      
               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
                 3h6z M  18 HRkVLR  23
                              |   
                              |   
                             20-MLZ

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 3H6Z)

(no "CATH Domain" information available for 3H6Z)

(no "Pfam Domain" information available for 3H6Z)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SMBT_DROME | Q9VK33)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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: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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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:0007446	imaginal disc growth	The increase in mass of imaginal discs by cell proliferation prior to metamorphosis. Imaginal discs are epithelial infoldings in the larvae of holometabolous insects that develop into adult structures (legs, antennae, wings, etc.) during metamorphosis from larval to adult form.
	GO:0010629	negative regulation of gene expression	Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0048477	oogenesis	The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
	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:0031519	PcG protein complex	A chromatin-associated multiprotein complex containing Polycomb Group proteins. In Drosophila, Polycomb group proteins are involved in the long-term maintenance of gene repression, and PcG protein complexes associate with Polycomb group response elements (PREs) in target genes to regulate higher-order chromatin structure.
	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.

Asymmetric Unit
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	3h6z
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(no "Related Entries Specified in the PDB File" available for 3H6Z)

Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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