2VYT - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   THE MBT REPEATS OF HUMAN SCML2 BIND TO PEPTIDES CONTAINING MONO METHYLATED LYSINE.

Authors :   C. M. Santiveri, B. C. Lechtenberg, M. D. Allen, A. Sathyamurthy, A. M. Jaulent, S. M. V. Freund, M. Bycroft

Date :   28 Jul 08 (Deposition) - 05 Aug 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Mono Methylated Peptides, Mbt Repeats, Transcription, Phosphoprotein, Alternative Splicing, Transcription Regulation, Nucleus, Repressor, Chromatin, Human Scml2 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. M. Santiveri, B. C. Lechtenberg, M. D. Allen, A. Sathyamurthy, A. M. Jaulent, S. M. V. Freund, M. Bycroft
The Malignant Brain Tumor Repeats Of Human Scml2 Bind To Peptides Containing Monomethylated Lysine.
J. Mol. Biol. V. 382 1107 2008
PubMed-ID: 18706910 | Reference-DOI: 10.1016/J.JMB.2008.07.081

Molecule 1 - SEX COMB ON MIDLEG-LIKE PROTEIN 2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	C41
	Expression System Taxid	:	562
	Expression System Vector	:	MODIFIED PRSETA
	Fragment	:	MBT REPEATS, RESIDUES 24-243
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SCML2, HUMAN MBT

		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, 3)

No.	Name	Count	Type	Full Name
1	MLZ	2	Mod. Residue	N-METHYL-LYSINE
2	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MLZ	1	Mod. Residue	N-METHYL-LYSINE
2	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	MLZ	1	Mod. Residue	N-METHYL-LYSINE
2	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:182 , ASN A:185 , PHE A:213 , HOH A:2104	BINDING SITE FOR RESIDUE MLZ A1244
2	AC2	SOFTWARE	VAL A:197 , GLY A:199 , LYS B:40 , GLU B:41 , ASP B:182 , TRP B:209 , PHE B:213 , HOH B:2083	BINDING SITE FOR RESIDUE MLZ B1244
3	AC3	SOFTWARE	TRP A:216 , ARG B:94 , ARG B:96	BINDING SITE FOR RESIDUE PGE B1245

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

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MBT	PS51079	MBT repeat profile.	SCML2_HUMAN	33-131 139-240	4	A:33-131 B:33-126 A:139-240 B:152-240

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MBT	PS51079	MBT repeat profile.	SCML2_HUMAN	33-131 139-240	2	A:33-131 - A:139-240 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MBT	PS51079	MBT repeat profile.	SCML2_HUMAN	33-131 139-240	2	- B:33-126 - B:152-240

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000251900	1a	ENSE00001341544	X:18372847-18372712	136	SCML2_HUMAN	-	0	0	-	-
1.2	ENST00000251900	2	ENSE00002195410	X:18352215-18352170	46	SCML2_HUMAN	1-8	8	0	-	-
1.3	ENST00000251900	3	ENSE00001740872	X:18348775-18348707	69	SCML2_HUMAN	8-31	24	2	A:30-31 B:31-31	2 1
1.4	ENST00000251900	4	ENSE00001722015	X:18343097-18343027	71	SCML2_HUMAN	31-54	24	2	A:31-54 B:31-54	24 24
1.5	ENST00000251900	5	ENSE00001761590	X:18342213-18341979	235	SCML2_HUMAN	55-133	79	2	A:55-133 B:55-126 (gaps)	79 72
1.6	ENST00000251900	6	ENSE00001802908	X:18338540-18338452	89	SCML2_HUMAN	133-162	30	2	A:133-162 B:152-162	30 11
1.7	ENST00000251900	7	ENSE00001780951	X:18323335-18323092	244	SCML2_HUMAN	163-244	82	2	A:163-243 B:163-243	81 81
1.8	ENST00000251900	8	ENSE00001602863	X:18283922-18283705	218	SCML2_HUMAN	244-316	73	0	-	-
1.9	ENST00000251900	9	ENSE00001692459	X:18278411-18278291	121	SCML2_HUMAN	317-357	41	0	-	-
1.10	ENST00000251900	10	ENSE00001801055	X:18276367-18276164	204	SCML2_HUMAN	357-425	69	0	-	-
1.11	ENST00000251900	11	ENSE00001720943	X:18275150-18274968	183	SCML2_HUMAN	425-486	62	0	-	-
1.12b	ENST00000251900	12b	ENSE00001776891	X:18266002-18265889	114	SCML2_HUMAN	486-524	39	0	-	-
1.13	ENST00000251900	13	ENSE00001632032	X:18264948-18264697	252	SCML2_HUMAN	524-608	85	0	-	-
1.14	ENST00000251900	14	ENSE00000666137	X:18260710-18260559	152	SCML2_HUMAN	608-658	51	0	-	-
1.15b	ENST00000251900	15b	ENSE00001765000	X:18259499-18257434	2066	SCML2_HUMAN	659-700	42	0	-	-

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:214
 aligned with SCML2_HUMAN | Q9UQR0 from UniProtKB/Swiss-Prot  Length:700

    Alignment length:214
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239    
          SCML2_HUMAN    30 RDDFHWEEYLKETGSISAPSECFRQSQIPPVNDFKVGMKLEARDPRNATSVCIATVIGITGARLRLRLDGSDNRNDFWRLVDSPDIQPVGTCEKEGDLLQPPLGYQMNTSSWPMFLLKTLNGSEMASATLFKKEPPKPPLNNFKVGMKLEAIDKKNPYLICPATIGDVKGDEVHITFDGWSGAFDYWCKYDSRDIFPAGWCRLTGDVLQPPGTS 243
               SCOP domains d2vyta1 A:30-135 Scml2 protein                                                                            ----d2vyta2 A:140-243 Scml2 protein                                                                          SCOP domains
               CATH domains 2vytA01 A:30-58,A:163-243    --------------------------------------------------------------------------------------------------------2vytA01 A:30-58,A:163-243  [code=2.30.30.160, no name defined]                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh....hhhhh...............eeeeee..eeeeeeeeeeeeee..eeeeee........eeee.....ee..hhhhhh............hhhhhhhhhhhhhh.....hhhhh................eeeeee..eeeeeeeeeeeeee..eeeeee...hhhhheeee.....ee..hhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---MBT  PDB: A:33-131 UniProt: 33-131                                                                 -------MBT  PDB: A:139-240 UniProt: 139-240                                                                  --- PROSITE
           Transcript 1 (1) 1.-----------------------Exon 1.5  PDB: A:55-133 UniProt: 55-133                                        -----------------------------Exon 1.7  PDB: A:163-243 UniProt: 163-244 [INCOMPLETE]                            Transcript 1 (1)
           Transcript 1 (2) -Exon 1.4  PDB: A:31-54  ------------------------------------------------------------------------------Exon 1.6  PDB: A:133-162      --------------------------------------------------------------------------------- Transcript 1 (2)
                 2vyt A  30 RDDFHWEEYLKETGSISAPSECFRQSQIPPVNDFKVGMKLEARDPRNATSVCIATVIGITGARLRLRLDGSDNRNDFWRLVDSPDIQPVGTCEKEGDLLQPPLGYQMNTSSWPMFLLETLNGSEMASATLFKKEPPKPPLNNFKVGMKLEAIDKKNPYLICPATIGDVKGDEVHITFDGWSGAFDYWCKYDSRDIFPAGWCRLTGDVLQPPGTS 243
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239

Chain B from PDB  Type:PROTEIN  Length:183
 aligned with SCML2_HUMAN | Q9UQR0 from UniProtKB/Swiss-Prot  Length:700

    Alignment length:213
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
          SCML2_HUMAN    31 DDFHWEEYLKETGSISAPSECFRQSQIPPVNDFKVGMKLEARDPRNATSVCIATVIGITGARLRLRLDGSDNRNDFWRLVDSPDIQPVGTCEKEGDLLQPPLGYQMNTSSWPMFLLKTLNGSEMASATLFKKEPPKPPLNNFKVGMKLEAIDKKNPYLICPATIGDVKGDEVHITFDGWSGAFDYWCKYDSRDIFPAGWCRLTGDVLQPPGTS 243
               SCOP domains d2vytb1 B:31-126 Scml2 protein                                                                                           d2vytb2 B:152-243 Scml2 protein                                                              SCOP domains
               CATH domains 2vytB01 B:31-58,B:163-243   --------------------------------------------------------------------------------------------------------2vytB01 B:31-58,B:163-243  [code=2.30.30.160, no name defined]                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh....hhhhh...............eeee.-----...eeeeeeeee..eeeeee........eeee.....ee..hhhhhhh.-------------------------....hhhhh................eeeee.......eeeeeeeeee..eeeeee...hhhhheeee.....ee..hhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --MBT  PDB: B:33-126 UniProt: 33-131                                                                 -------MBT  PDB: B:152-240 UniProt: 139-240                                                                  --- PROSITE
           Transcript 1 (1) 1-----------------------Exon 1.5  PDB: B:55-126 (gaps) UniProt: 55-133 [INCOMPLETE]                    -----------------------------Exon 1.7  PDB: B:163-243 UniProt: 163-244 [INCOMPLETE]                            Transcript 1 (1)
           Transcript 1 (2) Exon 1.4  PDB: B:31-54  ------------------------------------------------------------------------------Exon 1.6  PDB: B:152-162      --------------------------------------------------------------------------------- Transcript 1 (2)
                 2vyt B  31 DDFHWEEYLKETGSISAPSECFRQSQIPPVNDFKVGMKLEAR-----TSVCIATVIGITGARLRLRLDGSDNRNDFWRLVDSPDIQPVGTCEKEGD-------------------------SEMASATLFKKEPPKPPLNNFKVGMKLEAIDKKNPYLICPATIGDVKGDEVHITFDGWSGAFDYWCKYDSRDIFPAGWCRLTGDVLQPPGTS 243
                                    40        50        60        70 |     |80        90       100       110       120     |   -         -         - |     160       170       180       190       200       210       220       230       240   
                                                                    72    78                                             126                       152

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(

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Folds(

)

Superfamilies( (-)

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Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: Tudor/PWWP/MBT (72)

Family: MBT repeat (8)

Protein domain: Scml2 protein (2)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d2vyta1	A:30-135
1b	d2vyta2	A:140-243
1c	d2vytb1	B:31-126
1d	d2vytb2	B:152-243

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: [code=2.30.30.160, no name defined] (35)

Human (Homo sapiens) (27)

1a	2vytB01	B:31-58,B:163-243
1b	2vytA01	A:30-58,A:163-243

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (SCML2_HUMAN | Q9UQR0)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0009653	anatomical structure morphogenesis	The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
	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.

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	2vyt
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	SCML2_HUMAN \| Q9UQR0	:	1oi1 2biv 2mem 4edu

1oi1	CRYSTAL STRUCTURE OF THE MBT DOMAINS OF HUMAN SCML2
2biv	CRYSTAL STRUCTURE OF THE WILD-TYPE MBT DOMAINS OF HUMAN SCML2

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