2BIV - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE WILD-TYPE MBT DOMAINS OF HUMAN SCML2

Authors :   C. M. Santiveri, M. D. Allen, F. Sait, M. Bycroft

Date :   26 Jan 05 (Deposition) - 08 Feb 05 (Release) - 05 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Malignant Brain Tumor, Transcription Factor, Transcription (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, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSETA
	Expression System Strain	:	C41
	Expression System Taxid	:	562
	Expression System Vector	:	PRSETA
	Fragment	:	MBT DOMAIN, RESIDUES 1-243
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SCML2 PROTEIN

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	IOD	10	Ligand/Ion	IODIDE ION
2	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	IOD	3	Ligand/Ion	IODIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	IOD	3	Ligand/Ion	IODIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 3 (1, 4)

No.	Name	Count	Type	Full Name
1	IOD	4	Ligand/Ion	IODIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:216	BINDING SITE FOR RESIDUE IOD A1244
2	AC2	SOFTWARE	TRP B:35 , ARG B:231	BINDING SITE FOR RESIDUE IOD B1244
3	AC3	SOFTWARE	HIS B:34 , LYS B:162	BINDING SITE FOR RESIDUE IOD B1245
4	AC4	SOFTWARE	HOH B:2048	BINDING SITE FOR RESIDUE NA B1246
5	AC5	SOFTWARE	TRP B:216	BINDING SITE FOR RESIDUE IOD C1244
6	AC6	SOFTWARE	TRP C:107 , HOH C:2061	BINDING SITE FOR RESIDUE IOD C1245
7	AC7	SOFTWARE	TYR B:215 , TRP B:216 , HOH B:2208 , HOH C:2061	BINDING SITE FOR RESIDUE NA C1247
8	AC8	SOFTWARE	TRP C:35 , ARG C:231 , HOH C:2048	BINDING SITE FOR RESIDUE IOD C1248

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

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

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

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MBT	PS51079	MBT repeat profile.	SCML2_HUMAN	33-131 139-240	6	A:33-131 B:33-131 C:33-131 A:139-240 B:140-240 C:153-240

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:33-131 - - B:140-240 -

Biological Unit 3 (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	- - C:33-131 - - C:153-240

Asymmetric Unit (5, 13)

	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	1	- B:27-31 -	- 5 -
1.4	ENST00000251900	4	ENSE00001722015	X:18343097-18343027	71	SCML2_HUMAN	31-54	24	3	A:32-54 B:31-54 C:32-54	23 24 23
1.5	ENST00000251900	5	ENSE00001761590	X:18342213-18341979	235	SCML2_HUMAN	55-133	79	3	A:55-133 B:55-133 C:55-133	79 79 79
1.6	ENST00000251900	6	ENSE00001802908	X:18338540-18338452	89	SCML2_HUMAN	133-162	30	3	A:133-162 B:133-162 (gaps) C:133-162 (gaps)	30 30 30
1.7	ENST00000251900	7	ENSE00001780951	X:18323335-18323092	244	SCML2_HUMAN	163-244	82	3	A:163-243 B:163-243 C:163-243	81 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:212
 aligned with SCML2_HUMAN | Q9UQR0 from UniProtKB/Swiss-Prot  Length:700

    Alignment length:212
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
          SCML2_HUMAN    32 DFHWEEYLKETGSISAPSECFRQSQIPPVNDFKVGMKLEARDPRNATSVCIATVIGITGARLRLRLDGSDNRNDFWRLVDSPDIQPVGTCEKEGDLLQPPLGYQMNTSSWPMFLLKTLNGSEMASATLFKKEPPKPPLNNFKVGMKLEAIDKKNPYLICPATIGDVKGDEVHITFDGWSGAFDYWCKYDSRDIFPAGWCRLTGDVLQPPGTS 243
               SCOP domains d2biva1 A:32-138 automated matches                                                                         d2biva2 A:139-243 automated matches                                                                       SCOP domains
               CATH domains 2bivA01 A:32-58,A:163-243  2bivA02 A:59-162  [code=2.30.30.160, no name defined]                                                   2bivA01 A:32-58,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................eeeee.......eeeeeeeeee..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) -----------------------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:32-54 ------------------------------------------------------------------------------Exon 1.6  PDB: A:133-162      --------------------------------------------------------------------------------- Transcript 1 (2)
                 2biv A  32 DFHWEEYLKETGSISAPSECFRQSQIPPVNDFKVGMKLEARDPRNATSVCIATVIGITGARLRLRLDGSDNRNDFWRLVDSPDIQPVGTCEKEGDLLQPPLGYQMNTSSWPMFLLKTLNGSEMASATLFKKEPPKPPLNNFKVGMKLEAIDKKNPYLICPATIGDVKGDEVHITFDGWSGAFDYWCKYDSRDIFPAGWCRLTGDVLQPPGTS 243
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain B from PDB  Type:PROTEIN  Length:211
 aligned with SCML2_HUMAN | Q9UQR0 from UniProtKB/Swiss-Prot  Length:700

    Alignment length:217
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       
          SCML2_HUMAN    27 SVQRDDFHWEEYLKETGSISAPSECFRQSQIPPVNDFKVGMKLEARDPRNATSVCIATVIGITGARLRLRLDGSDNRNDFWRLVDSPDIQPVGTCEKEGDLLQPPLGYQMNTSSWPMFLLKTLNGSEMASATLFKKEPPKPPLNNFKVGMKLEAIDKKNPYLICPATIGDVKGDEVHITFDGWSGAFDYWCKYDSRDIFPAGWCRLTGDVLQPPGTS 243
               SCOP domains d2bivb1 B:27-133 automated matches                                                                         ------d2bivb2 B:140-243 automated matches                                                                      SCOP domains
               CATH domains 2bivB01 B:27-58,B:163-243       2bivB02 B:59-162  [code=2.30.30.160, no name defined]                                                   2bivB01 B:27-58,B:163-243  [code=2.30.30.160, no name defined]                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh.....hhhhh...............eeeeee..eeeeeeeeeeeeee..eeeeee........eeee.....ee..hhhhhh.........------hhhhhhhhhhh.....hhhhh................eeeee.......eeeeeeeeee..eeeeee........eeee.....ee..hhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------MBT  PDB: B:33-131 UniProt: 33-131                                                                 -------MBT  PDB: B:140-240 UniProt: 139-240                                                                  --- PROSITE
           Transcript 1 (1) 1.3  -----------------------Exon 1.5  PDB: B:55-133 UniProt: 55-133                                        -----------------------------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:133-162 (gaps--------------------------------------------------------------------------------- Transcript 1 (2)
                 2biv B  27 SVQRDDFHWEEYLKETGSISAPSECFRQSQIPPVNDFKVGMKLEARDPRNATSVCIATVIGITGARLRLRLDGSDNRNDFWRLVDSPDIQPVGTCEKEGDLLQPPLG------SWPMFLLKTLNGSEMASATLFKKEPPKPPLNNFKVGMKLEAIDKKNPYLICPATIGDVKGDEVHITFDGWSGAFDYWCKYDSRDIFPAGWCRLTGDVLQPPGTS 243
                                    36        46        56        66        76        86        96       106       116       126      |  -   |   146       156       166       176       186       196       206       216       226       236       
                                                                                                                                    133    140

Chain C from PDB  Type:PROTEIN  Length:193
 aligned with SCML2_HUMAN | Q9UQR0 from UniProtKB/Swiss-Prot  Length:700

    Alignment length:212
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
          SCML2_HUMAN    32 DFHWEEYLKETGSISAPSECFRQSQIPPVNDFKVGMKLEARDPRNATSVCIATVIGITGARLRLRLDGSDNRNDFWRLVDSPDIQPVGTCEKEGDLLQPPLGYQMNTSSWPMFLLKTLNGSEMASATLFKKEPPKPPLNNFKVGMKLEAIDKKNPYLICPATIGDVKGDEVHITFDGWSGAFDYWCKYDSRDIFPAGWCRLTGDVLQPPGTS 243
               SCOP domains d2bivc1 C:32-133 automated matches                                                                    -------------------d2bivc2 C:153-243 automated matches                                                         SCOP domains
               CATH domains 2bivC01 C:32-58,C:163-243  2bivC02 C:59-162  [code=2.30.30.160, no name defined]                                                   2bivC01 C:32-58,C:163-243  [code=2.30.30.160, no name defined]                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.....hhhhh...............eeeeee..eeeeeeeeeeeeee..eeeeee........eeee.....ee..hhhhhh.........-------------------...hhhhh................eeeee.......eeeeeeeeee..eeeeee...hhhhheeee.....ee..hhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -MBT  PDB: C:33-131 UniProt: 33-131                                                                 -------MBT  PDB: C:153-240 UniProt: 139-240                                                                  --- PROSITE
           Transcript 1 (1) -----------------------Exon 1.5  PDB: C:55-133 UniProt: 55-133                                        -----------------------------Exon 1.7  PDB: C:163-243 UniProt: 163-244 [INCOMPLETE]                            Transcript 1 (1)
           Transcript 1 (2) Exon 1.4  PDB: C:32-54 ------------------------------------------------------------------------------Exon 1.6  PDB: C:133-162 (gaps--------------------------------------------------------------------------------- Transcript 1 (2)
                 2biv C  32 DFHWEEYLKETGSISAPSECFRQSQIPPVNDFKVGMKLEARDPRNATSVCIATVIGITGARLRLRLDGSDNRNDFWRLVDSPDIQPVGTCEKEGDLLQPPLG-------------------EMASATLFKKEPPKPPLNNFKVGMKLEAIDKKNPYLICPATIGDVKGDEVHITFDGWSGAFDYWCKYDSRDIFPAGWCRLTGDVLQPPGTS 243
                                    41        51        61        71        81        91       101       111       121       131 |       -         - |     161       171       181       191       201       211       221       231       241  
                                                                                                                               133                 153

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: SH3-like barrel (1035)

Superfamily: Tudor/PWWP/MBT (72)

Family: automated matches (24)

Protein domain: automated matches (24)

Human (Homo sapiens) [TaxId: 9606] (20)

1a	d2biva1	A:32-138
1b	d2biva2	A:139-243
1c	d2bivb1	B:27-133
1d	d2bivb2	B:140-243
1e	d2bivc1	C:32-133
1f	d2bivc2	C:153-243

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

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	2bivA02	A:59-162
1b	2bivC02	C:59-162
1c	2bivA01	A:32-58,A:163-243
1d	2bivC01	C:32-58,C:163-243
1e	2bivB01	B:27-58,B:163-243
1f	2bivB02	B:59-162

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (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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	2biv
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	SCML2_HUMAN \| Q9UQR0	:	1oi1 2mem 2vyt 4edu

1oi1	CRYSTAL STRUCTURE OF THE MBT DOMAINS OF HUMAN SCML2
2vyt	THE MBT REPEATS OF HUMAN SCML2 BIND TO PEPTIDES CONTAINING MONO METHYLATED LYSINE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (5, 13)

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