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Description

Title :   CRYSTAL STRUCTURE OF SCMH1

Authors :   N. Herzanych, G. Senisterra, Y. Liu, L. Crombet, P. Loppnau, I. Koziera M. Vedadi, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, J. Min, Structural Genomics Consortium (Sgc)

Date :   28 Feb 07 (Deposition) - 27 Mar 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Scmh1, Structural Genomics, Structural Genomics Consortium, Sgc, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Herzanych, G. Senisterra, Y. Liu, L. Crombet, P. Loppnau, I. Kozieradzki, M. Vedadi, J. Weigelt, M. Sundstrom, C. H. Arrowsmith A. M. Edwards, A. Bochkarev, J. Min
Structure Of Scmh1
To Be Published
PubMed: search

Compounds

Molecule 1 - POLYCOMB PROTEIN SCMH1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A-MHL
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	SCMH1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SEX COMB ON MIDLEG HOMOLOG 1

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 8)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CL	6	Ligand/Ion	CHLORIDE ION
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	PO4	6	Ligand/Ion	PHOSPHATE ION

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:115 , LYS A:118	BINDING SITE FOR RESIDUE CL A 301
2	AC2	SOFTWARE	ASN A:145 , HOH A:584	BINDING SITE FOR RESIDUE CL A 302
3	AC3	SOFTWARE	LYS A:142 , GLY A:194 , HOH A:445	BINDING SITE FOR RESIDUE CL A 303
4	AC4	SOFTWARE	PHE A:47 , PRO A:160 , HOH A:484 , HOH A:593	BINDING SITE FOR RESIDUE CL A 304
5	AC5	SOFTWARE	LYS A:63 , ASP A:93 , LYS A:168 , MET A:169 , PO4 A:401 , HOH A:557	BINDING SITE FOR RESIDUE CL A 305
6	AC6	SOFTWARE	MET A:138	BINDING SITE FOR RESIDUE CL A 306
7	AC7	SOFTWARE	ASP A:93 , GLY A:94 , ARG A:130 , PHE A:139 , GLU A:191 , VAL A:192 , CL A:305 , HOH A:560	BINDING SITE FOR RESIDUE PO4 A 401
8	AC8	SOFTWARE	MET A:149 , ALA A:150 , PRO A:151 , SER A:161 , ARG A:213 , ASP A:215 , HOH A:424 , HOH A:512 , HOH A:598	BINDING SITE FOR RESIDUE PO4 A 402

SS Bonds (0, 0)

(no "SS Bond" information available for 2P0K)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2P0K)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2P0K)

PROSITE Motifs (1, 2)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MBT	PS51079	MBT repeat profile.	SCMH1_HUMAN	28-126 134-235	2	A:28-126 A:134-235

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MBT	PS51079	MBT repeat profile.	SCMH1_HUMAN	28-126 134-235	2	A:28-126 A:134-235

Biological Unit 2 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MBT	PS51079	MBT repeat profile.	SCMH1_HUMAN	28-126 134-235	6	A:28-126 A:134-235

Exons (4, 4)

Asymmetric Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.7b	ENST00000397174	7b	ENSE00001527590	chr1:41618346-41618271	76	SCMH1_HUMAN	1-26	26	0	-	-
1.8	ENST00000397174	8	ENSE00001726473	chr1:41617356-41617286	71	SCMH1_HUMAN	26-49	24	1	A:27-49	23
1.9	ENST00000397174	9	ENSE00001731684	chr1:41608784-41608550	235	SCMH1_HUMAN	50-128	79	1	A:50-128	79
1.10	ENST00000397174	10	ENSE00000870127	chr1:41582682-41582594	89	SCMH1_HUMAN	128-157	30	1	A:128-157	30
1.11	ENST00000397174	11	ENSE00000768876	chr1:41579198-41578955	244	SCMH1_HUMAN	158-239	82	1	A:158-235	78
1.12	ENST00000397174	12	ENSE00000768714	chr1:41541123-41540891	233	SCMH1_HUMAN	239-316	78	0	-	-
1.13a	ENST00000397174	13a	ENSE00000768679	chr1:41536393-41536267	127	SCMH1_HUMAN	317-359	43	0	-	-
1.14a	ENST00000397174	14a	ENSE00000768644	chr1:41514562-41514362	201	SCMH1_HUMAN	359-426	68	0	-	-
1.15c	ENST00000397174	15c	ENSE00000574832	chr1:41512270-41512079	192	SCMH1_HUMAN	426-490	65	0	-	-
1.18a	ENST00000397174	18a	ENSE00001144641	chr1:41503213-41503034	180	SCMH1_HUMAN	490-550	61	0	-	-
1.19	ENST00000397174	19	ENSE00001144632	chr1:41499720-41499655	66	SCMH1_HUMAN	550-572	23	0	-	-
1.20b	ENST00000397174	20b	ENSE00001144620	chr1:41494398-41494256	143	SCMH1_HUMAN	572-619	48	0	-	-
1.21b	ENST00000397174	21b	ENSE00001304971	chr1:41493991-41492877	1115	SCMH1_HUMAN	620-660	41	0	-	-

Sequences/Alignments

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:209
 aligned with SCMH1_HUMAN | Q96GD3 from UniProtKB/Swiss-Prot  Length:660

    Alignment length:209
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226         
          SCMH1_HUMAN    27 HFTWDKYLKETCSVPAPVHCFKQSYTPPSNEFKISMKLEAQDPRNTTSTCIATVVGLTGARLRLRLDGSDNKNDFWRLVDSAEIQPIGNCEKNGGMLQPPLGFRLNASSWPMFLLKTLNGAEMAPIRIFHKEPPSPSHNFFKMGMKLEAVDRKNPHFICPATIGEVRGSEVLVTFDGWRGAFDYWCRFDSRDIFPVGWCSLTGDNLQPP 235
               SCOP domains d2p0ka1 A:27-133 automated matches                                                                         d2p0ka2 A:134-235 automated matches                                                                    SCOP domains
               CATH domains 2p0kA01 A:27-53,A:158-235  --------------------------------------------------------------------------------------------------------2p0kA01 A:27-53,A:158-235  [code=2.30.30.160, no name defined]                 CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------MBT-2p0kA01 A:171-235                                             Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------MBT-2p0kA02 A:171-235                                             Pfam domains (2)
         Sec.struct. author ..hhhhhhhhh.....hhhhh...............eeeeee..eeeeeeeeeeeeee..eeeeee........eeee.....ee..hhhhhh............hhhhhhhhhhhhhh.....hhhhh................eeeee.......eeeeeeeeee..eeeeee........eeee.....ee..hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -MBT  PDB: A:28-126 UniProt: 28-126                                                                 -------MBT  PDB: A:134-235 UniProt: 134-235                                                                   PROSITE
           Transcript 1 (1) Exon 1.8  PDB: A:27-49 ------------------------------------------------------------------------------Exon 1.10  PDB: A:128-157     Exon 1.11  PDB: A:158-235 UniProt: 158-239 [INCOMPLETE]                        Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.9  PDB: A:50-128 UniProt: 50-128                                        ----------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2p0k A  27 HFTWDKYLKETCSVPAPVHCFKQSYTPPSNEFKISMKLEAQDPRNTTSTCIATVVGLTGARLRLRLDGSDNKNDFWRLVDSAEIQPIGNCEKNGGMLQPPLGFRLNASSWPMFLLKTLNGAEMAPIRIFHKEPPSPSHNFFKMGMKLEAVDRKNPHFICPATIGEVRGSEVLVTFDGWRGAFDYWCRFDSRDIFPVGWCSLTGDNLQPP 235
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

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	d2p0ka1	A:27-133
1b	d2p0ka2	A:134-235

CATH Domains (1, 1)

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)

2p0kA01

A:27-53,A:158-235

Pfam Domains (1, 2)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Tudor (88)

Family: MBT (24)

Homo sapiens (Human) (20)

1a	MBT-2p0kA01	A:171-235
1b	MBT-2p0kA02	A:171-235

Gene Ontology (16, 16)

Asymmetric Unit(hide GO term definitions)

Chain A (SCMH1_HUMAN | Q96GD3)

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: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:0009952	anterior/posterior pattern specification	The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
	GO:0006338	chromatin remodeling	Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
	GO:0016458	gene silencing	Any process carried out at the cellular level that results in either long-term transcriptional repression via action on chromatin structure or RNA mediated, post-transcriptional repression of gene expression.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0016925	protein sumoylation	The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0010369	chromocenter	A region in which centric, heterochromatic portions of one or more chromosomes form a compact structure.
	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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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (4, 4)

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Related Entries

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Related Entries Specified in the PDB File