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Description

Title :   SOLUTION STRUCTURE OF THE 2ND MBT DOMAIN FROM HUMAN KIAA1617 PROTEIN

Authors :   T. Tomizawa, T. Kigawa, S. Koshiba, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   29 May 04 (Deposition) - 29 Nov 04 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Mbt Domain, Kiaa1617 Protein, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Tomizawa, T. Kigawa, S. Koshiba, M. Inoue, S. Yokoyama
Solution Structure Of The 2Nd Mbt Domain From Human Kiaa1617 Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - KIAA1617 PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P040119-21
	Expression System Vector Type	:	PLASMID
	Fragment	:	MBT DOMAIN
	Gene	:	KAZUSA CDNA FJ13890
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS

Structural Features

Chains, Units


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1WJR)

Sites (0, 0)

(no "Site" information available for 1WJR)

SS Bonds (0, 0)

(no "SS Bond" information available for 1WJR)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1WJR)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1WJR)

PROSITE Motifs (1, 1)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MBT	PS51079	MBT repeat profile.	SMBT2_HUMAN	44-144 152-256 266-372 380-477	1	- - A:92-126 -

Exons (4, 4)

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000397167	1a	ENSE00001527591	chr10:7453450-7453307	144	SMBT2_HUMAN	-	0	0	-	-
1.4	ENST00000397167	4	ENSE00001215204	chr10:7423911-7423761	151	SMBT2_HUMAN	1-34	34	0	-	-
1.5	ENST00000397167	5	ENSE00000915095	chr10:7412337-7412243	95	SMBT2_HUMAN	34-65	32	0	-	-
1.6	ENST00000397167	6	ENSE00000915094	chr10:7409851-7409611	241	SMBT2_HUMAN	66-146	81	0	-	-
1.8a	ENST00000397167	8a	ENSE00001215170	chr10:7327916-7327828	89	SMBT2_HUMAN	146-175	30	1	A:1-4 (gaps)	12
1.9	ENST00000397167	9	ENSE00000837273	chr10:7326112-7325866	247	SMBT2_HUMAN	176-258	83	1	A:5-84	80
1.10	ENST00000397167	10	ENSE00000837272	chr10:7318951-7318854	98	SMBT2_HUMAN	258-290	33	1	A:84-116	33
1.11	ENST00000397167	11	ENSE00000689524	chr10:7290611-7290510	102	SMBT2_HUMAN	291-324	34	1	A:117-127 (gaps)	32
1.12	ENST00000397167	12	ENSE00000915093	chr10:7285667-7285520	148	SMBT2_HUMAN	325-374	50	0	-	-
1.13	ENST00000397167	13	ENSE00000837270	chr10:7269899-7269817	83	SMBT2_HUMAN	374-401	28	0	-	-
1.14	ENST00000397167	14	ENSE00000915092	chr10:7262499-7262373	127	SMBT2_HUMAN	402-444	43	0	-	-
1.15	ENST00000397167	15	ENSE00000985193	chr10:7247890-7247777	114	SMBT2_HUMAN	444-482	39	0	-	-
1.16	ENST00000397167	16	ENSE00000985194	chr10:7244484-7244442	43	SMBT2_HUMAN	482-496	15	0	-	-
1.17	ENST00000397167	17	ENSE00000985195	chr10:7242446-7242376	71	SMBT2_HUMAN	496-520	25	0	-	-
1.18	ENST00000397167	18	ENSE00000985196	chr10:7239649-7239510	140	SMBT2_HUMAN	520-566	47	0	-	-
1.19	ENST00000397167	19	ENSE00000985197	chr10:7230695-7230586	110	SMBT2_HUMAN	567-603	37	0	-	-
1.20	ENST00000397167	20	ENSE00000985198	chr10:7218127-7217952	176	SMBT2_HUMAN	603-662	60	0	-	-
1.21	ENST00000397167	21	ENSE00000985199	chr10:7214623-7214457	167	SMBT2_HUMAN	662-717	56	0	-	-
1.22	ENST00000397167	22	ENSE00000985200	chr10:7214120-7213857	264	SMBT2_HUMAN	718-805	88	0	-	-
1.23	ENST00000397167	23	ENSE00000985201	chr10:7213018-7212890	129	SMBT2_HUMAN	806-848	43	0	-	-
1.24a	ENST00000397167	24a	ENSE00001527573	chr10:7205872-7204249	1624	SMBT2_HUMAN	849-894	46	0	-	-

Sequences/Alignments

NMR Structure

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
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Chain A from PDB  Type:PROTEIN  Length:127
 aligned with SMBT2_HUMAN | Q5VUG0 from UniProtKB/Swiss-Prot  Length:894

    Alignment length:159
                                   173       183       193       203       213       223       233       243       253       263       273       283       293       303       313         
          SMBT2_HUMAN   164 GSRTAPANLLEGPLRGKGPIDLITVGSLIELQDSQNPFQYWIVSVIENVGGRLRLRYVGLEDTESYDQWLFYLDYRLRPVGWCQENKYRMDPPSEIYPLKMASEWKCTLEKSLIDAAKFPLPMEVFKDHADLRSHFFTVGMKLETVNMCEPFYISPASV 322
               SCOP domains d1        wj   ra_ A: Scm-like with four MBT domains protein 2, SFMBT2 (KIAA1617)                                                                               SCOP domains
               CATH domains 1w        jr   A00 A:1-127  [code=2.30.30.160, no name defined]                                                                                                 CATH domains
               Pfam domains ---------------------------MBT-1wjrA01 A:17-89                                                      ----------------------------------------------------------- Pfam domains
         Sec.struct. author ..--------..---..hhhhhh....eeeee.......eeeee...ee..eeee............eeee..........hhhhhh.............hhhhhhhhhhhhhhhhhhh..hhhhhh......---------------------..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE MBT  PDB: - UniProt: 152-256                                                                 ---------MBT  PDB: A:92-126 UniProt: 266-372                       PROSITE
           Transcript 1 (1) Exon 1.8a   ----------------------------------------------------------------------------------Exon 1.10  PDB: A:84-116         Exon 1.11  PDB: A:117-127 (gaps) Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.9  PDB: A:5-84 UniProt: 176-258 [INCOMPLETE]                                ---------------------------------------------------------------- Transcript 1 (2)
                 1wjr A   1 GS--------SG---SSGPIDLITVGSLIELQDSQNPFQYWIVSVIENVGGRLRLRYVGLEDTESYDQWLFYLDYRLRPVGWCQENKYRMDPPSEIYPLKMASEWKCTLEKSLIDAAKFPLPMEVFKDHADLS---------------------GPSSG 127
                             |       -||   |   9        19        29        39        49        59        69        79        89        99       109       119  |      -         -    |    
                             2        3|   5                                                                                                                  122                   123    
                                       4

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, 1)

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

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: Scm-like with four MBT domains protein 2, SFMBT2 (KIAA1617) (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d1wjra_

CATH Domains (1, 1)

NMR Structure

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)

1wjrA00

A:1-127

Pfam Domains (1, 1)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Tudor (88)

Family: MBT (24)

Homo sapiens (Human) (20)

MBT-1wjrA01

A:17-89

Gene Ontology (8, 8)

NMR Structure(hide GO term definitions)

Chain A (SMBT2_HUMAN | Q5VUG0)

molecular function
	GO:0042393	histone binding	Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
	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).
biological process
	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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
	GO:0016235	aggresome	An inclusion body formed by dynein-dependent retrograde transport of an aggregated protein on microtubules.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	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 (0, 0)

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SS Bonds (0, 0)

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Exons (4, 4)

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