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Description

Title :   SOLUTION STRUCTURE OF THE UBA DOMAIN OF HUMAN TUDOR DOMAIN CONTAINING PROTEIN 3

Authors :   Y. O. Kamatari, N. Tochio, T. Nakanishi, K. Miyamoto, H. Li, N. Kobayashi, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, 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 :   Uba Domain, Tudor Domain Containing 3, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. O. Kamatari, N. Tochio, T. Nakanishi, K. Miyamoto, H. Li, N. Kobayashi, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Uba Domain Of Human Tudor Domain Containing Protein 3
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - TUDOR DOMAIN CONTAINING PROTEIN 3
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P040301-26
	Expression System Vector Type	:	PLASMID
	Fragment	:	UBA DOMAIN
	Gene	:	IMS CDNA CAE03871
	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 1WJI)

Sites (0, 0)

(no "Site" information available for 1WJI)

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (1, 1)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBA	PS50030	Ubiquitin-associated domain (UBA) profile.	TDRD3_HUMAN	193-233	1	A:8-47

Exons (3, 3)

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1d	ENST00000377894	1d	ENSE00001475419	chr13:60971122-60971144	23	TDRD3_HUMAN	-	0	0	-	-
1.3b	ENST00000377894	3b	ENSE00002151362	chr13:61013822-61013906	85	TDRD3_HUMAN	-	0	0	-	-
1.4b	ENST00000377894	4b	ENSE00001423039	chr13:61018821-61018882	62	TDRD3_HUMAN	-	0	0	-	-
1.5a	ENST00000377894	5a	ENSE00002163556	chr13:61034514-61034674	161	TDRD3_HUMAN	1-25	25	0	-	-
1.6	ENST00000377894	6	ENSE00001205839	chr13:61041372-61041513	142	TDRD3_HUMAN	25-72	48	0	-	-
1.7	ENST00000377894	7	ENSE00001205834	chr13:61057909-61057980	72	TDRD3_HUMAN	73-96	24	0	-	-
1.9b	ENST00000377894	9b	ENSE00000923617	chr13:61059933-61060082	150	TDRD3_HUMAN	97-146	50	0	-	-
1.10	ENST00000377894	10	ENSE00000923618	chr13:61068569-61068709	141	TDRD3_HUMAN	147-193	47	1	A:1-7 (gaps)	18
1.11b	ENST00000377894	11b	ENSE00000923619	chr13:61083897-61084053	157	TDRD3_HUMAN	194-246	53	1	A:8-56	49
1.12	ENST00000377894	12	ENSE00000923620	chr13:61084764-61084889	126	TDRD3_HUMAN	246-288	43	1	A:57-63 (gaps)	16
1.13b	ENST00000377894	13b	ENSE00000923621	chr13:61102501-61103351	851	TDRD3_HUMAN	288-571	284	0	-	-
1.14a	ENST00000377894	14a	ENSE00000923622	chr13:61109242-61109367	126	TDRD3_HUMAN	572-613	42	0	-	-
1.15	ENST00000377894	15	ENSE00000923623	chr13:61141659-61141784	126	TDRD3_HUMAN	614-651	38	0	-	-
1.16c	ENST00000377894	16c	ENSE00001475429	chr13:61147750-61148011	262	TDRD3_HUMAN	-	0	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:63
 aligned with TDRD3_HUMAN | Q9H7E2 from UniProtKB/Swiss-Prot  Length:651

    Alignment length:116
                                   176       186       196       206       216       226       236       246       256       266       276      
          TDRD3_HUMAN   167 GNRNREVLQKEKSTKSEGKHEGVYRELVDEKALKHITEMGFSKEASRQALMDNGNNLEAALNVLLTSNKQKPVMGPPLRGRGKGRGRIRSEDEEDLGNARPSAPSTLFDFLESKMG 282
               SCOP domains d           1wjia_          A: Tudor domain containing protein 3, TDRD3                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------UBA-1wjiA01 A:8-44                   ---------------------------------------------------- Pfam domains
         Sec.struct. author .-----------......---------.hhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhh........------------------------......---------. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------UBA  PDB: A:8-47 UniProt: 193-233        ------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.10  PDB: A:1-7 (gapsExon 1.11b  PDB: A:8-56 UniProt: 194-246 [INCOMPLETE]------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------Exon 1.12  PDB: A:57-63 (gaps)        Transcript 1 (2)
                 1wji A   1 G-----------SSGSSG---------VDEKALKHITEMGFSKEASRQALMDNGNNLEAALNVLLTSNKQKPVMGP------------------------PSGPSS---------G  63
                            |        -  |    | -       |10        20        30        40        50     |   -         -         -|    |   -     |
                            |           2    7         8                                              56                       57   62        63
                            1

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 alpha proteins (14657)

Fold: RuvA C-terminal domain-like (106)

Superfamily: UBA-like (64)

Family: UBA domain (48)

Protein domain: Tudor domain containing protein 3, TDRD3 (1)

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

d1wjia_

CATH Domains (0, 0)

(no "CATH Domain" information available for 1WJI)

Pfam Domains (1, 1)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: UBA (32)

Family: UBA (23)

Homo sapiens (Human) (13)

UBA-1wjiA01

A:8-44

Gene Ontology (8, 8)

NMR Structure(hide GO term definitions)

Chain A (TDRD3_HUMAN | Q9H7E2)

molecular function
	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: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:0003713	transcription coactivator activity	Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
biological process
	GO:1903506	regulation of nucleic acid-templated transcription	Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0035145	exon-exon junction complex	A multi-subunit complex deposited by the spliceosome upstream of messenger RNA exon-exon junctions. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay.
	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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	TDRD3_HUMAN \| Q9H7E2	:	2lto 3pmt 3pnw 3s6w 5gvd 5gve

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