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Asym./Biol. Unit

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Description

Title :   CRYSTAL STRUCTURE OF THE TUDOR DOMAIN OF HUMAN TUDOR DOMAIN-CONTAINING PROTEIN 3

Authors :   R. Lam, C. B. Bian, Y. H. Guo, C. Xu, J. Kania, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, J. Min, Structural Gen Consortium (Sgc)

Date :   18 Nov 10 (Deposition) - 01 Dec 10 (Release) - 28 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Tudor Domain, Structural Genomics Consortium, Sgc, Sulfur Phasing, Nucleus, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Liu, Y. Guo, H. Liu, C. Bian, R. Lam, Y. Liu, F. Mackenzie, L. A. Rojas, D. Reinberg, M. T. Bedford, R. M. Xu, J. Min
Crystal Structure Of Tdrd3 And Methyl-Arginine Binding Characterization Of Tdrd3, Smn And Spf30.
Plos One V. 7 30375 2012
PubMed-ID: 22363433 | Reference-DOI: 10.1371/JOURNAL.PONE.0030375

Compounds

Molecule 1 - TUDOR DOMAIN-CONTAINING PROTEIN 3
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28-MHL
	Expression System Strain	:	BL21-(DE3)-V2R-PRARE2
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	TUDOR DOMAIN, UNP RESIDUES 553-611
	Gene	:	TDRD3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 1)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL

Sites (1, 1)

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:566 , LYS A:571 , PHE A:591 , TYR A:594 , ASN A:596	BINDING SITE FOR RESIDUE PG4 A 800

SS Bonds (0, 0)

(no "SS Bond" information available for 3PMT)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 3PMT)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 3PMT)

PROSITE Motifs (1, 1)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TUDOR	PS50304	Tudor domain profile.	TDRD3_HUMAN	555-615	1	A:555-608

Exons (2, 2)

Asymmetric/Biological Unit (2, 2)

	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	0	-	-
1.11b	ENST00000377894	11b	ENSE00000923619	chr13:61083897-61084053	157	TDRD3_HUMAN	194-246	53	0	-	-
1.12	ENST00000377894	12	ENSE00000923620	chr13:61084764-61084889	126	TDRD3_HUMAN	246-288	43	0	-	-
1.13b	ENST00000377894	13b	ENSE00000923621	chr13:61102501-61103351	851	TDRD3_HUMAN	288-571	284	1	A:554-571	18
1.14a	ENST00000377894	14a	ENSE00000923622	chr13:61109242-61109367	126	TDRD3_HUMAN	572-613	42	1	A:572-608	37
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

Asymmetric/Biological 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:55
 aligned with TDRD3_HUMAN | Q9H7E2 from UniProtKB/Swiss-Prot  Length:651

    Alignment length:55
                                   563       573       583       593       603     
          TDRD3_HUMAN   554 KMWKPGDECFALYWEDNKFYRAEVEALHSSGMTAVVKFIDYGNYEEVLLSNIKPI 608
               SCOP domains d3pmta_ A: Tudor domain-containing protein 3, TDRD3     SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....eeeeeeeeee.....eeeeee.....eeeee...eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE -TUDOR  PDB: A:555-608 UniProt: 555-615                 PROSITE
               Transcript 1 Exon 1.13b        Exon 1.14a  PDB: A:572-608            Transcript 1
                 3pmt A 554 KMWKPGDECFALYWEDNKFYRAEVEALHSSGMTAVVKFIDYGNYEEVLLSNIKPI 608
                                   563       573       583       593       603

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)

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: Tudor/PWWP/MBT (72)

Family: Tudor domain (24)

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

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

d3pmta_

CATH Domains (0, 0)

(no "CATH Domain" information available for 3PMT)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 3PMT)

Gene Ontology (8, 8)

Asymmetric/Biological Unit(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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	3pmt
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	TDRD3_HUMAN \| Q9H7E2	:	1wji 2lto 3pnw 3s6w 5gvd 5gve

Related Entries Specified in the PDB File

3s6w