3FDR - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TDRD2

Authors :   M. F Amaya, M. A. Adams, Y. Guo, Y. Li, I. Kozieradzki, A. M. Edwards, C. H. Arrowsmith, J. Weigelt, C. Bountra, A. Bochkarev, J. Min, Structural Genomics Consortium (Sgc)

Date :   26 Nov 08 (Deposition) - 06 Jan 09 (Release) - 15 Dec 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym./Biol. Unit : A

Keywords :   Tdrd2, Tudor, Structural Genomics, Structural Genomics Consortium, Sgc, Alternative Splicing, Rna-Binding, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Chen, J. Jin, D. A. James, M. A. Adams-Cioaba, J. G. Park, Y. Guo, E. Tenaglia, C. Xu, G. Gish, J. Min, T. Pawson
Mouse Piwi Interactome Identifies Binding Mechanism Of Tdrkh Tudor Domain To Arginine Methylated Miwi
Proc. Natl. Acad. Sci. Usa V. 106 20336 2009
PubMed-ID: 19918066 | Reference-DOI: 10.1073/PNAS.0911640106
(for further references see the PDB file header)

Molecule 1 - TUDOR AND KH DOMAIN-CONTAINING PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	TUDOR DOMAIN
	Gene	:	TDRKH, TDRD2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3FDR)

(no "Site" information available for 3FDR)

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

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

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TUDOR	PS50304	Tudor domain profile.	TDRKH_HUMAN	353-412	1	A:27-86

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000368827	2b	ENSE00001941603	chr1:151762998-151762856	143	TDRKH_HUMAN	-	0	0	-	-
1.4b	ENST00000368827	4b	ENSE00002159845	chr1:151755525-151755375	151	TDRKH_HUMAN	1-42	42	0	-	-
1.6	ENST00000368827	6	ENSE00001296403	chr1:151754063-151753957	107	TDRKH_HUMAN	42-77	36	0	-	-
1.7e	ENST00000368827	7e	ENSE00001311108	chr1:151752616-151752427	190	TDRKH_HUMAN	78-141	64	0	-	-
1.8a	ENST00000368827	8a	ENSE00001325745	chr1:151751718-151751579	140	TDRKH_HUMAN	141-187	47	0	-	-
1.9a	ENST00000368827	9a	ENSE00001300321	chr1:151751482-151751161	322	TDRKH_HUMAN	188-295	108	0	-	-
1.10	ENST00000368827	10	ENSE00001294518	chr1:151749075-151748915	161	TDRKH_HUMAN	295-348	54	1	A:5-22	18
1.11	ENST00000368827	11	ENSE00001311139	chr1:151748744-151748572	173	TDRKH_HUMAN	349-406	58	1	A:23-80	58
1.12	ENST00000368827	12	ENSE00001317063	chr1:151748360-151748296	65	TDRKH_HUMAN	406-428	23	1	A:80-93	14
1.13	ENST00000368827	13	ENSE00001316963	chr1:151748019-151747868	152	TDRKH_HUMAN	428-478	51	0	-	-
1.14	ENST00000368827	14	ENSE00001307144	chr1:151747642-151747541	102	TDRKH_HUMAN	479-512	34	0	-	-
1.15	ENST00000368827	15	ENSE00001291350	chr1:151747282-151747186	97	TDRKH_HUMAN	513-545	33	0	-	-
1.16a	ENST00000368827	16a	ENSE00001325167	chr1:151746980-151746889	92	TDRKH_HUMAN	545-561	17	0	-	-
1.17	ENST00000368827	17	ENSE00001419045	chr1:151744462-151744040	423	TDRKH_HUMAN	-	0	0	-	-

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:89
 aligned with TDRKH_HUMAN | Q9Y2W6 from UniProtKB/Swiss-Prot  Length:561

    Alignment length:89
                                   340       350       360       370       380       390       400       410         
          TDRKH_HUMAN   331 LQLDKLVNEMTQHYENSVPEDLTVHVGDIVAAPLPTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIEC 419
               SCOP domains d3fdra_ A: Tudor and KH domain-containing protein TDRKH                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.............eeeee......eeeeeeeee.....eeeee.....eeeehhhhhee.hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------TUDOR  PDB: A:27-86 UniProt: 353-412                        ------- PROSITE
           Transcript 1 (1) Exon 1.10         Exon 1.11  PDB: A:23-80 UniProt: 349-406                  ------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------Exon 1.12      Transcript 1 (2)
                 3fdr A   5 LQLDKLVNEMTQHYENSVPEDLTVHVGDIVAAPLPTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIEC  93
                                    14        24        34        44        54        64        74        84

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Asymmetric/Biological Unit

Classes(

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Families(

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Protein Domains( (-)

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Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: Tudor/PWWP/MBT (72)

Family: Tudor domain (24)

Protein domain: Tudor and KH domain-containing protein TDRKH (2)

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

d3fdra_

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TDRKH_HUMAN | Q9Y2W6)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
biological process
	GO:0043046	DNA methylation involved in gamete generation	The covalent transfer of a methyl group to C-5 of cytosine that contributes to the establishment of DNA methylation patterns in the gamete.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0009566	fertilization	The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).
	GO:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	GO:0007140	male meiotic nuclear division	A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline.
	GO:0034587	piRNA metabolic process	The chemical reactions and pathways involving piRNAs, Piwi-associated RNAs, a class of 24- to 30-nucleotide RNA derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0071546	pi-body	A P granule that contains the PIWIL2-TDRD1 module, a set of proteins that act in the primary piRNA pathway. The pi-body corresponds to the cementing material between mitochondria found in gonocytes.
	GO:0071547	piP-body	A P granule that contains the PIWIL4-TDRD9 module, a set of proteins that act in the secondary piRNA pathway.

Asymmetric/Biological Unit
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	TDRKH_HUMAN \| Q9Y2W6	:	2diq 5j39

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