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Description

Title :   SOLUTION STRUCTURE OF THE TUDOR DOMAIN OF TUDOR DOMAIN-CONTAINING PROTEIN 4

Authors :   W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   30 Mar 07 (Deposition) - 02 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Nmr, Tudor Domain, Tudor Domain-Containing Protein 4, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of The Tudor Domain Of Tudor Domain-Containing Protein 4
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - TUDOR DOMAIN-CONTAINING PROTEIN 4
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P060911-18
	Expression System Vector Type	:	PLASMID
	Fragment	:	TUDOR DOMAIN
	Gene	:	TDRD4
	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 2EQK)

Sites (0, 0)

(no "Site" information available for 2EQK)

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (1, 1)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TUDOR	PS50304	Tudor domain profile.	RNF17_HUMAN	726-784 962-1021 1228-1285 1479-1539	1	- A:21-80 - -

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
1.1a	ENST00000255324	1a	ENSE00001843925	chr13:25338290-25338471	182	RNF17_HUMAN	1-44	44	0	-	-
1.2	ENST00000255324	2	ENSE00001696954	chr13:25341410-25341504	95	RNF17_HUMAN	44-75	32	0	-	-
1.3	ENST00000255324	3	ENSE00001619772	chr13:25348951-25349042	92	RNF17_HUMAN	76-106	31	0	-	-
1.4	ENST00000255324	4	ENSE00001782677	chr13:25352433-25352544	112	RNF17_HUMAN	106-143	38	0	-	-
1.5	ENST00000255324	5	ENSE00001798456	chr13:25353805-25353885	81	RNF17_HUMAN	144-170	27	0	-	-
1.6	ENST00000255324	6	ENSE00001630455	chr13:25355982-25356082	101	RNF17_HUMAN	171-204	34	0	-	-
1.7b	ENST00000255324	7b	ENSE00001794042	chr13:25362126-25362297	172	RNF17_HUMAN	204-261	58	0	-	-
1.8	ENST00000255324	8	ENSE00001758443	chr13:25363486-25363562	77	RNF17_HUMAN	262-287	26	0	-	-
1.9	ENST00000255324	9	ENSE00001800443	chr13:25363836-25363910	75	RNF17_HUMAN	287-312	26	0	-	-
1.10	ENST00000255324	10	ENSE00001723012	chr13:25367180-25367484	305	RNF17_HUMAN	312-414	103	0	-	-
1.12b	ENST00000255324	12b	ENSE00001687093	chr13:25370275-25370433	159	RNF17_HUMAN	414-467	54	0	-	-
1.13	ENST00000255324	13	ENSE00001646722	chr13:25373533-25373722	190	RNF17_HUMAN	467-530	64	0	-	-
1.14	ENST00000255324	14	ENSE00001767298	chr13:25374504-25374672	169	RNF17_HUMAN	530-586	57	0	-	-
1.15	ENST00000255324	15	ENSE00001695592	chr13:25376519-25376709	191	RNF17_HUMAN	587-650	64	0	-	-
1.17	ENST00000255324	17	ENSE00001684621	chr13:25378426-25378567	142	RNF17_HUMAN	650-697	48	0	-	-
1.20	ENST00000255324	20	ENSE00001706074	chr13:25399757-25399910	154	RNF17_HUMAN	698-749	52	0	-	-
1.22	ENST00000255324	22	ENSE00001671772	chr13:25404622-25404737	116	RNF17_HUMAN	749-787	39	0	-	-
1.23	ENST00000255324	23	ENSE00001786297	chr13:25405996-25406116	121	RNF17_HUMAN	788-828	41	0	-	-
1.24	ENST00000255324	24	ENSE00001729598	chr13:25416179-25416299	121	RNF17_HUMAN	828-868	41	0	-	-
1.25a	ENST00000255324	25a	ENSE00001731008	chr13:25417882-25418109	228	RNF17_HUMAN	868-944	77	1	A:1-3	3
1.26	ENST00000255324	26	ENSE00001621489	chr13:25418790-25418940	151	RNF17_HUMAN	944-994	51	1	A:3-53	51
1.27	ENST00000255324	27	ENSE00001144924	chr13:25419099-25419217	119	RNF17_HUMAN	995-1034	40	1	A:54-85	32
1.28	ENST00000255324	28	ENSE00001144918	chr13:25424479-25424581	103	RNF17_HUMAN	1034-1068	35	0	-	-
1.29	ENST00000255324	29	ENSE00001144911	chr13:25425594-25425709	116	RNF17_HUMAN	1069-1107	39	0	-	-
1.30	ENST00000255324	30	ENSE00001144905	chr13:25427993-25428282	290	RNF17_HUMAN	1107-1204	98	0	-	-
1.31	ENST00000255324	31	ENSE00001144899	chr13:25433139-25433302	164	RNF17_HUMAN	1204-1258	55	0	-	-
1.32	ENST00000255324	32	ENSE00001144895	chr13:25435406-25435525	120	RNF17_HUMAN	1259-1298	40	0	-	-
1.33b	ENST00000255324	33b	ENSE00001391074	chr13:25436851-25436931	81	RNF17_HUMAN	1299-1325	27	0	-	-
1.34	ENST00000255324	34	ENSE00001375546	chr13:25439011-25439136	126	RNF17_HUMAN	1326-1367	42	0	-	-
1.35	ENST00000255324	35	ENSE00001144882	chr13:25440282-25440341	60	RNF17_HUMAN	1368-1387	20	0	-	-
1.36	ENST00000255324	36	ENSE00001144876	chr13:25442738-25442854	117	RNF17_HUMAN	1388-1426	39	0	-	-
1.37	ENST00000255324	37	ENSE00001144871	chr13:25444709-25444877	169	RNF17_HUMAN	1427-1483	57	0	-	-
1.38a	ENST00000255324	38a	ENSE00001144865	chr13:25448252-25448387	136	RNF17_HUMAN	1483-1528	46	0	-	-
1.39	ENST00000255324	39	ENSE00000906526	chr13:25451135-25451324	190	RNF17_HUMAN	1528-1591	64	0	-	-
1.40	ENST00000255324	40	ENSE00000906525	chr13:25453325-25453433	109	RNF17_HUMAN	1592-1623	32	0	-	-
1.41b	ENST00000255324	41b	ENSE00001490241	chr13:25453875-25454059	185	RNF17_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:85
 aligned with RNF17_HUMAN | Q9BXT8 from UniProtKB/Swiss-Prot  Length:1623

    Alignment length:85
                                   951       961       971       981       991      1001      1011      1021     
         RNF17_HUMAN    942 LNSLEEKMIAAYENSKWEPVKWENDMHCAVKIQDKNQWRRGQIIRMVTDTLVEVLLYDVGVELVVNVDCLRKLEENLKTMGRLSL 1026
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhh............eeeee......eeeeeeeee....eeeee......eeeee...eee..hhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------TUDOR  PDB: A:21-80 UniProt: 962-1021                       ----- PROSITE
           Transcript 1 (1) 1.2--------------------------------------------------Exon 1.27  PDB: A:54-85          Transcript 1 (1)
           Transcript 1 (2) --Exon 1.26  PDB: A:3-53 UniProt: 944-994            -------------------------------- Transcript 1 (2)
                2eqk A    1 GSSGSSGMIAAYENSKWEPVKWENDMHCAVKIQDKNQWRRGQIIRMVTDTLVEVLLYDVGVELVVNVDCLRKLEENLKTMGRLSL   85
                                    10        20        30        40        50        60        70        80

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 (0, 0)

(no "SCOP Domain" information available for 2EQK)

CATH Domains (0, 0)

(no "CATH Domain" information available for 2EQK)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2EQK)

Gene Ontology (9, 9)

NMR Structure(hide GO term definitions)

Chain A (RNF17_HUMAN | Q9BXT8)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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: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:0007286	spermatid development	The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure.
	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: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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