3S93 - JenaLib

Title :   CRYSTAL STRUCTURE OF CONSERVED MOTIF IN TDRD5

Authors :   X. Chao, W. Tempel, C. Bian, J. Kania, A. K. Wernimont, C. Bountra, J. Wei C. H. Arrowsmith, A. M. Edwards, J. Min, Structural Genomics Consor (Sgc)

Date :   31 May 11 (Deposition) - 31 Aug 11 (Release) - 31 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.28

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Structural Genomics Consortium, Sgc, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Chao, W. Tempel, C. Bian, J. Kania, A. K. Wernimont, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, J. Min
Crystal Structure Of Conserved Motif In Tdrd5
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Asymmetric 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:80
 aligned with TDRD5_HUMAN | Q8NAT2 from UniProtKB/Swiss-Prot  Length:981

    Alignment length:80
                             1                                                                              
                             |       9        19        29        39        49        59        69        79
           TDRD5_HUMAN    - -MSEQERIQECLRKEIRSLLISTKDGLSPQELEKEYLLMVGNHLPLRILGYRSTMELVLDMPDVVRVCPGAGGTVILKAI 79
               SCOP domains -------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....hhhhh..hhhhhhhh....eeee.hhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------HTH_OST  PDB: A:7-79 UniProt: 7-80                                        PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                  3s93 A  0 GMSEQERIQECLRKEIRSLLISTKDGLSPQELEKEYLLMVGNHLPLRILGYRSTMELVLDMPDVVRVCPGAGGTVILKAI 79
                                     9        19        29        39        49        59        69        79

Chain B from PDB  Type:PROTEIN  Length:81
 aligned with TDRD5_HUMAN | Q8NAT2 from UniProtKB/Swiss-Prot  Length:981

    Alignment length:81
                             1                                                                               
                             |       9        19        29        39        49        59        69        79 
           TDRD5_HUMAN    - -MSEQERIQECLRKEIRSLLISTKDGLSPQELEKEYLLMVGNHLPLRILGYRSTMELVLDMPDVVRVCPGAGGTVILKAIP 80
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....hhhhh..hhhhhhhh....eeeee.hhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------HTH_OST  PDB: B:7-80 UniProt: 7-80                                         PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  3s93 B  0 GMSEQERIQECLRKEIRSLLISTKDGLSPQELEKEYLLMVGNHLPLRILGYRSTMELVLDMPDVVRVCPGAGGTVILKAIP 80
                                     9        19        29        39        49        59        69        79

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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A,B (TDRD5_HUMAN | Q8NAT2)

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:0030719	P granule organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of polar granules, cytoplasmic, non-membranous RNA/protein complex aggregates in the primordial germ cells of many higher eukaryotes.
	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:0033391	chromatoid body	A ribonucleoprotein complex found in the cytoplasm of male germ cells, composed of exceedingly thin filaments that are consolidated into a compact mass or into dense strands of varying thickness that branch to form an irregular network. Contains mRNAs, miRNAs, and protein components involved in miRNA processing (such as Argonaute proteins and the endonuclease Dicer) and in RNA decay (such as the decapping enzyme DCP1a and GW182).
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

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