2VC8 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE LSM DOMAIN OF HUMAN EDC3 (ENHANCER OF DECAPPING 3)

Authors :   F. Tritschler, M. D. Hartmann, O. Weichenrieder

Date :   19 Sep 07 (Deposition) - 16 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.31

Chains :   Asym./Biol. Unit : A

Keywords :   P-Body Component, Enhancer Of Mrna Decapping, Rna, Cytoplasm, Sm-Like Protein, Protein-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Tritschler, A. Eulalio, V. Truffault, M. D. Hartmann, S. Helms, S. Schmidt, M. Coles, E. Izaurralde, O. Weichenrieder
A Divergent Sm Fold In Edc3 Proteins Mediates Dcp1 Binding And P-Body Targeting.
Mol. Cell. Biol. V. 27 8600 2007
PubMed-ID: 17923697 | Reference-DOI: 10.1128/MCB.01506-07

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (0, 0)

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
1.1	ENST00000315127	1	ENSE00001292931	chr15:74988384-74988221	164	EDC3_HUMAN	-	0	0	-	-
1.2b	ENST00000315127	2b	ENSE00001253727	chr15:74967483-74967302	182	EDC3_HUMAN	1-55	55	1	A:3-55	53
1.3	ENST00000315127	3	ENSE00001253676	chr15:74964115-74963796	320	EDC3_HUMAN	55-162	108	1	A:55-74	20
1.4	ENST00000315127	4	ENSE00001253669	chr15:74948409-74948074	336	EDC3_HUMAN	162-274	113	0	-	-
1.5	ENST00000315127	5	ENSE00001253663	chr15:74932960-74932807	154	EDC3_HUMAN	274-325	52	0	-	-
1.6	ENST00000315127	6	ENSE00001253655	chr15:74927967-74927750	218	EDC3_HUMAN	325-398	74	0	-	-
1.7b	ENST00000315127	7b	ENSE00001856853	chr15:74925287-74922899	2389	EDC3_HUMAN	398-508	111	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
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Chain A from PDB  Type:PROTEIN  Length:72
 aligned with EDC3_HUMAN | Q96F86 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:72
                                    12        22        32        42        52        62        72  
            EDC3_HUMAN    3 TDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPFHNGVKCLVPEVTFRAGDITELKILEIPGPGDNQ 74
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee......eeeeeeeeee....eeeeeeeee..ee....eeeee.hhh.eeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------S-------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:3-55 UniProt: 1-55 [INCOMPLETE]    ------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------Exon 1.3             Transcript 1 (2)
                  2vc8 A  3 TDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPFHNGVKCLVPEVTFRAGDITELKILEIPGPGDNQ 74
                                    12        22        32        42        52        62        72

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 (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (EDC3_HUMAN | Q96F86)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	GO:1990174	phosphodiesterase decapping endonuclease activity	Catalysis of the removal of the cap from an unmethylated 5'-end capped RNA resulting in the release of the entire cap structure (GpppN) and a 5' monophosphorylated RNA.
	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).
biological process
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0033962	cytoplasmic mRNA processing body assembly	The aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.
	GO:0031087	deadenylation-independent decapping of nuclear-transcribed mRNA	Cleavage of the 5'-cap of a nuclear-transcribed mRNA that is independent of poly(A) tail shortening.
	GO:0043928	exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 3'-poly(A) tail.
cellular component
	GO:0000932	P-body	A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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