2VC8
Crystal structure of the LSm domain of human EDC3 (enhancer of decapping 3)
Summary for 2VC8
| Entry DOI | 10.2210/pdb2vc8/pdb |
| Related | 2RM4 |
| Descriptor | ENHANCER OF MRNA-DECAPPING PROTEIN 3 (2 entities in total) |
| Functional Keywords | p-body component, enhancer of mrna decapping, rna, cytoplasm, sm-like protein, protein-binding, protein binding |
| Biological source | HOMO SAPIENS (HUMAN) |
| Cellular location | Cytoplasm, P-body: Q96F86 |
| Total number of polymer chains | 1 |
| Total formula weight | 8988.08 |
| Authors | Tritschler, F.,Hartmann, M.D.,Weichenrieder, O. (deposition date: 2007-09-19, release date: 2007-10-16, Last modification date: 2024-05-08) |
| Primary citation | Tritschler, F.,Eulalio, A.,Truffault, V.,Hartmann, M.D.,Helms, S.,Schmidt, S.,Coles, M.,Izaurralde, E.,Weichenrieder, O. A Divergent Sm Fold in Edc3 Proteins Mediates Dcp1 Binding and P-Body Targeting. Mol.Cell.Biol., 27:8600-, 2007 Cited by PubMed Abstract: Members of the (L)Sm (Sm and Sm-like) protein family are found across all kingdoms of life and play crucial roles in RNA metabolism. The P-body component EDC3 (enhancer of decapping 3) is a divergent member of this family that functions in mRNA decapping. EDC3 is composed of a N-terminal LSm domain, a central FDF domain, and a C-terminal YjeF-N domain. We show that this modular architecture enables EDC3 to interact with multiple components of the decapping machinery, including DCP1, DCP2, and Me31B. The LSm domain mediates DCP1 binding and P-body localization. We determined the three-dimensional structures of the LSm domains of Drosophila melanogaster and human EDC3 and show that the domain adopts a divergent Sm fold that lacks the characteristic N-terminal alpha-helix and has a disrupted beta4-strand. This domain remains monomeric in solution and lacks several features that canonical (L)Sm domains require for binding RNA. The structures also revealed a conserved patch of surface residues that are required for the interaction with DCP1 but not for P-body localization. The conservation of surface and of critical structural residues indicates that LSm domains in EDC3 proteins adopt a similar fold that has separable novel functions that are absent in canonical (L)Sm proteins. PubMed: 17923697DOI: 10.1128/MCB.01506-07 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.31 Å) |
Structure validation
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