2VGM	Cell Cycle	date	Nov 14, 2007
title	Structure Of S. Cerevisiae Dom34, A Translation Termination- Factor Involved In Rna Quality Control Pathways And Interac Hbs1 (Unlabeled Protein)
authors	M.Graille, M.Chaillet, H.Van Tilbeurgh
compound		source
Molecule: Dom34 Chain: A Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 559292 Strain: S288c Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_variant: Rosetta Plyss Expression_system_plasmid: Pet9
symmetry	Space Group: P 32 2 1	R_factor 0.226 R_Free 0.288
crystal cell	length a length b length c angle alpha angle beta angle gamma 75.500 75.500 163.981 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.60 Å
Gene Ontology	Chain Function Process Component A nuclease activity endonuclease activity endoribonuclease activity
Primary reference	Structure of yeast Dom34: a protein related to translation termination factor eRF1 and involved in No-Go decay., Graille M, Chaillet M, van Tilbeurgh H, J Biol Chem. 2008 Jan 7;. PMID:18180287

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (63 Kb) [Save to disk] Biological Unit Coordinates (2vgm.pdb1.gz) 58 Kb CSU: Contacts of Structural Units for 2VGM Likely Quarternary Molecular Structure file(s) for 2VGM Structure Factors (119 Kb) Retrieve 2VGM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2VGM from S2C, [Save to disk] Re-refined 2vgm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2VGM in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 2VGM

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 2VGM, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2vgm_A] [2vgm] SWISS-PROT database: [P33309] Domain organization of [DOM34_YEAST] by SWISSPFAM Domain found in 2VGM: [eRF1_1 ] by SMART

Other resources with information on 2VGM

Community annotation for 2VGM at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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