+Open data
-Basic information
Entry | Database: PDB / ID: 2iw3 | ||||||
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Title | Elongation Factor 3 in complex with ADP | ||||||
Components | ELONGATION FACTOR 3A | ||||||
Keywords | TRANSLATION / ACETYLATION / ATP-BINDING / ELONGATION FACTOR / PROTEIN BIOSYNTHESIS / NUCLEOTIDE-BINDING / PHOSPHORYLATION / RNA-BINDING / RRNA-BINDING | ||||||
Function / homology | Function and homology information translational elongation / translational termination / translation elongation factor activity / cytosolic ribosome / negative regulation of protein phosphorylation / : / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / negative regulation of protein kinase activity / cytoplasmic stress granule / ribosome ...translational elongation / translational termination / translation elongation factor activity / cytosolic ribosome / negative regulation of protein phosphorylation / : / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / negative regulation of protein kinase activity / cytoplasmic stress granule / ribosome / rRNA binding / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.4 Å | ||||||
Authors | Andersen, C.B.F. / Becker, T. / Blau, M. / Anand, M. / Halic, M. / Balar, B. / Mielke, T. / Boesen, T. / Pedersen, J.S. / Spahn, C.M.T. ...Andersen, C.B.F. / Becker, T. / Blau, M. / Anand, M. / Halic, M. / Balar, B. / Mielke, T. / Boesen, T. / Pedersen, J.S. / Spahn, C.M.T. / Kinzy, T.G. / Andersen, G.R. / Beckmann, R. | ||||||
Citation | Journal: Nature / Year: 2006 Title: Structure of eEF3 and the mechanism of transfer RNA release from the E-site. Authors: Christian B F Andersen / Thomas Becker / Michael Blau / Monika Anand / Mario Halic / Bharvi Balar / Thorsten Mielke / Thomas Boesen / Jan Skov Pedersen / Christian M T Spahn / Terri Goss ...Authors: Christian B F Andersen / Thomas Becker / Michael Blau / Monika Anand / Mario Halic / Bharvi Balar / Thorsten Mielke / Thomas Boesen / Jan Skov Pedersen / Christian M T Spahn / Terri Goss Kinzy / Gregers R Andersen / Roland Beckmann / Abstract: Elongation factor eEF3 is an ATPase that, in addition to the two canonical factors eEF1A and eEF2, serves an essential function in the translation cycle of fungi. eEF3 is required for the binding of ...Elongation factor eEF3 is an ATPase that, in addition to the two canonical factors eEF1A and eEF2, serves an essential function in the translation cycle of fungi. eEF3 is required for the binding of the aminoacyl-tRNA-eEF1A-GTP ternary complex to the ribosomal A-site and has been suggested to facilitate the clearance of deacyl-tRNA from the E-site. Here we present the crystal structure of Saccharomyces cerevisiae eEF3, showing that it consists of an amino-terminal HEAT repeat domain, followed by a four-helix bundle and two ABC-type ATPase domains, with a chromodomain inserted in ABC2. Moreover, we present the cryo-electron microscopy structure of the ATP-bound form of eEF3 in complex with the post-translocational-state 80S ribosome from yeast. eEF3 uses an entirely new factor binding site near the ribosomal E-site, with the chromodomain likely to stabilize the ribosomal L1 stalk in an open conformation, thus allowing tRNA release. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iw3.cif.gz | 407.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iw3.ent.gz | 338.9 KB | Display | PDB format |
PDBx/mmJSON format | 2iw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/2iw3 ftp://data.pdbj.org/pub/pdb/validation_reports/iw/2iw3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.58167, -2.3E-5, 0.81343), Vector: |
-Components
#1: Protein | Mass: 110699.914 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-980 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P16521 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Compound details | RELEASES DEACYLATED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 50 % |
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Crystal grow | pH: 5.2 / Details: pH 5.20 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 4, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 175271 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.93 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.27 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.36 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.4→35 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3241467.18 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.8603 Å2 / ksol: 0.34978 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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