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- PDB-2iw3: Elongation Factor 3 in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 2iw3
TitleElongation Factor 3 in complex with ADP
ComponentsELONGATION FACTOR 3A
KeywordsTRANSLATION / ACETYLATION / ATP-BINDING / ELONGATION FACTOR / PROTEIN BIOSYNTHESIS / NUCLEOTIDE-BINDING / PHOSPHORYLATION / RNA-BINDING / RRNA-BINDING
Function / homology
Function and homology information


translational elongation / translation elongation factor activity / translational termination / cytosolic ribosome / negative regulation of protein phosphorylation / negative regulation of protein kinase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic stress granule / ribosome binding / rRNA binding ...translational elongation / translation elongation factor activity / translational termination / cytosolic ribosome / negative regulation of protein phosphorylation / negative regulation of protein kinase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic stress granule / ribosome binding / rRNA binding / ribosome / ATP hydrolysis activity / ATP binding
Similarity search - Function
PWI domain - #20 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #990 / PWI domain / Four helical bundle domain / : / Four helical bundle domain / Elongation Factor 3 / : / : / HEAT repeat profile. ...PWI domain - #20 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #990 / PWI domain / Four helical bundle domain / : / Four helical bundle domain / Elongation Factor 3 / : / : / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Armadillo-like helical / Alpha Horseshoe / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Elongation factor 3A
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.4 Å
AuthorsAndersen, 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.
CitationJournal: 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
DepositionJun 26, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ELONGATION FACTOR 3A
B: ELONGATION FACTOR 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,50317
Polymers221,4002
Non-polymers2,10315
Water17,421967
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.800, 107.700, 209.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.58167, -2.3E-5, 0.81343), (-0.049912, -0.99811, -0.03572), (0.81189, -0.061377, 0.58057)
Vector: 257.14, -212.95, -137.79)

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Components

#1: Protein ELONGATION FACTOR 3A / ELONGATION FACTOR 3 / EF-3A / EF-3 / TRANSLATION ELONGATION FACTOR 3A / EUKARYOTIC ELONGATION ...ELONGATION FACTOR 3 / EF-3A / EF-3 / TRANSLATION ELONGATION FACTOR 3A / EUKARYOTIC ELONGATION FACTOR 3 / EEF3 / YEAST ELONGATION FACTOR 3


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 ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 967 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRELEASES DEACYLATED TRNA FROM THE RIBOSOMAL E-SITE DURING PROTEIN BIOSYNTHESIS, IN PRESENCE OF ATP.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 50 %
Crystal growpH: 5.2 / Details: pH 5.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.4→2.5 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.36 / % possible all: 94.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.242 4384 5 %RANDOM
Rwork0.202 ---
obs0.202 87434 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.8603 Å2 / ksol: 0.34978 e/Å3
Displacement parametersBiso mean: 42.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.711 Å20 Å20 Å2
2--5.168 Å20 Å2
3----10.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.4→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15226 0 119 967 16312
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.16
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 718 5.1 %
Rwork0.255 13385 -
obs--97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4SO4_XPLOR_PAR.TXTSO4_XPLOR_TOP.TXT
X-RAY DIFFRACTION5ADP_XPLOR_PAR.TXTADP_XPLOR_TOP.TXT

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