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- EMDB-6584: The structure of elongation factor 4 (EF4/LepA) in GTP form bound... -

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Database: EMDB / ID: 6584
TitleThe structure of elongation factor 4 (EF4/LepA) in GTP form bound to the ribosome
Map dataReconstruction of EF4 bound to the ribosome
SampleThe structure of elongation factor 4 (EF4/LepA) in GTP form bound to the ribosome:
ribosome-prokaryote
KeywordsLepA / EF4 / ribosome / 70S
Function / homologyec:3.6.5.n1: / Ribosomal protein L25, C-terminal / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / Elongation factor Tu GTP binding domain / Ribosomal protein L19 superfamily / Ribosomal protein L33 superfamily / LepA, C-terminal domain superfamily / Ribosomal protein L35 superfamily / RNA-binding S4 domain superfamily ...ec:3.6.5.n1: / Ribosomal protein L25, C-terminal / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / Elongation factor Tu GTP binding domain / Ribosomal protein L19 superfamily / Ribosomal protein L33 superfamily / LepA, C-terminal domain superfamily / Ribosomal protein L35 superfamily / RNA-binding S4 domain superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S11 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S3, C-terminal domain / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein S15 / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ribosomal protein L6 / Ribosomal protein S10p/S20e / Ribosomal protein S5, N-terminal domain / Ribosomal protein L30p/L7e / Ribosomal protein S2 / Ribosomal protein L11, RNA binding domain / Ribosomal protein S19 / Ribosomal protein L3 / Ribosomal protein L5 / Ribosomal protein L23 / Ribosomal protein S14p/S29e / Ribosomal protein L16p/L10e / Ribosomal protein L14p/L23e / Ribosomal protein L22p/L17e / Ribosomal protein S7 domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S11 / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L31 type A / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L1, conserved site / Ribosomal protein L25 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein S14, type Z / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L10 / Ribosomal protein L21-like / 30S ribosomal protein / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L17 superfamily / Ribosomal L18e/L15P superfamily / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L15 / Ribosomal protein L36 superfamily / Elongation factor 4, domain IV / EF-G domain III/V-like / Ribosomal protein L20, C-terminal / 30S ribosomal protein Thx / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Tr-type G domain, conserved site / Ribosomal protein S8 / Ribosomal protein S13/S18 / Ribosomal protein S4/S9 / Ribosomal protein L22 signature. / Ribosomal protein L33 signature. / Ribosomal protein L29 signature. / Ribosomal protein S3 signature. / Ribosomal protein S14 signature. / Ribosomal protein L15 signature. / Ribosomal protein L3 signature. / Ribosomal protein L2 signature. / Ribosomal protein S15 signature. / Ribosomal protein S4 signature. / Ribosomal protein S10 signature. / Ribosomal protein S9 signature. / Ribosomal protein L11 signature. / Ribosomal protein L5 signature. / Ribosomal protein S19 signature. / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein S18 signature. / Ribosomal protein S5 signature.
Function and homology information
SourceThermus thermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsKumar V / Ahmed T / Ero R / Jian G-K / Yin Z / Gao Y / Bhushan S
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Structure of the GTP Form of Elongation Factor 4 (EF4) Bound to the Ribosome.
Authors: Veerendra Kumar / Rya Ero / Tofayel Ahmed / Kwok Jian Goh / Yin Zhan / Shashi Bhushan / Yong-Gui Gao
Abstract: Elongation factor 4 (EF4) is a member of the family of ribosome-dependent translational GTPase factors, along with elongation factor G and BPI-inducible protein A. Although EF4 is highly conserved in ...Elongation factor 4 (EF4) is a member of the family of ribosome-dependent translational GTPase factors, along with elongation factor G and BPI-inducible protein A. Although EF4 is highly conserved in bacterial, mitochondrial, and chloroplast genomes, its exact biological function remains controversial. Here we present the cryo-EM reconstitution of the GTP form of EF4 bound to the ribosome with P and E site tRNAs at 3.8-Å resolution. Interestingly, our structure reveals an unrotated ribosome rather than a clockwise-rotated ribosome, as observed in the presence of EF4-GDP and P site tRNA. In addition, we also observed a counterclockwise-rotated form of the above complex at 5.7-Å resolution. Taken together, our results shed light on the interactions formed between EF4, the ribosome, and the P site tRNA and illuminate the GTPase activation mechanism at previously unresolved detail.
Validation ReportPDB-ID: 5imq

SummaryFull reportAbout validation report
DateDeposition: Feb 3, 2016 / Header (metadata) release: Mar 9, 2016 / Map release: May 18, 2016 / Last update: Jun 29, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.095
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.095
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5imq
  • Surface level: 0.095
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6584.map.gz (map file in CCP4 format, 132862 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
324 pix
1.28 Å/pix.
= 414.72 Å
324 pix
1.28 Å/pix.
= 414.72 Å
324 pix
1.28 Å/pix.
= 414.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.28 Å
Density
Contour Level:0.095 (by author), 0.095 (movie #1):
Minimum - Maximum-0.38665524 - 0.61588430
Average (Standard dev.)0.00301005 (0.02501679)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions324324324
Origin000
Limit323323323
Spacing324324324
CellA=B=C: 414.72 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.281.281.28
M x/y/z324324324
origin x/y/z0.0000.0000.000
length x/y/z414.720414.720414.720
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS324324324
D min/max/mean-0.3870.6160.003

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Supplemental data

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Sample components

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Entire The structure of elongation factor 4 (EF4/LepA) in GTP form bound...

EntireName: The structure of elongation factor 4 (EF4/LepA) in GTP form bound to the ribosome
Number of components: 1 / Oligomeric State: 1
MassTheoretical: 2.5 MDa / Experimental: 2.5 MDa / Measured by: Sedimentation

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Component #1: ribosome-prokaryote, Thermus thermophilus

Ribosome-prokaryoteName: Thermus thermophilus / a.k.a: 70S ribosomeRibosome / Prokaryote: ALL / Recombinant expression: No
MassTheoretical: 2.5 MDa / Experimental: 2.5 MDa
SourceSpecies: Thermus thermophilus (bacteria)
Source (natural)Location in cell: Translation

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 5mM HEPES, pH 7.5, 10mM MgOAc, 50mM KCl, 10mM NH4Cl, 6mM 2-mercaptoethanol
pH: 7.5
Support film300 mesh copper grid with 2 nm carbon support, glow-discharged
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 4 K / Humidity: 100 % / Method: Blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Nov 17, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 78000 X (nominal), 109375 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 73684 times magnification
Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 2500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2026
Details: Every image is the average of seven frames recorded by the direct electron detector

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 110981
Details: Particles were selected using EMAN and processed using Relion
3D reconstructionAlgorithm: Every image is the average of two frames recorded by the direct electron detector
Software: Relion / CTF correction: Ctffind3 / Resolution: 3.8 Å / Resolution method: FSC 0.143, gold-standard

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