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- EMDB-6550: Cryo-EM map of EF4-bound ribosomal complexe -

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Entry
Database: EMDB / ID: 6550
TitleCryo-EM map of EF4-bound ribosomal complexe
Map dataReconstruction of PRE-EF4 complex
SampleEF4 bound to PRE 70S ribosome:
EF4 / ribosome-prokaryote
Keywordsribosome elongation / GTPase EF4 / tRNA back-translocation / P-loop
Function / homologyec:3.6.5.n1: / Ribosomal protein L11, C-terminal domain 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 S7 domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L9, C-terminal domain superfamily ...ec:3.6.5.n1: / Ribosomal protein L11, C-terminal domain 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 S7 domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein L9, N-terminal domain 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 S8 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein S11 superfamily / EF-G domain III/V-like / Ribosomal protein S3, C-terminal domain / Ribosomal protein L11, RNA binding domain / 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 S19 / Ribosomal Proteins L2, RNA binding domain / RNA-binding S4 domain superfamily / Ribosomal protein S7p/S5e / 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 / Ribosomal protein S21 superfamily / LepA, C-terminal domain superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L28/L24 superfamily / Elongation factor 4, domain IV / Ribosomal protein L20, C-terminal / Ribosomal protein S2 / Ribosomal protein L11, conserved site / Ribosomal protein L35 / Ribosomal protein L18e/L15P / Ribosomal protein L34, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L16, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L2, C-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L9, N-terminal / Ribosomal protein L9, C-terminal / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S4/S9 / L28p-like / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Tr-type G domain, conserved site / Ribosomal protein L15 / Ribosomal protein L25 / Ribosomal protein L21-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein L28/L24 / Ribosomal protein L5 domain superfamily / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L1-like / Ribosomal protein L1, conserved site / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S15 / Ribosomal protein L30p/L7e / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L3 signature.
Function and homology information
SourceEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsZhang D / Yan K / Liu G / Song G / Luo J / Shi Y / Cheng E / Wu S / Jiang T / Low J / Gao N / Qin Y
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2016
Title: EF4 disengages the peptidyl-tRNA CCA end and facilitates back-translocation on the 70S ribosome.
Authors: Dejiu Zhang / Kaige Yan / Guangqiao Liu / Guangtao Song / Jiejian Luo / Yi Shi / Erchao Cheng / Shan Wu / Taijiao Jiang / Jizhong Lou / Ning Gao / Yan Qin
Validation ReportPDB-ID: 3jce

SummaryFull reportAbout validation report
DateDeposition: Nov 30, 2015 / Header (metadata) release: Dec 30, 2015 / Map release: Dec 30, 2015 / Last update: May 25, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-3jce
  • Surface level: 0.01
  • 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_6550.map.gz (map file in CCP4 format, 128001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.32 Å/pix.
= 422.4 Å
320 pix
1.32 Å/pix.
= 422.4 Å
320 pix
1.32 Å/pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:0.01 (by author), 0.01 (movie #1):
Minimum - Maximum-0.01396657 - 0.03598515
Average (Standard dev.)-0.00002502 (0.00229444)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z422.400422.400422.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0140.036-0.000

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Supplemental data

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Sample components

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Entire EF4 bound to PRE 70S ribosome

EntireName: EF4 bound to PRE 70S ribosome / Number of components: 2

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Component #1: protein, EF4

ProteinName: EF4 / Recombinant expression: Yes
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: ribosome-prokaryote, ribosome 70S

Ribosome-prokaryoteName: ribosome 70S / Prokaryote: ALL / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Oct 20, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 107706
Details: The particles were selected using an automatic selection program.
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143, gold-standard
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 4V9O
Output model

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