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- EMDB-3618: Bypassing 70S ribosome -

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Entry
Database: EMDB / ID: 3618
TitleBypassing 70S ribosome
Map dataraw map
SampleBypassing 70S take-off complex:
Function / homologyRibosomal protein L5 domain superfamily / Ribosomal protein S19 conserved site / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L35 / Ribosomal protein L18e/L15P / Ribosomal protein L34, conserved site / Ribosomal protein L5, bacterial-type / Ribosomal L25p family ...Ribosomal protein L5 domain superfamily / Ribosomal protein S19 conserved site / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L35 / Ribosomal protein L18e/L15P / Ribosomal protein L34, conserved site / Ribosomal protein L5, bacterial-type / Ribosomal L25p family / Ribosomal protein L5, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L16, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S4/S9 / Ribosomal protein L10 / Ribosomal protein L9, bacteria/chloroplast / 30s ribosomal protein S13, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / Ribosomal protein L25 / Ribosomal protein L21-like / Ribosomal protein L31 type A / Ribosomal protein S10 domain / Ribosomal protein L28/L24 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / 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 S7, conserved site / Ribosomal protein S16, conserved site / L28p-like / Ribosomal protein L29, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein L33, conserved site / Ribosomal protein L27, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / Ribosomal protein L30, conserved site / Ribosomal protein L10e/L16 / Ribosomal protein L30, ferredoxin-like fold domain / K homology domain-like, alpha/beta / Ribosomal protein S10, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S11, bacterial-type / 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 protein L25, short-form / Ribosomal protein L6, alpha-beta domain / 30S ribosomal protein S17 / Ribosomal protein S13, bacterial-type / Ribosomal protein S18, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L3, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, conserved site / Ribosomal protein S21, conserved site / C-terminal associated domain of TOPRIM / Ribosomal protein L20, C-terminal / Ribosomal protein L2, domain 2 / Ribosomal protein L6 / Ribosomal protein L36 / Ribosomal protein S13/S18 / Ribosomal protein S11 / Ribosomal protein S8 / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ribosomal protein S10p/S20e / Ribosomal protein L10 / Ribosomal protein S5, N-terminal domain / Ribosomal protein L30p/L7e / Ribosomal protein S2 / Ribosomal protein S15 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L3 / Ribosomal protein L5 / Ribosomal protein L20 / KOW motif / Ribosomal protein S14p/S29e / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L19
Function and homology information
SourceEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsAgirrezabala X / Samatova E / Klimova M / Zamora M / Gil-Carton D / Rodnina M / Valle M
CitationJournal: Sci Adv / Year: 2017
Title: Ribosome rearrangements at the onset of translational bypassing.
Authors: Xabier Agirrezabala / Ekaterina Samatova / Mariia Klimova / Miguel Zamora / David Gil-Carton / Marina V Rodnina / Mikel Valle
Validation ReportPDB-ID: 5np6

SummaryFull reportAbout validation report
DateDeposition: Mar 7, 2017 / Header (metadata) release: May 31, 2017 / Map release: Jun 14, 2017 / Last update: Aug 2, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5np6
  • Surface level: 0.0045
  • 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_3618.map.gz (map file in CCP4 format, 157217 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
340 pix
1.06 Å/pix.
= 360.4 Å
340 pix
1.06 Å/pix.
= 360.4 Å
340 pix
1.06 Å/pix.
= 360.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.0045 (by author), 0.0045 (movie #1):
Minimum - Maximum-0.014063428 - 0.033133972
Average (Standard dev.)-0.000106188396 (0.0026842528)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions340340340
Origin0.00.00.0
Limit339.0339.0339.0
Spacing340340340
CellA=B=C: 360.4 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z360.400360.400360.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.0140.033-0.000

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Supplemental data

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Sample components

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Entire Bypassing 70S take-off complex

EntireName: Bypassing 70S take-off complex / Number of components: 1

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Component #1: protein, Bypassing 70S take-off complex

ProteinName: Bypassing 70S take-off complex / Recombinant expression: No
MassTheoretical: 2.3 MDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 26 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 47170.0 X (calibrated) / Cs: 0.01 mm / Imaging mode: BRIGHT FIELD / Defocus: 600.0 - 3000.0 nm
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: 37000
3D reconstructionSoftware: RELION / CTF correction: Wiener filter / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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