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- EMDB-3919: Stalled E. coli ribosomes (Fo-c SecM nascent chains) and native E... -

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Basic information

Entry
Database: EMDB / ID: 3919
TitleStalled E. coli ribosomes (Fo-c SecM nascent chains) and native E. coli membranes containing recombinant YidC
SampleRibosome-nascent chains with native E.coli membranes containing YidC
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataAverage of class 1
Methodsubtomogram averaging, at 100 Å resolution
AuthorsBaker LA / Gruenewald K
CitationStructure, 2018, 26, 161-170.e3

Structure, 2018, 26, 161-170.e3 Yorodumi Papers
Combined 1H-Detected Solid-State NMR Spectroscopy and Electron Cryotomography to Study Membrane Proteins across Resolutions in Native Environments.
Lindsay A Baker / Tessa Sinnige / Pascale Schellenberger / Jeanine de Keyzer / C Alistair Siebert / Arnold J M Driessen / Marc Baldus / Kay Grünewald

DateDeposition: Oct 12, 2017 / Header (metadata) release: Dec 20, 2017 / Map release: Dec 27, 2017 / Last update: Jan 10, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0055
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.0055
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_3919.map.gz (map file in CCP4 format, 321 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
40 pix
9.04 Å/pix.
= 361.6 Å
50 pix
9.04 Å/pix.
= 452. Å
40 pix
9.04 Å/pix.
= 361.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 9.04 Å
Density
Contour Level:0.0055 (by author), 0.0055 (movie #1):
Minimum - Maximum-0.03396017 - 0.034291007
Average (Standard dev.)-0.00652426 (0.01028893)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions504040
Origin504040
Limit997979
Spacing405040
CellA: 361.6 Å / B: 452 Å / C: 361.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z9.049.049.04
M x/y/z405040
origin x/y/z0.0000.0000.000
length x/y/z361.600452.000361.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS405040
NC/NR/NS405040
D min/max/mean-0.0340.034-0.007

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Supplemental data

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Sample components

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Entire Ribosome-nascent chains with native E.coli membranes containing YidC

EntireName: Ribosome-nascent chains with native E.coli membranes containing YidC
Number of components: 3

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Component #1: cellular-component, Ribosome-nascent chains with native E.coli me...

Cellular-componentName: Ribosome-nascent chains with native E.coli membranes containing YidC
Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pHisLIC_YidC/pJK763 / Strain: LEMO/BL21delta Trigger Factor
Source (natural)Location in cell: membrane

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Component #2: cellular-component, E. coli native membranes containing YidC

Cellular-componentName: E. coli native membranes containing YidC / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pHisLIC_YidC / Strain: LEMO
Source (natural)Location in cell: membrane

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Component #3: protein, Ribosomes with SecM stalled nascent chains of ATP syntha...

ProteinName: Ribosomes with SecM stalled nascent chains of ATP synthase subunit c
Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pJK763 / Strain: BL21 delta Trigger Factor
Source (natural)Location in cell: cytoplasm

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.4
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE MIXTURE

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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: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2500 - 5000 nm / Energy filter: GIF Quantum LS / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt Angle: -45 - 45 deg.
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging
Details: Tomograms were built with IMOD, after correction of movie stacks with Unblur.
3D reconstructionAlgorithm: BACK PROJECTION / Resolution: 100 Å / Resolution method: OTHER

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