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- EMDB-8434: Structure of bL17-depleted large ribosomal subunit assembly inter... -

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Basic information

Entry
Database: EMDB / ID: 8434
TitleStructure of bL17-depleted large ribosomal subunit assembly intermediate - Class A
SamplebL17-depleted large ribosomal subunit assembly intermediate - Class A
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataClass A L17-Depleted 50S Ribosomal Intermediate - Sharpened
Methodsingle particle reconstruction, at 6.5 Å resolution
AuthorsTan Y / Davis JH / Lyumkis D
CitationCell, 2016, 167, 1610-1622.e15

Cell, 2016, 167, 1610-1622.e15 Yorodumi Papers
Modular Assembly of the Bacterial Large Ribosomal Subunit.
Joseph H Davis / Yong Zi Tan / Bridget Carragher / Clinton S Potter / Dmitry Lyumkis / James R Williamson

DateDeposition: Oct 21, 2016 / Header (metadata) release: Dec 14, 2016 / Map release: Dec 14, 2016 / Last update: Apr 12, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.035
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_8434.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.31 Å/pix.
= 419.2 Å
320 pix
1.31 Å/pix.
= 419.2 Å
320 pix
1.31 Å/pix.
= 419.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.31 Å
Density
Contour Level:0.0436 (by author), 0.035 (movie #1):
Minimum - Maximum-0.065385886 - 0.11887856
Average (Standard dev.)-0.0011801925 (0.008011028)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 419.19998 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z419.200419.200419.200
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-0.0650.119-0.001

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Supplemental data

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Mask #1

Fileemd_8434_msk_1.map ( map file in CCP4 format, 131073 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsClass A L17-Depleted 50S Ribosomal Intermediate - Mask
Space group number1

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Mask #1~

Fileemd_8434_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire bL17-depleted large ribosomal subunit assembly intermediate - Class A

EntireName: bL17-depleted large ribosomal subunit assembly intermediate - Class A
Details: E. coli large ribosome subunit purified from bL17-depleted cells.
Number of components: 1

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Component #1: protein, bL17-depleted large ribosomal subunit assembly intermedi...

ProteinName: bL17-depleted large ribosomal subunit assembly intermediate - Class A
Details: E. coli large ribosome subunit purified from bL17-depleted cells.
Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: NCM3722 rplQ::cat, pHSL-rplQ

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: Most of the sucrose was removed by spin concentration
pH: 7.5
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 80 % / Details: 3 microliter of the sample was added.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Details: In order to account for highly preferred orientation of the specimen, data was acquired using tilts ranging from 10-60 degrees, in addition to untilted images at 0 degrees. The CTF was estimated on a per-particle basis to account for the gradient of CTF values across individual micrographs
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 34.27 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500 X (nominal), 38167 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2479 / Sampling size: 5 microns
Raw dataEMPIAR-10076 (Title: CryoEM Dataset of L17-Depleted 50S Ribosomal Intermediates
Data size: 50.3
Data #1: Particle stack of L17-depleted 50S Ribosomal Assembly Intermediates [picked particles - single frame - unprocessed])

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 2018
3D reconstructionAlgorithm: FOURIER SPACE / Software: Frealign / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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