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- EMDB-24515: E. coli bL17-limitation ribosome assembly intermediate #8 -

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Basic information

Entry
Database: EMDB / ID: EMD-24515
TitleE. coli bL17-limitation ribosome assembly intermediate #8
Map dataE. coli bL17-limitation ribosome assembly intermediate #8 (E-class)
Sample
  • Complex: bL17-depleted large ribosomal subunit assembly intermediate #8
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.6 Å
AuthorsRabuck-Gibbons JN / Lyumkis D / Williamson JR
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP5-OD021396 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 AI150472 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM136412 United States
CitationJournal: Structure / Year: 2022
Title: Quantitative mining of compositional heterogeneity in cryo-EM datasets of ribosome assembly intermediates.
Authors: Rabuck-Gibbons JN / Lyumkis D / Williamson JR
History
DepositionJul 23, 2021-
Header (metadata) releaseDec 29, 2021-
Map releaseDec 29, 2021-
UpdateApr 20, 2022-
Current statusApr 20, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_24515.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE. coli bL17-limitation ribosome assembly intermediate #8 (E-class)
Voxel sizeX=Y=Z: 1.31 Å
Density
Contour LevelBy AUTHOR: 7.6 / Movie #1: 6
Minimum - Maximum-9.674385 - 20.58844
Average (Standard dev.)-0.61405456 (±1.3388466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 419.19998 Å
α=β=γ: 90.0 °

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/NZ000
NX/NY/NZ448448448
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-9.67420.588-0.614

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Supplemental data

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Sample components

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Entire : bL17-depleted large ribosomal subunit assembly intermediate #8

EntireName: bL17-depleted large ribosomal subunit assembly intermediate #8
Components
  • Complex: bL17-depleted large ribosomal subunit assembly intermediate #8

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Supramolecule #1: bL17-depleted large ribosomal subunit assembly intermediate #8

SupramoleculeName: bL17-depleted large ribosomal subunit assembly intermediate #8
type: complex / ID: 1 / Parent: 0
Details: bL17-depleted large ribosomal subunit assembly intermediate #8
Source (natural)Organism: Escherichia coli (E. coli) / Strain: NCM3722
Molecular weightTheoretical: 1.5 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormula
20.0 mMTrisHCl
100.0 mMNH4Cl
10.0 mMMgCl2
0.5 mMEDTA
6.0 mMb-mercaptoethanol
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: 3 ul of this sample was added to 3 plasma cleaned (Gatan, Solarus) 1.2mm hole, 1.3mm spacing holey gold grids (Russo and Passmore, 2014). Grids were manually frozen in liquid ethane..
Detailsdepleted ribosome assembly intermediate purified by sucrose gradient

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsIn order to account for highly preferred orientation of the specimen, data was acquired using a tilt of -20 degrees.
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 833 / Average exposure time: 10.0 sec. / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. X) / Number images used: 1826
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: FREALIGN (ver. X) / Details: FrealignX
Final 3D classificationSoftware - Name: FREALIGN (ver. X)

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