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- EMDB-3579: 30S ribosomal subunit with partial density for ribosomal protein S1 -

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Basic information

Entry
Database: EMDB / ID: EMD-3579
Title30S ribosomal subunit with partial density for ribosomal protein S1
Map dataNone
Sample
  • Complex: the sample contained a mixture of in vitro assembled E.coli expressomes and free ribosomes (see related entry EMDB 3580 and related publication). This structure shows additional density for ribosomal protein S1 and weak density for the RNA Polymerase.
    • Other: ribosome
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsKohler R / Mooney RA / Mills DJ / Landick R / Cramer P
CitationJournal: Science / Year: 2017
Title: Architecture of a transcribing-translating expressome.
Authors: R Kohler / R A Mooney / D J Mills / R Landick / P Cramer /
Abstract: DNA transcription is functionally coupled to messenger RNA (mRNA) translation in bacteria, but how this is achieved remains unclear. Here we show that RNA polymerase (RNAP) and the ribosome of can ...DNA transcription is functionally coupled to messenger RNA (mRNA) translation in bacteria, but how this is achieved remains unclear. Here we show that RNA polymerase (RNAP) and the ribosome of can form a defined transcribing and translating "expressome" complex. The cryo-electron microscopic structure of the expressome reveals continuous protection of ~30 nucleotides of mRNA extending from the RNAP active center to the ribosome decoding center. The RNAP-ribosome interface includes the RNAP subunit α carboxyl-terminal domain, which is required for RNAP-ribosome interaction in vitro and for pronounced cell growth defects upon translation inhibition in vivo, consistent with its function in transcription-translation coupling. The expressome structure can only form during transcription elongation and explains how translation can prevent transcriptional pausing, backtracking, and termination.
History
DepositionJan 25, 2017-
Header (metadata) releaseFeb 22, 2017-
Map releaseApr 26, 2017-
UpdateApr 26, 2017-
Current statusApr 26, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0245
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0245
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3579.png

Downloads & links

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Map

FileDownload / File: emd_3579.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 1.86 Å
Density
Contour LevelBy AUTHOR: 0.0245 / Movie #1: 0.0245
Minimum - Maximum-0.0736037 - 0.15664811
Average (Standard dev.)0.00044244496 (±0.0048991847)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 483.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.861.861.86
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z483.600483.600483.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-0.0740.1570.000

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Supplemental data

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Sample components

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Entire : the sample contained a mixture of in vitro assembled E.coli expre...

EntireName: the sample contained a mixture of in vitro assembled E.coli expressomes and free ribosomes (see related entry EMDB 3580 and related publication). This structure shows additional density for ...Name: the sample contained a mixture of in vitro assembled E.coli expressomes and free ribosomes (see related entry EMDB 3580 and related publication). This structure shows additional density for ribosomal protein S1 and weak density for the RNA Polymerase.
Components
  • Complex: the sample contained a mixture of in vitro assembled E.coli expressomes and free ribosomes (see related entry EMDB 3580 and related publication). This structure shows additional density for ribosomal protein S1 and weak density for the RNA Polymerase.
    • Other: ribosome

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Supramolecule #1: the sample contained a mixture of in vitro assembled E.coli expre...

SupramoleculeName: the sample contained a mixture of in vitro assembled E.coli expressomes and free ribosomes (see related entry EMDB 3580 and related publication). This structure shows additional density for ...Name: the sample contained a mixture of in vitro assembled E.coli expressomes and free ribosomes (see related entry EMDB 3580 and related publication). This structure shows additional density for ribosomal protein S1 and weak density for the RNA Polymerase.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: ribosome

MacromoleculeName: ribosome / type: other / ID: 1 / Classification: other
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString:
not applic able

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 16.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 1.4)
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 71835

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