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- EMDB-6057: Structure of the E. coli 50S subunit with ErmCL nascent chain -

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Basic information

Entry
Database: EMDB / ID: EMD-6057
TitleStructure of the E. coli 50S subunit with ErmCL nascent chain
Map dataReconstruction of ErmCL-stalled ribosome complex (30S masked out)
Sample
  • Sample: ErmCL-stalled E. coli ribosome
  • Complex: 50S ribosomal subunit
Keywordserythromycin / stalling / RIBOSOME-ANTIBIOTIC complex / ErmCL
Function / homology
Function and homology information


stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation ...stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / protein homodimerization activity / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Leader peptide, Erm / : / Erm Leader peptide / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like ...Leader peptide, Erm / : / Erm Leader peptide / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Ribosomal protein L25, short-form / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / : / Ribosomal protein L11 signature. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal protein L11, N-terminal / Ribosomal L25p family / Ribosomal protein L11, N-terminal domain / Ribosomal protein L25 / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / : / : / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L34, conserved site / Ribosomal L28 family / Ribosomal protein L34 signature. / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / : / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein
Similarity search - Domain/homology
Large ribosomal subunit protein uL15 / 23S rRNA methylase leader peptide / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL12 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 ...Large ribosomal subunit protein uL15 / 23S rRNA methylase leader peptide / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL12 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsArenz S / Meydan S / Starosta AL / Berninghausen O / Beckmann R / Vazquez-Laslop N / Wilson DN
CitationJournal: Mol Cell / Year: 2014
Title: Drug sensing by the ribosome induces translational arrest via active site perturbation.
Authors: Stefan Arenz / Sezen Meydan / Agata L Starosta / Otto Berninghausen / Roland Beckmann / Nora Vázquez-Laslop / Daniel N Wilson /
Abstract: During protein synthesis, nascent polypeptide chains within the ribosomal tunnel can act in cis to induce ribosome stalling and regulate expression of downstream genes. The Staphylococcus aureus ...During protein synthesis, nascent polypeptide chains within the ribosomal tunnel can act in cis to induce ribosome stalling and regulate expression of downstream genes. The Staphylococcus aureus ErmCL leader peptide induces stalling in the presence of clinically important macrolide antibiotics, such as erythromycin, leading to the induction of the downstream macrolide resistance methyltransferase ErmC. Here, we present a cryo-electron microscopy (EM) structure of the erythromycin-dependent ErmCL-stalled ribosome at 3.9 Å resolution. The structure reveals how the ErmCL nascent chain directly senses the presence of the tunnel-bound drug and thereby induces allosteric conformational rearrangements at the peptidyltransferase center (PTC) of the ribosome. ErmCL-induced perturbations of the PTC prevent stable binding and accommodation of the aminoacyl-tRNA at the A-site, leading to inhibition of peptide bond formation and translation arrest.
History
DepositionAug 27, 2014-
Header (metadata) releaseOct 1, 2014-
Map releaseOct 22, 2014-
UpdateDec 10, 2014-
Current statusDec 10, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.003
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.003
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j7z
  • Surface level: 0.003
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6057.gif

Downloads & links

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Map

FileDownload / File: emd_6057.map.gz / Format: CCP4 / Size: 27.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of ErmCL-stalled ribosome complex (30S masked out)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 231 pix.
= 255.948 Å		1.11 Å/pix.
x 183 pix.
= 202.764 Å		1.11 Å/pix.
x 177 pix.
= 196.116 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.108 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003 / Movie #1: 0.003
Minimum - Maximum-0.01293502 - 0.01906713
Average (Standard dev.)0.00029695 (±0.00148553)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin927079
Dimensions183177231
Spacing183177231
CellA: 196.11601 Å / B: 202.764 Å / C: 255.94801 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1081.1081.108
M x/y/z177183231
origin x/y/z0.0000.0000.000
length x/y/z196.116202.764255.948
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS709279
NC/NR/NS177183231
D min/max/mean-0.0130.0190.000

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Supplemental data

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Sample components

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Entire : ErmCL-stalled E. coli ribosome

EntireName: ErmCL-stalled E. coli ribosome
Components
  • Sample: ErmCL-stalled E. coli ribosome
  • Complex: 50S ribosomal subunit

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Supramolecule #1000: ErmCL-stalled E. coli ribosome

SupramoleculeName: ErmCL-stalled E. coli ribosome / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: 50S ribosomal subunit

SupramoleculeName: 50S ribosomal subunit / type: complex / ID: 1 / Details: ErmCL-stalled / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: LSU 50S
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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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: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Cs0
DateMar 12, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 6118
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal magnification: 125085 / Cs: mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: defocus groups
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: OTHER / Software - Name: SPIDER
Details: Since the microscopy images were processed in the absence of spatial frequencies higher than 8 A, an FSC cut-off value of 0.143 was used for average resolution determination of 3.9 A (Scheres and Chen, 2012).
Number images used: 269163

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Atomic model buiding 1

Initial modelPDB ID:

4kix
PDB Unreleased entry

SoftwareName: Chimera
DetailsThe crystal structure of the E. coli 50S subunit was fitted as a rigid body.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3j7z:
Structure of the E. coli 50S subunit with ErmCL nascent chain

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