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- EMDB-8647: Cryo-EM structure of the 70S ribosome from Mycobacterium smegmatis -

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Basic information

Entry
Database: EMDB / ID: EMD-8647
TitleCryo-EM structure of the 70S ribosome from Mycobacterium smegmatis
Map data70S ribosome from Mycobacterium smegmatis
Sample
  • Complex: Ribosome from Mycobacterium smegmatis
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A ...Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L16 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / 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 L25p family / Ribosomal protein L25 / 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 L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S14/S29 / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein L28/L24 / Ribosomal protein S18 signature. / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / : / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein L27 / Ribosomal protein S6 superfamily / Ribosomal L27 protein / Ribosomal protein S12, bacterial-type / Ribosomal protein L20
Similarity search - Domain/homology
Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 ...Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL33 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein uS17 / Mitochondrial domain of uncharacterized function (DUF1713) / 50S ribosomal protein L15 / Large ribosomal subunit protein uL13 / 50S ribosomal protein L14 / : / : / : / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS12
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsYang K / Chang J-Y / Cui Z / Zhang J
CitationJournal: Nucleic Acids Res / Year: 2017
Title: Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis.
Authors: Kailu Yang / Jeng-Yih Chang / Zhicheng Cui / Xiaojun Li / Ran Meng / Lijun Duan / Jirapat Thongchol / Joanita Jakana / Christoph M Huwe / James C Sacchettini / Junjie Zhang /
Abstract: Ribosomes from Mycobacterium tuberculosis (Mtb) possess species-specific ribosomal RNA (rRNA) expansion segments and ribosomal proteins (rProtein). Here, we present the near-atomic structures of the ...Ribosomes from Mycobacterium tuberculosis (Mtb) possess species-specific ribosomal RNA (rRNA) expansion segments and ribosomal proteins (rProtein). Here, we present the near-atomic structures of the Mtb 50S ribosomal subunit and the complete Mtb 70S ribosome, solved by cryo-electron microscopy. Upon joining of the large and small ribosomal subunits, a 100-nt long expansion segment of the Mtb 23S rRNA, named H54a or the 'handle', switches interactions from with rRNA helix H68 and rProtein uL2 to with rProtein bS6, forming a new intersubunit bridge 'B9'. In Mtb 70S, bridge B9 is mostly maintained, leading to correlated motions among the handle, the L1 stalk and the small subunit in the rotated and non-rotated states. Two new protein densities were discovered near the decoding center and the peptidyl transferase center, respectively. These results provide a structural basis for studying translation in Mtb as well as developing new tuberculosis drugs.
History
DepositionMar 23, 2017-
Header (metadata) releaseApr 19, 2017-
Map releaseSep 20, 2017-
UpdateNov 1, 2017-
Current statusNov 1, 2017Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8647.png

Downloads & links

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Map

FileDownload / File: emd_8647.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation70S ribosome from Mycobacterium smegmatis
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.5 Å/pix.
x 128 pix.
= 320. Å		2.5 Å/pix.
x 128 pix.
= 320. Å		2.5 Å/pix.
x 128 pix.
= 320. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.027 / Movie #1: 0.027
Minimum - Maximum-0.063424 - 0.12682697
Average (Standard dev.)0.0024691701 (±0.0108328555)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 320.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.52.52.5
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z320.000320.000320.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0630.1270.002

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Supplemental data

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Sample components

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Entire : Ribosome from Mycobacterium smegmatis

EntireName: Ribosome from Mycobacterium smegmatis
Components
  • Complex: Ribosome from Mycobacterium smegmatis

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Supramolecule #1: Ribosome from Mycobacterium smegmatis

SupramoleculeName: Ribosome from Mycobacterium smegmatis / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#51
Source (natural)Organism: Mycobacterium smegmatis (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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.27 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 106000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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