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- EMDB-17959: Structure of bacterial ribosome determined by cryoEM at 100 keV -
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Open data
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Basic information
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Title | Structure of bacterial ribosome determined by cryoEM at 100 keV | |||||||||||||||||||||
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![]() | RIBOSOME | |||||||||||||||||||||
Function / homology | ![]() negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis ...negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||||||||||||||
![]() | McMullan G / Naydenova K / Mihaylov D / Peet MJ / Wilson H / Yamashita K / Dickerson JL / Chen S / Cannone G / Lee Y ...McMullan G / Naydenova K / Mihaylov D / Peet MJ / Wilson H / Yamashita K / Dickerson JL / Chen S / Cannone G / Lee Y / Hutchings KA / Gittins O / Sobhy M / Wells T / El-Gomati MM / Dalby J / Meffert M / Schulze-Briese C / Henderson R / Russo CJ | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure determination by cryoEM at 100 keV. Authors: Greg McMullan / Katerina Naydenova / Daniel Mihaylov / Keitaro Yamashita / Mathew J Peet / Hugh Wilson / Joshua L Dickerson / Shaoxia Chen / Giuseppe Cannone / Yang Lee / Katherine A ...Authors: Greg McMullan / Katerina Naydenova / Daniel Mihaylov / Keitaro Yamashita / Mathew J Peet / Hugh Wilson / Joshua L Dickerson / Shaoxia Chen / Giuseppe Cannone / Yang Lee / Katherine A Hutchings / Olivia Gittins / Mohamed A Sobhy / Torquil Wells / Mohamed M El-Gomati / Jason Dalby / Matthias Meffert / Clemens Schulze-Briese / Richard Henderson / Christopher J Russo / ![]() ![]() ![]() Abstract: Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose- ...Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose-built instrument operating at 100 keV-including advances in electron optics, detection, and processing-that makes structure determination fast and simple at a fraction of current costs. The instrument attains its theoretical performance limits, allowing atomic resolution imaging of gold test specimens and biological molecular structure determination in hours. We demonstrate its capabilities by determining the structures of eleven different specimens, ranging in size from 140 kDa to 2 MDa, using a fraction of the data normally required. CryoEM with a microscope designed specifically for high-efficiency, on-the-spot imaging of biological molecules will expand structural biology to a wide range of previously intractable problems. | |||||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 31.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 73.5 KB 73.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.3 KB | Display | ![]() |
Images | ![]() | 126.5 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Filedesc metadata | ![]() | 14.8 KB | ||
Others | ![]() ![]() | 194.3 MB 194.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pvaMC ![]() 8pv9C ![]() 8pvbC ![]() 8pvcC ![]() 8pvdC ![]() 8pveC ![]() 8pvfC ![]() 8pvgC ![]() 8pvhC ![]() 8pviC ![]() 8pvjC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.031 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
+Entire : E. coli 70S ribosome
+Supramolecule #1: E. coli 70S ribosome
+Macromolecule #1: 16S rRNA
+Macromolecule #22: 23S rRNA
+Macromolecule #23: 5S rRNA
+Macromolecule #53: mRNA
+Macromolecule #54: A-site tRNA-val
+Macromolecule #55: P-site tRNA-fMet
+Macromolecule #56: E-site tRNA
+Macromolecule #2: Small ribosomal subunit protein uS2
+Macromolecule #3: Small ribosomal subunit protein uS3
+Macromolecule #4: Small ribosomal subunit protein uS4
+Macromolecule #5: Small ribosomal subunit protein uS5
+Macromolecule #6: Small ribosomal subunit protein bS6, fully modified isoform
+Macromolecule #7: Small ribosomal subunit protein uS7
+Macromolecule #8: Small ribosomal subunit protein uS8
+Macromolecule #9: Small ribosomal subunit protein uS9
+Macromolecule #10: Small ribosomal subunit protein uS10
+Macromolecule #11: Small ribosomal subunit protein uS11
+Macromolecule #12: Small ribosomal subunit protein uS12
+Macromolecule #13: Small ribosomal subunit protein uS13
+Macromolecule #14: Small ribosomal subunit protein uS14
+Macromolecule #15: Small ribosomal subunit protein uS15
+Macromolecule #16: Small ribosomal subunit protein bS16
+Macromolecule #17: Small ribosomal subunit protein uS17
+Macromolecule #18: Small ribosomal subunit protein bS18
+Macromolecule #19: Small ribosomal subunit protein uS19
+Macromolecule #20: Small ribosomal subunit protein bS20
+Macromolecule #21: Small ribosomal subunit protein bS21
+Macromolecule #24: Large ribosomal subunit protein uL2
+Macromolecule #25: Large ribosomal subunit protein uL3
+Macromolecule #26: Large ribosomal subunit protein uL4
+Macromolecule #27: Large ribosomal subunit protein uL5
+Macromolecule #28: Large ribosomal subunit protein uL6
+Macromolecule #29: Large ribosomal subunit protein bL9
+Macromolecule #30: Large ribosomal subunit protein uL13
+Macromolecule #31: 50S ribosomal protein L14
+Macromolecule #32: 50S ribosomal protein L15
+Macromolecule #33: Large ribosomal subunit protein uL16
+Macromolecule #34: 50S ribosomal protein L17
+Macromolecule #35: 50S ribosomal protein L18
+Macromolecule #36: 50S ribosomal protein L19
+Macromolecule #37: 50S ribosomal protein L20
+Macromolecule #38: 50S ribosomal protein L21
+Macromolecule #39: 50S ribosomal protein L22
+Macromolecule #40: 50S ribosomal protein L23
+Macromolecule #41: 50S ribosomal protein L24
+Macromolecule #42: 50S ribosomal protein L25
+Macromolecule #43: 50S ribosomal protein L27
+Macromolecule #44: 50S ribosomal protein L28
+Macromolecule #45: 50S ribosomal protein L29
+Macromolecule #46: 50S ribosomal protein L30
+Macromolecule #47: 50S ribosomal protein L32
+Macromolecule #48: 50S ribosomal protein L33
+Macromolecule #49: 50S ribosomal protein L34
+Macromolecule #50: 50S ribosomal protein L35
+Macromolecule #51: 50S ribosomal protein L36
+Macromolecule #52: Large ribosomal subunit protein bL31A
+Macromolecule #57: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: UltrAuFoil R0./1 / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | JEOL 1400/HR + YPS FEG |
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Image recording | Film or detector model: DECTRIS SINGLA (1k x 1k) / Digitization - Dimensions - Width: 1030 pixel / Digitization - Dimensions - Height: 1066 pixel / Average electron dose: 24.0 e/Å2 |
Electron beam | Acceleration voltage: 100 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm |