+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20756 | ||||||||||||
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Title | SAM-bound SAM-IV riboswitch | ||||||||||||
Map data | SAM-bound SAM-IV riboswitch | ||||||||||||
Sample |
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Keywords | SAM-IV riboswitch / Cryo-EM / Small RNA / RNA | ||||||||||||
Biological species | Helicobacter pylori (bacteria) / Mycobacterium sp. MCS (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||||||||
Authors | Zhang K / Li S | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution. Authors: Kaiming Zhang / Shanshan Li / Kalli Kappel / Grigore Pintilie / Zhaoming Su / Tung-Chung Mou / Michael F Schmid / Rhiju Das / Wah Chiu / Abstract: Specimens below 50 kDa have generally been considered too small to be analyzed by single-particle cryo-electron microscopy (cryo-EM). The high flexibility of pure RNAs makes it difficult to obtain ...Specimens below 50 kDa have generally been considered too small to be analyzed by single-particle cryo-electron microscopy (cryo-EM). The high flexibility of pure RNAs makes it difficult to obtain high-resolution structures by cryo-EM. In bacteria, riboswitches regulate sulfur metabolism through binding to the S-adenosylmethionine (SAM) ligand and offer compelling targets for new antibiotics. SAM-I, SAM-I/IV, and SAM-IV are the three most commonly found SAM riboswitches, but the structure of SAM-IV is still unknown. Here, we report the structures of apo and SAM-bound SAM-IV riboswitches (119-nt, ~40 kDa) to 3.7 Å and 4.1 Å resolution, respectively, using cryo-EM. The structures illustrate homologies in the ligand-binding core but distinct peripheral tertiary contacts in SAM-IV compared to SAM-I and SAM-I/IV. Our results demonstrate the feasibility of resolving small RNAs with enough detail to enable detection of their ligand-binding pockets and suggest that cryo-EM could play a role in structure-assisted drug design for RNA. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20756.map.gz | 17 MB | EMDB map data format | |
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Header (meta data) | emd-20756-v30.xml emd-20756.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
Images | emd_20756.png | 114.2 KB | ||
Filedesc metadata | emd-20756.cif.gz | 4.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20756 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20756 | HTTPS FTP |
-Validation report
Summary document | emd_20756_validation.pdf.gz | 521.2 KB | Display | EMDB validaton report |
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Full document | emd_20756_full_validation.pdf.gz | 520.8 KB | Display | |
Data in XML | emd_20756_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | emd_20756_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20756 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20756 | HTTPS FTP |
-Related structure data
Related structure data | 6uetMC 6uesC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20756.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | SAM-bound SAM-IV riboswitch | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : SAM-bound SAM-IV riboswitch
Entire | Name: SAM-bound SAM-IV riboswitch |
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Components |
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-Supramolecule #1: SAM-bound SAM-IV riboswitch
Supramolecule | Name: SAM-bound SAM-IV riboswitch / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Helicobacter pylori (bacteria) / Strain: 60190 |
Molecular weight | Theoretical: 40 KDa |
-Supramolecule #2: SAM-bound SAM-IV riboswitch
Supramolecule | Name: SAM-bound SAM-IV riboswitch / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Helicobacter pylori (bacteria) / Strain: 60190 |
-Macromolecule #1: RNA (119-MER)
Macromolecule | Name: RNA (119-MER) / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: Mycobacterium sp. MCS (bacteria) |
Molecular weight | Theoretical: 38.522906 KDa |
Sequence | String: GGUCAUGAGU GCCAGCGUCA AGCCCCGGCU UGCUGGCCGG CAACCCUCCA ACCGCGGUGG GGUGCCCCGG GUGAUGACCA GGUUGAGUA GCCGUGACGG CUACGCGGCA AGCGCGGGUC GENBANK: GENBANK: CP000384.1 |
-Macromolecule #2: S-ADENOSYLMETHIONINE
Macromolecule | Name: S-ADENOSYLMETHIONINE / type: ligand / ID: 2 / Number of copies: 1 / Formula: SAM |
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Molecular weight | Theoretical: 398.437 Da |
Chemical component information | ChemComp-SAM: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.2 mg/mL |
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Buffer | pH: 7.2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
Details | SAM-bound SAM-IV riboswitch |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-30 / Number grids imaged: 2 / Number real images: 6030 / Average exposure time: 6.0 sec. / Average electron dose: 7.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: BACKBONE TRACE |
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Output model | PDB-6uet: |