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- EMDB-20756: SAM-bound SAM-IV riboswitch -

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Basic information

Entry
Database: EMDB / ID: EMD-20756
TitleSAM-bound SAM-IV riboswitch
Map dataSAM-bound SAM-IV riboswitch
Sample
  • Complex: SAM-bound SAM-IV riboswitch
    • Complex: SAM-bound SAM-IV riboswitch
      • RNA: RNA (119-MER)
  • Ligand: S-ADENOSYLMETHIONINE
KeywordsSAM-IV riboswitch / Cryo-EM / Small RNA / RNA
Biological speciesHelicobacter pylori (bacteria) / Mycobacterium sp. MCS (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsZhang K / Li S
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P41GM103832 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM079429 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)S10OD021600 United States
CitationJournal: 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
DepositionSep 23, 2019-
Header (metadata) releaseNov 20, 2019-
Map releaseDec 18, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6uet
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20756.png

Downloads & links

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Map

FileDownload / File: emd_20756.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSAM-bound SAM-IV riboswitch
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 168 pix.
= 178.08 Å		1.06 Å/pix.
x 168 pix.
= 178.08 Å		1.06 Å/pix.
x 168 pix.
= 178.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0 / Movie #1: 5
Minimum - Maximum-14.384168000000001 - 24.313755
Average (Standard dev.)0.000000000000189 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 178.07999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z178.080178.080178.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-14.38424.3140.000

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Supplemental data

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Sample components

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Entire : SAM-bound SAM-IV riboswitch

EntireName: SAM-bound SAM-IV riboswitch
Components
  • Complex: SAM-bound SAM-IV riboswitch
    • Complex: SAM-bound SAM-IV riboswitch
      • RNA: RNA (119-MER)
  • Ligand: S-ADENOSYLMETHIONINE

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Supramolecule #1: SAM-bound SAM-IV riboswitch

SupramoleculeName: SAM-bound SAM-IV riboswitch / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Helicobacter pylori (bacteria) / Strain: 60190
Molecular weightTheoretical: 40 KDa

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Supramolecule #2: SAM-bound SAM-IV riboswitch

SupramoleculeName: SAM-bound SAM-IV riboswitch / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Helicobacter pylori (bacteria) / Strain: 60190

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Macromolecule #1: RNA (119-MER)

MacromoleculeName: RNA (119-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Mycobacterium sp. MCS (bacteria)
Molecular weightTheoretical: 38.522906 KDa
SequenceString:
GGUCAUGAGU GCCAGCGUCA AGCCCCGGCU UGCUGGCCGG CAACCCUCCA ACCGCGGUGG GGUGCCCCGG GUGAUGACCA GGUUGAGUA GCCGUGACGG CUACGCGGCA AGCGCGGGUC

GENBANK: GENBANK: CP000384.1

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Macromolecule #2: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 2 / Number of copies: 1 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE

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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

Concentration1.2 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
DetailsSAM-bound SAM-IV riboswitch

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1830706
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 588580
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final 3D classificationNumber classes: 10 / Software - Name: cryoSPARC (ver. 2)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-6uet:
SAM-bound SAM-IV riboswitch

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