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- EMDB-40264: Adenosylcobalamin-bound riboswitch dimer, form 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-40264
TitleAdenosylcobalamin-bound riboswitch dimer, form 3
Map dataunsharpened map
Sample
  • Organelle or cellular component: holodimer 3
    • RNA: adenosylcobalamin riboswitch form 3
  • Ligand: Adenosylcobalamin
KeywordsRNA cobalamin riboswitch / RNA
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDing J / Deme JC / Stagno JR / Yu P / Lea SM / Wang YX
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CCR Core Funding for Lea Group United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CCR Core Funding for Wang Group United States
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Capturing heterogeneous conformers of cobalamin riboswitch by cryo-EM.
Authors: Jienyu Ding / Justin C Deme / Jason R Stagno / Ping Yu / Susan M Lea / Yun-Xing Wang /
Abstract: RNA conformational heterogeneity often hampers its high-resolution structure determination, especially for large and flexible RNAs devoid of stabilizing proteins or ligands. The adenosylcobalamin ...RNA conformational heterogeneity often hampers its high-resolution structure determination, especially for large and flexible RNAs devoid of stabilizing proteins or ligands. The adenosylcobalamin riboswitch exhibits heterogeneous conformations under 1 mM Mg2+ concentration and ligand binding reduces conformational flexibility. Among all conformers, we determined one apo (5.3 Å) and four holo cryo-electron microscopy structures (overall 3.0-3.5 Å, binding pocket 2.9-3.2 Å). The holo dimers exhibit global motions of helical twisting and bending around the dimer interface. A backbone comparison of the apo and holo states reveals a large structural difference in the P6 extension position. The central strand of the binding pocket, junction 6/3, changes from an 'S'- to a 'U'-shaped conformation to accommodate ligand. Furthermore, the binding pocket can partially form under 1 mM Mg2+ and fully form under 10 mM Mg2+ within the bound-like structure in the absence of ligand. Our results not only demonstrate the stabilizing ligand-induced conformational changes in and around the binding pocket but may also provide further insight into the role of the P6 extension in ligand binding and selectivity.
History
DepositionMar 31, 2023-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40264.png

Downloads & links

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Map

FileDownload / File: emd_40264.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 400 pix.
= 415.8 Å		1.04 Å/pix.
x 400 pix.
= 415.8 Å		1.04 Å/pix.
x 400 pix.
= 415.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0395 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.377
Minimum - Maximum-0.67032516 - 2.1650977
Average (Standard dev.)-0.0004181067 (±0.022508645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 415.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40264_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: B-factor sharpened map

Fileemd_40264_additional_1.map
AnnotationB-factor sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_40264_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_40264_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : holodimer 3

EntireName: holodimer 3
Components
  • Organelle or cellular component: holodimer 3
    • RNA: adenosylcobalamin riboswitch form 3
  • Ligand: Adenosylcobalamin

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Supramolecule #1: holodimer 3

SupramoleculeName: holodimer 3 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)

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Macromolecule #1: adenosylcobalamin riboswitch form 3

MacromoleculeName: adenosylcobalamin riboswitch form 3 / type: rna / ID: 1 / Number of copies: 2
Source (natural)Organism: Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Molecular weightTheoretical: 68.273664 KDa
SequenceString: GGUUAAAGCC UUAUGGUCGC UACCAUUGCA CUCCGGUAGC GUUAAAAGGG AAGACGGGUG AGAAUCCCGC GCAGCCCCCG CUACUGUGA GGGAGGACGA AGCCCUAGUA AGCCACUGCC GAAAGGUGGG AAGGCAGGGU GGAGGAUGAG UCCCGAGCCA G GAGACCUG ...String:
GGUUAAAGCC UUAUGGUCGC UACCAUUGCA CUCCGGUAGC GUUAAAAGGG AAGACGGGUG AGAAUCCCGC GCAGCCCCCG CUACUGUGA GGGAGGACGA AGCCCUAGUA AGCCACUGCC GAAAGGUGGG AAGGCAGGGU GGAGGAUGAG UCCCGAGCCA G GAGACCUG CCAUAAGGUU UUAGAAGUUC GCCUUCGGGG GGAAGGUGAA CA

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Macromolecule #2: Adenosylcobalamin

MacromoleculeName: Adenosylcobalamin / type: ligand / ID: 2 / Number of copies: 1 / Formula: B1Z
Molecular weightTheoretical: 1.58059 KDa
Chemical component information

ChemComp-B1Z:
Adenosylcobalamin / medication*YM

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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: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 54.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 272327
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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