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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | apo form of adenosylcobalamin riboswitch dimer | |||||||||
![]() | unsharpened map | |||||||||
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![]() | RNA cobalamin riboswitch / RNA | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.3 Å | |||||||||
![]() | Ding J / Deme JC / Stagno JR / Yu P / Lea SM / Wang YX | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 875.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.8 KB 19.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 24.1 KB | Display | ![]() |
Images | ![]() | 30.5 KB | ||
Masks | ![]() | 1000 MB | ![]() | |
Filedesc metadata | ![]() | 4.7 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() | 942.8 MB 942.9 MB 875.4 MB 929.2 MB 929.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sa6MC ![]() 8sa2C ![]() 8sa3C ![]() 8sa4C ![]() 8sa5C M: atomic model generated by this map C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | unsharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.693 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 |
-Additional map: local refinement of binding pocket, B-factor sharpened
File | emd_40266_additional_1.map | ||||||||||||
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Annotation | local refinement of binding pocket, B-factor sharpened | ||||||||||||
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Density Histograms |
-Additional map: B-factor sharpened map
File | emd_40266_additional_2.map | ||||||||||||
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Annotation | B-factor sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: local refinement of binding pocket, unsharpened
File | emd_40266_additional_3.map | ||||||||||||
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Annotation | local refinement of binding pocket, unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_40266_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
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Density Histograms |
-Half map: half map 2
File | emd_40266_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : apodimer
Entire | Name: apodimer |
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Components |
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-Supramolecule #1: apodimer
Supramolecule | Name: apodimer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: apo form of adenosylcobalamin riboswitch dimer
Macromolecule | Name: apo form of adenosylcobalamin riboswitch dimer / type: rna / ID: 1 / Number of copies: 2 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 68.273664 KDa |
Sequence | String: 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 |
-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: 6 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 54.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 |