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Open data
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Basic information
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Title | Adenosylcobalamin-bound riboswitch dimer, form 2 | |||||||||
![]() | unsharpened map | |||||||||
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![]() | RNA cobalamin riboswitch / RNA | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 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 | ![]() | 217.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.9 KB 15.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.9 KB | Display | ![]() |
Images | ![]() | 43.1 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Filedesc metadata | ![]() | 4.7 KB | ||
Others | ![]() ![]() ![]() | 230.3 MB 226.2 MB 226.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 767.6 KB | Display | ![]() |
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Full document | ![]() | 767.1 KB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sa3MC ![]() 8sa2C ![]() 8sa4C ![]() 8sa5C ![]() 8sa6C 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: 1.0395 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: b-factor sharpened map
File | emd_40263_additional_1.map | ||||||||||||
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Annotation | b-factor sharpened map | ||||||||||||
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Density Histograms |
-Half map: half map 1
File | emd_40263_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_40263_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 : holodimer 2
Entire | Name: holodimer 2 |
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Components |
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-Supramolecule #1: holodimer 2
Supramolecule | Name: holodimer 2 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: adenosylcobalamin riboswitch form 2
Macromolecule | Name: adenosylcobalamin riboswitch form 2 / 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 |
-Macromolecule #2: Adenosylcobalamin
Macromolecule | Name: Adenosylcobalamin / type: ligand / ID: 2 / Number of copies: 2 / Formula: B1Z |
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Molecular weight | Theoretical: 1.58059 KDa |
Chemical component information | ![]() ChemComp-B1Z: |
-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: 54.5 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 |