+Open data
-Basic information
Entry | Database: PDB / ID: 8sa4 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Adenosylcobalamin-bound riboswitch dimer, form 3 | |||||||||
Components | adenosylcobalamin riboswitch form 3 | |||||||||
Keywords | RNA / RNA cobalamin riboswitch | |||||||||
Function / homology | Adenosylcobalamin / RNA / RNA (> 10) / RNA (> 100) Function and homology information | |||||||||
Biological species | Caldanaerobacter subterraneus subsp. tengcongensis (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Ding, J. / Deme, J.C. / Stagno, J.R. / Yu, P. / Lea, S.M. / Wang, Y.X. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8sa4.cif.gz | 128.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8sa4.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 8sa4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sa4_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8sa4_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8sa4_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 8sa4_validation.cif.gz | 40.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sa/8sa4 ftp://data.pdbj.org/pub/pdb/validation_reports/sa/8sa4 | HTTPS FTP |
-Related structure data
Related structure data | 40264MC 8sa2C 8sa3C 8sa5C 8sa6C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: RNA chain | Mass: 68273.664 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Caldanaerobacter subterraneus subsp. tengcongensis (bacteria) #2: Chemical | ChemComp-B1Z / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: holodimer 3 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL |
---|---|
Source (natural) | Organism: Caldanaerobacter subterraneus subsp. tengcongensis (bacteria) |
Buffer solution | pH: 6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 54.5 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 272327 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|