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- PDB-9n3i: Vibrio cholerae Glycine Riboswitch - glycine bound at 2.9A resolution -

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Basic information

Entry
Database: PDB / ID: 9n3i
TitleVibrio cholerae Glycine Riboswitch - glycine bound at 2.9A resolution
ComponentsGlycine Riboswitch
KeywordsRNA / Riboswitch / Glycine / Magnesium / Holo
Function / homologyGLYCINE / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsJespersen, N. / Singhal, A. / Prajapati, J.D. / Sanbonmatsu, K.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)20230044DR United States
CitationJournal: To Be Published
Title: Vibrio cholerae Glycine Riboswitch - glycine bound at 2.9A resolution
Authors: Jespersen, N. / Singhal, A. / Prajapati, J.D. / Sanbonmatsu, K.
History
DepositionJan 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycine Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,55417
Polymers76,0631
Non-polymers49016
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain Glycine Riboswitch


Mass: 76063.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria) / References: GenBank: 2772158317
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Holo structure of the glycine riboswitch with 10mM Magnesium and 2mM Glycine
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: .0757 MDa / Experimental value: NO
Source (natural)Organism: Vibrio cholerae (bacteria)
Buffer solutionpH: 6 / Details: 25mM MES (pH 6.0), 10mM MgCl2, 2mM Glycine
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMMES1
22 mMGlycine1
310 mMMagnesium ChlorideMgCl21
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15mA / Grid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 59 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 5338

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
4cryoSPARC4.6.0CTF correction
7Coot0.9.8.95model fitting
11cryoSPARC4.6.0classification
12cryoSPARC4.6.03D reconstruction
13PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 476789
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 215269 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6WLT

6wlt


Pdb chain-ID: A / Accession code: 6WLT / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.86 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0065531
ELECTRON MICROSCOPYf_angle_d0.5018618
ELECTRON MICROSCOPYf_dihedral_angle_d21.5723311
ELECTRON MICROSCOPYf_chiral_restr0.0311150
ELECTRON MICROSCOPYf_plane_restr0.003232

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