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- EMDB-48851: Vibrio cholerae Glycine Riboswitch - glycine bound at 2.9A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-48851
TitleVibrio cholerae Glycine Riboswitch - glycine bound at 2.9A resolution
Map dataVibrio cholerae Glycine Riboswitch - glycine bound at 2.9A resolution
Sample
  • Complex: Holo structure of the glycine riboswitch with 10mM Magnesium and 2mM Glycine
    • RNA: Glycine Riboswitch
  • Ligand: GLYCINE
  • Ligand: MAGNESIUM ION
KeywordsRiboswitch / Glycine / Magnesium / Holo / RNA
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsJespersen N / Singhal A / Prajapati JD / Sanbonmatsu K
Funding support United States, 1 items
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 JD / Sanbonmatsu K
History
DepositionJan 31, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48851.png

Downloads & links

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Map

FileDownload / File: emd_48851.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVibrio cholerae Glycine Riboswitch - glycine bound at 2.9A resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 210.688 Å		0.82 Å/pix.
x 256 pix.
= 210.688 Å		0.82 Å/pix.
x 256 pix.
= 210.688 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.823 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.16715337 - 0.3287338
Average (Standard dev.)0.0003778004 (±0.007275842)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 210.688 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48851_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Raw Map

Fileemd_48851_additional_1.map
AnnotationRaw Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_48851_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_48851_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Holo structure of the glycine riboswitch with 10mM Magnesium and ...

EntireName: Holo structure of the glycine riboswitch with 10mM Magnesium and 2mM Glycine
Components
  • Complex: Holo structure of the glycine riboswitch with 10mM Magnesium and 2mM Glycine
    • RNA: Glycine Riboswitch
  • Ligand: GLYCINE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Holo structure of the glycine riboswitch with 10mM Magnesium and ...

SupramoleculeName: Holo structure of the glycine riboswitch with 10mM Magnesium and 2mM Glycine
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 75.7 KDa

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Macromolecule #1: Glycine Riboswitch

MacromoleculeName: Glycine Riboswitch / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 76.063195 KDa
SequenceString: GUCCGUUGAA GACUGCAGGA GAGUGGUUGU UAACCAGAUU UUAACAUCUG AGCCAAAUAA CCCGCCGAAG AAGUAAAUCU UUCAGGUGC AUUAUUCUUA GCCAUAUAUU GGCAACGAAU AAGCGAGGAC UGUAGUUGGA GGAACCUCUG GAGAGAACCG U UUAAUCGG ...String:
GUCCGUUGAA GACUGCAGGA GAGUGGUUGU UAACCAGAUU UUAACAUCUG AGCCAAAUAA CCCGCCGAAG AAGUAAAUCU UUCAGGUGC AUUAUUCUUA GCCAUAUAUU GGCAACGAAU AAGCGAGGAC UGUAGUUGGA GGAACCUCUG GAGAGAACCG U UUAAUCGG UCGCCGAAGG AGCAAGCUCU GCGCAUAUGC AGAGUGAAAC UCUCAGGCAA AAGGACAGAG GAGUGAA

GENBANK: GENBANK: CP160480.1

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Macromolecule #2: GLYCINE

MacromoleculeName: GLYCINE / type: ligand / ID: 2 / Number of copies: 2 / Formula: GLY
Molecular weightTheoretical: 75.067 Da
Chemical component information

ChemComp-GLY:
GLYCINE

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 14 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration1.2 mg/mL
BufferpH: 6
Component:
ConcentrationNameFormula
25.0 mMMES
2.0 mMGlycine
10.0 mMMagnesium ChlorideMgCl2

Details: 25mM MES (pH 6.0), 10mM MgCl2, 2mM Glycine
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 15mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 5338 / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 476789
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 215269
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 10 / Avg.num./class: 25000 / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6wlt


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

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

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