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- EMDB-26631: Pseudomonas aeruginosa 70S ribosome initiation complex bound to c... -

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Basic information

Entry
Database: EMDB / ID: EMD-26631
TitlePseudomonas aeruginosa 70S ribosome initiation complex bound to compact IF2-GDP (I-B)
Map data
Sample
  • Complex: Pseudomonas aeruginosa 70S ribosome initiation complex bound to compact IF2-GDP (I-B)
KeywordsInitiation Factor 2 / 70S ribosome / cryo-EM / translation initiation / initiator tRNA / conformational changes / RIBOSOME
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsBasu RS / Sherman MB / Gagnon MG
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM136936 United States
Robert A. Welch FoundationH-2032-20200401 United States
CitationJournal: Nat Commun / Year: 2022
Title: Compact IF2 allows initiator tRNA accommodation into the P site and gates the ribosome to elongation
Authors: Basu RS / Sherman MB / Gagnon MG
History
DepositionApr 11, 2022-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26631.png

Downloads & links

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Map

FileDownload / File: emd_26631.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 512 pix.
= 435.2 Å		0.85 Å/pix.
x 512 pix.
= 435.2 Å		0.85 Å/pix.
x 512 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.6629317 - 1.7981621
Average (Standard dev.)-0.00179459 (±0.06766914)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26631_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Pseudomonas aeruginosa 70S ribosome initiation complex bound to...

Fileemd_26631_additional_1.map
AnnotationPseudomonas aeruginosa 70S ribosome initiation complex bound to compact IF2-GDP (I-B). Sharpened map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Pseudomonas aeruginosa 70S ribosome initiation complex bound to...

Fileemd_26631_half_map_1.map
AnnotationPseudomonas aeruginosa 70S ribosome initiation complex bound to compact IF2-GDP (I-B). Half-map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Pseudomonas aeruginosa 70S ribosome initiation complex bound to...

Fileemd_26631_half_map_2.map
AnnotationPseudomonas aeruginosa 70S ribosome initiation complex bound to compact IF2-GDP (I-B). Half-map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pseudomonas aeruginosa 70S ribosome initiation complex bound to c...

EntireName: Pseudomonas aeruginosa 70S ribosome initiation complex bound to compact IF2-GDP (I-B)
Components
  • Complex: Pseudomonas aeruginosa 70S ribosome initiation complex bound to compact IF2-GDP (I-B)

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Supramolecule #1: Pseudomonas aeruginosa 70S ribosome initiation complex bound to c...

SupramoleculeName: Pseudomonas aeruginosa 70S ribosome initiation complex bound to compact IF2-GDP (I-B)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)

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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

BufferpH: 7.6
GridModel: Quantifoil R2/1 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 295 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8056 / Average exposure time: 1.0 sec. / Average electron dose: 31.0 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: 2.1 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 878576
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1.0) / Number images used: 24614
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.1.0)

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