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- EMDB-19199: Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin... -

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Basic information

Entry
Database: EMDB / ID: EMD-19199
TitleStructure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61, bound TRAP-alpha TMD
Map data
Sample
  • Complex: 80S ribosome translating a stalled, two-TMD nascent chain (derived from rhodopsin), and bound to Sec61, the TRAP complex, and RAMP4
KeywordsRibosome / Membrane protein / Translocon / Transport
Biological speciesCanis lupus familiaris (dog)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69243 Å
AuthorsLewis AJO / Hegde RS
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_A022_1007 United Kingdom
CitationJournal: To Be Published
Title: Structural analysis of the dynamic ribosome-translocon complex
Authors: Lewis AJO / Hegde RS
History
DepositionDec 20, 2023-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateJan 24, 2024-
Current statusJan 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19199.png

Downloads & links

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Map

FileDownload / File: emd_19199.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.3398 Å
Density
Contour LevelBy AUTHOR: 0.0231
Minimum - Maximum-0.07814522 - 0.24408749
Average (Standard dev.)0.0005007235 (±0.0067392085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 562.716 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19199_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19199_half_map_2.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 : 80S ribosome translating a stalled, two-TMD nascent chain (derive...

EntireName: 80S ribosome translating a stalled, two-TMD nascent chain (derived from rhodopsin), and bound to Sec61, the TRAP complex, and RAMP4
Components
  • Complex: 80S ribosome translating a stalled, two-TMD nascent chain (derived from rhodopsin), and bound to Sec61, the TRAP complex, and RAMP4

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Supramolecule #1: 80S ribosome translating a stalled, two-TMD nascent chain (derive...

SupramoleculeName: 80S ribosome translating a stalled, two-TMD nascent chain (derived from rhodopsin), and bound to Sec61, the TRAP complex, and RAMP4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#56 / Details: Sample prepared by in vitro translation
Source (natural)Organism: Canis lupus familiaris (dog)

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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: 7.5
Component:
ConcentrationNameFormula
50.0 mMHEPES-KOH buffer, pH 7.5
200.0 mMpotassium acetateKOAc
5.0 mMmagnesium acetateMg(OAc)2
0.25 % (w/w)digitonin
50.0 mMbiotin
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 17540 / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.9000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69243 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 121515
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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