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- EMDB-24557: RACK1-WT, 40S head masked from 80S rotated state, locally refined... -

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Basic information

Entry
Database: EMDB / ID: EMD-24557
TitleRACK1-WT, 40S head masked from 80S rotated state, locally refined and filtered
Map dataRACK1-WT; 40S head from rotated 80S after local refinement and filtering
Sample
  • Complex: RACK1-S278E 80S rotated state, consensus reconstruction
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsShen PS / Rollins MG / Shasmal M / Meade N / Astar H / Walsh D
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 390GM133772 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI127456 United States
CitationJournal: Cell Rep / Year: 2021
Title: Negative charge in the RACK1 loop broadens the translational capacity of the human ribosome.
Authors: Madeline G Rollins / Manidip Shasmal / Nathan Meade / Helen Astar / Peter S Shen / Derek Walsh /
Abstract: Although the roles of initiation factors, RNA binding proteins, and RNA elements in regulating translation are well defined, how the ribosome functionally diversifies remains poorly understood. In ...Although the roles of initiation factors, RNA binding proteins, and RNA elements in regulating translation are well defined, how the ribosome functionally diversifies remains poorly understood. In their human hosts, poxviruses phosphorylate serine 278 (S) at the tip of a loop domain in the small subunit ribosomal protein RACK1, thereby mimicking negatively charged residues in the RACK1 loops of dicot plants and protists to stimulate translation of transcripts with 5' poly(A) leaders. However, how a negatively charged RACK1 loop affects ribosome structure and its broader translational output is not known. Here, we show that although ribotoxin-induced stress signaling and stalling on poly(A) sequences are unaffected, negative charge in the RACK1 loop alters the swivel motion of the 40S head domain in a manner similar to several internal ribosome entry sites (IRESs), confers resistance to various protein synthesis inhibitors, and broadly supports noncanonical modes of translation.
History
DepositionJul 26, 2021-
Header (metadata) releaseSep 22, 2021-
Map releaseSep 22, 2021-
UpdateSep 22, 2021-
Current statusSep 22, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.28
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.28
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24557.png

Downloads & links

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Map

FileDownload / File: emd_24557.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRACK1-WT; 40S head from rotated 80S after local refinement and filtering
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 420 pix.
= 444.36 Å		1.06 Å/pix.
x 420 pix.
= 444.36 Å		1.06 Å/pix.
x 420 pix.
= 444.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28 / Movie #1: 0.28
Minimum - Maximum-0.60830086 - 1.4279261
Average (Standard dev.)0.0023300052 (±0.033080466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 444.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0581.0581.058
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z444.360444.360444.360
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ330330330
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.6081.4280.002

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Supplemental data

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Sample components

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Entire : RACK1-S278E 80S rotated state, consensus reconstruction

EntireName: RACK1-S278E 80S rotated state, consensus reconstruction
Components
  • Complex: RACK1-S278E 80S rotated state, consensus reconstruction

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Supramolecule #1: RACK1-S278E 80S rotated state, consensus reconstruction

SupramoleculeName: RACK1-S278E 80S rotated state, consensus reconstruction
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.5 MDa

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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: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10413
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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