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- EMDB-3037: Density map of the engaged state of the mammalian SRP-ribosome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-3037
TitleDensity map of the engaged state of the mammalian SRP-ribosome complex
Map dataThis is a sharpened post-processed, masked map
Sample
  • Sample: Mammalian ribosome in complex with the signal recognition particle interacting with its hydrophobic substrate
  • Complex: mammalian ribosome
  • RNA: Signal recognition particle
Keywordsribosomes / SRP / mammal / translocation
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsVoorhees RM / Hegde RS
CitationJournal: Elife / Year: 2015
Title: Structures of the scanning and engaged states of the mammalian SRP-ribosome complex.
Authors: Rebecca M Voorhees / Ramanujan S Hegde /
Abstract: The universally conserved signal recognition particle (SRP) is essential for the biogenesis of most integral membrane proteins. SRP scans the nascent chains of translating ribosomes, preferentially ...The universally conserved signal recognition particle (SRP) is essential for the biogenesis of most integral membrane proteins. SRP scans the nascent chains of translating ribosomes, preferentially engaging those with hydrophobic targeting signals, and delivers these ribosome-nascent chain complexes to the membrane. Here, we present structures of native mammalian SRP-ribosome complexes in the scanning and engaged states. These structures reveal the near-identical SRP architecture of these two states, show many of the SRP-ribosome interactions at atomic resolution, and suggest how the polypeptide-binding M domain selectively engages hydrophobic signals. The scanning M domain, pre-positioned at the ribosomal exit tunnel, is auto-inhibited by a C-terminal amphipathic helix occluding its hydrophobic binding groove. Upon engagement, the hydrophobic targeting signal displaces this amphipathic helix, which then acts as a protective lid over the signal. Biochemical experiments suggest how scanning and engagement are coordinated with translation elongation to minimize exposure of hydrophobic signals during membrane targeting.
History
DepositionJun 2, 2015-
Header (metadata) releaseAug 12, 2015-
Map releaseAug 12, 2015-
UpdateDec 16, 2015-
Current statusDec 16, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3jaj
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3037.png

Downloads & links

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Map

FileDownload / File: emd_3037.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a sharpened post-processed, masked map
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.47114572 - 0.63764018
Average (Standard dev.)0.00140738 (±0.02118861)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 562.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z562.800562.800562.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.4710.6380.001

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Supplemental data

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Supplemental map: engaged half1 unfil.map

Fileengaged_half1_unfil.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: engaged half2 unfil.map

Fileengaged_half2_unfil.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 : Mammalian ribosome in complex with the signal recognition particl...

EntireName: Mammalian ribosome in complex with the signal recognition particle interacting with its hydrophobic substrate
Components
  • Sample: Mammalian ribosome in complex with the signal recognition particle interacting with its hydrophobic substrate
  • Complex: mammalian ribosome
  • RNA: Signal recognition particle

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Supramolecule #1000: Mammalian ribosome in complex with the signal recognition particl...

SupramoleculeName: Mammalian ribosome in complex with the signal recognition particle interacting with its hydrophobic substrate
type: sample / ID: 1000
Oligomeric state: monomeric ribosome with monomeric signal recognition particle
Number unique components: 2

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Supramolecule #1: mammalian ribosome

SupramoleculeName: mammalian ribosome / type: complex / ID: 1 / Name.synonym: 80S ribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: rabbit / Cell: reticulocyte

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Macromolecule #1: Signal recognition particle

MacromoleculeName: Signal recognition particle / type: rna / ID: 1 / Name.synonym: SRP / Details: Ribonucleoprotein particle / Classification: OTHER / Structure: OTHER / Synthetic?: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: rabbit

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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 / Details: 50 mM HEPES, 200 mM KAc, 15 mM MgAc2, and 1 mM DTT
GridDetails: Quantifoil R2/2 400 mesh copper grids.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Method: 3uL of sampled was incubated on the grid for 30 seconds before blotting for 3 second

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateJun 16, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 27 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 52061

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