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- EMDB-1169: ERj1p uses a universal ribosomal adaptor site to coordinate the 8... -

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Basic information

Entry
Database: EMDB / ID: EMD-1169
TitleERj1p uses a universal ribosomal adaptor site to coordinate the 80S ribosome at the membrane.
Map dataVolume of canine 80S+ErjC-dC
Sample
  • Sample: canine ribosome with bound ERj
  • Complex: canine ribosome
  • Protein or peptide: ERjIp
Biological speciesCanis lupus familiaris (dog) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsBlau M / Mullapudi S / Becker T / Dudek J / Zimmermann R / Penczek PA / Beckmann R
CitationJournal: Nat Struct Mol Biol / Year: 2005
Title: ERj1p uses a universal ribosomal adaptor site to coordinate the 80S ribosome at the membrane.
Authors: Michael Blau / Srinivas Mullapudi / Thomas Becker / Johanna Dudek / Richard Zimmermann / Pawel A Penczek / Roland Beckmann /
Abstract: Ribosomes translating secretory and membrane proteins are targeted to the endoplasmic reticulum membrane and attach to the protein-conducting channel and ribosome-associated membrane proteins (RAMPs). ...Ribosomes translating secretory and membrane proteins are targeted to the endoplasmic reticulum membrane and attach to the protein-conducting channel and ribosome-associated membrane proteins (RAMPs). Recently, a new RAMP, ERj1p, has been identified that recruits BiP to ribosomes and regulates translational activity. Here we present the cryo-EM structure of a ribosome-ERj1p complex, revealing how ERj1p coordinates the ribosome at the membrane and how allosteric effects may mediate ERj1p's regulatory activity.
History
DepositionAug 17, 2005-
Header (metadata) releaseOct 10, 2005-
Map releaseOct 10, 2006-
UpdateNov 20, 2013-
Current statusNov 20, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00047
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.00047
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1169.gif

Downloads & links

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Map

FileDownload / File: emd_1169.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVolume of canine 80S+ErjC-dC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.5 Å/pix.
x 144 pix.
= 504. Å		3.5 Å/pix.
x 144 pix.
= 504. Å		3.5 Å/pix.
x 144 pix.
= 504. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.5 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.000695 / Movie #1: 0.00047
Minimum - Maximum-0.00252685 - 0.00531806
Average (Standard dev.)-0.00039273 (±0.000642063)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144144144
Spacing144144144
CellA=B=C: 504 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.53.53.5
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z504.000504.000504.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-77-770
NX/NY/NZ15515578
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS144144144
D min/max/mean-0.0030.005-0.000

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Supplemental data

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Sample components

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Entire : canine ribosome with bound ERj

EntireName: canine ribosome with bound ERj
Components
  • Sample: canine ribosome with bound ERj
  • Complex: canine ribosome
  • Protein or peptide: ERjIp

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Supramolecule #1000: canine ribosome with bound ERj

SupramoleculeName: canine ribosome with bound ERj / type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: canine ribosome

SupramoleculeName: canine ribosome / type: complex / ID: 1 / Name.synonym: ribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Canis lupus familiaris (dog) / synonym: Dog

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Macromolecule #1: ERjIp

MacromoleculeName: ERjIp / type: protein_or_peptide / ID: 1 / Name.synonym: ERjC-dC / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: House mouse

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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

VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL KYOTO-3000SFF
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Gathan / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å

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