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- EMDB-1063: Structure of the signal recognition particle interacting with the... -

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Basic information

Entry
Database: EMDB / ID: 1063
TitleStructure of the signal recognition particle interacting with the elongation-arrested ribosome.
Sample80S RNC-SRP complex fron canis sp.
SourceCanis lupus familiaris / mammal / Dog /
Map dataStructure of signal recognition particle interacting with elongation arested ribosome
Methodsingle particle reconstruction, at 12 Å resolution
AuthorsHalic M / Beckmann R
CitationNature, 2004, 427, 808-814

Nature, 2004, 427, 808-814 StrPapers
Structure of the signal recognition particle interacting with the elongation-arrested ribosome.
Mario Halic / Thomas Becker / Martin R Pool / Christian M T Spahn / Robert A Grassucci / Joachim Frank / Roland Beckmann

Validation ReportPDB-ID: 1ry1

SummaryFull reportAbout validation report
DateDeposition: Dec 19, 2003 / Header (metadata) release: Dec 19, 2003 / Map release: Dec 19, 2004 / Last update: May 26, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00019
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.00019
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-1ry1
  • Surface level: 0.00014
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_1063.map.gz (map file in CCP4 format, 8584 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
130 pix
3.26 Å/pix.
= 423.8 Å
130 pix
3.26 Å/pix.
= 423.8 Å
130 pix
3.26 Å/pix.
= 423.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.26 Å
Density
Contour Level:0.00055, 0.00019 (movie #1):
Minimum - Maximum-0.000663056 - 0.00216205
Average (Standard dev.)3.37914e-05 (0.000236399)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions130130130
Origin-65-65-65
Limit646464
Spacing130130130
CellA=B=C: 423.8 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.263.263.26
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z423.800423.800423.800
α/β/γ90.00090.00090.000
start NX/NY/NZ0052
NX/NY/NZ12812855
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
D min/max/mean-0.0010.0020.000

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Supplemental data

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Sample components

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Entire 80S RNC-SRP complex fron canis sp.

EntireName: 80S RNC-SRP complex fron canis sp. / Oligomeric State: one srp binds one ribosome / Number of components: 3

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Component #1: ribosome-eukaryote, 80S ribosome

Ribosome-eukaryoteName: 80S ribosome / a.k.a: 80S RNC / Details: q / Eukaryote: ALL / Recombinant expression: No
MassTheoretical: 4 MDa / Experimental: 4 MDa
SourceSpecies: Canis lupus familiaris / mammal / Dog /

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Component #2: ligand, mammalian SRP

LigandName: mammalian SRP / a.k.a: SRP / Oligomeric Details: monomer / Details: q / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 400 kDa / Experimental: 400 kDa
SourceSpecies: Canis lupus familiaris / mammal / Dog / / Strain: beagle
Source (engineered)Expression System: Canis lupus familiaris / mammal /
Source (natural)Organelle: ER / Location in cell: ER / Cell: secretory cells / Organ or tissue: pancreas

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Component #3: ligand, tRNA

LigandName: tRNA / a.k.a: tRNA / Oligomeric Details: monomer / Details: q / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 25 kDa / Experimental: 25 kDa
SourceSpecies: Canis lupus familiaris / mammal / Dog /
Source (engineered)Expression System: Wheat germ

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Experimental details

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Sample preparation

Specimen stateparticle
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 4300 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionScanner: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: projection matching / Software: spider / Resolution: 12 Å / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Details: The domains were separately fitted by manual docking using program O
Output model

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