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- EMDB-1484: Ribosome Binding of a Single Copy of the SecY Complex: Implicatio... -

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Database: EMDB / ID: 1484
TitleRibosome Binding of a Single Copy of the SecY Complex: Implications for Protein Translocation
Keywordsribosome / secY / translocation / electron microscopy
SampleRibosome SecY complex
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataEscherichia coli ribosome secY complex
Methodsingle particle reconstruction, at 9.6 Å resolution
AuthorsMenetret JF / Schaletzky J / Clemons WM Jr / Osborne AR / Skanland SS / Denison C / Gygi SP / Kirkpatrick DS / Park E / Ludtke SJ / Rapoport TA / Akey CW
CitationMol. Cell, 2007, 28, 1083-1092

Mol. Cell, 2007, 28, 1083-1092 Yorodumi Papers
Ribosome binding of a single copy of the SecY complex: implications for protein translocation.
Jean-François Ménétret / Julia Schaletzky / William M Clemons / Andrew R Osborne / Sigrid S Skånland / Carilee Denison / Steven P Gygi / Don S Kirkpatrick / Eunyong Park / Steven J Ludtke / Tom A Rapoport / Christopher W Akey

Validation ReportPDB-ID: 3bo0

SummaryFull report
PDB-ID: 3bo1

SummaryFull report
PDB-ID: 4v7i

SummaryFull report
About validation report
DateDeposition: Feb 26, 2008 / Header (metadata) release: Feb 26, 2008 / Map release: May 29, 2009 / Last update: Oct 24, 2012

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 1.5
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  • Surface view colored by height
  • Surface level: 1.5
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  • Surface view with fitted model
  • Atomic models: : PDB-3bo0
  • Surface level: 1.5
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-4v7i
  • Surface level: 1.5
  • Imaged by UCSF CHIMERA
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-3bo0
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-3bo1
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3D viewer

View / / Stereo:
Slabnear <=> far

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Supplemental images

Downloads & links


Fileemd_1484.map.gz (map file in CCP4 format, 11665 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
144 pix
2.73 Å/pix.
= 393.12 Å
144 pix
2.73 Å/pix.
= 393.12 Å
144 pix
2.73 Å/pix.
= 393.12 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.73 Å
Contour Level:0.95 (by author), 1.5 (movie #1):
Minimum - Maximum-4.99671 - 10.6495
Average (Standard dev.)0.149684 (0.868322)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 393.12 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.732.732.73
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z393.120393.120393.120
start NX/NY/NZ-55-55-55
MAP C/R/S123
start NC/NR/NS-72-72-72
D min/max/mean-4.99710.6490.150

Supplemental data

Sample components

Entire Ribosome SecY complex

EntireName: Ribosome SecY complex / Number of components: 1 / Oligomeric State: monomer
MassTheoretical: 3.2 MDa

Component #1: ribosome-prokaryote, 70S ribosome

Ribosome-prokaryoteName: 70S ribosome / a.k.a: ribosome / Prokaryote: ALL / Recombinant expression: No
MassTheoretical: 3.2 MDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.3 mg/ml
Buffer solution: 50mM Hepes-KOH, 100mM KOAc, 10mM Mg(OAc)2, 0.05% DDM
pH: 7.5
Support film400 mesh Cu grids with continuous carbon film
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 95 % / Method: 1 second blot / Details: Vitrification instrument: home-made

Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20
Details: About 30 percent of the data were collected at 30 degree tilt and micrographs were processed in small strips parallel to the tilt axis to correct for the defocus ramp.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 51000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2500 nm
Specimen HolderHolder: eucentric / Model: GATAN LIQUID NITROGEN / Tilt Angle: 0 - 30 deg. / Temperature: 90 K
CameraDetector: KODAK SO-163 FILM

Image acquisition

Image acquisitionNumber of digital images: 351 / Scanner: OTHER / Sampling size: 4.5 microns / Bit depth: 16 / OD range: 1 / Details: Creoscitex Eversmart scanner was used

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 39000 / Details: 1900 classes were used in EMAN 3D refinement / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: projection matching / Software: EMAN / CTF correction: by micrograph / Resolution: 9.6 Å / Resolution method: FSC 0.5

Atomic model buiding

Modeling #1Software: coot / Refinement protocol: rigid body / Refinement space: REAL
Details: Protocol: manual in O and Chimera. Loop geometry was regularized in Coot.
Input PDB model: 1RHZ, 2I2T, 2I2P
Output model

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