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

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Basic information

Entry
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 A 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 StrPapers
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

DateDeposition: Feb 26, 2008 / Header (metadata) release: Feb 26, 2008 / Map release: May 29, 2009 / Last update: Feb 26, 2008

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 1.5
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-3bo0
  • Surface level: 1.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-4v7i
  • Surface level: 1.5
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_1484.map.gz (map file in CCP4 format, 11665 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
144 pix
2.73 A/pix
= 393.12 A
144 pix
2.73 A/pix
= 393.12 A
144 pix
2.73 A/pix
= 393.12 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

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

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions144144144
Origin-72-72-72
Limit717171
Spacing144144144
CellA=B=C: 393.12 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-55-55-55
NX/NY/NZ111111111
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
D min/max/mean-4.99710.6490.150

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Supplemental data

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Sample components

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Entire Ribosome SecY complex

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

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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 /

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Experimental details

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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

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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/A2 / 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

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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

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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 A / Resolution method: FSC 0.5

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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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