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- EMDB-1143: Structure of the E. coli protein-conducting channel bound to a tr... -

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Basic information

Entry
Database: EMDB / ID: 1143
TitleStructure of the E. coli protein-conducting channel bound to a translating ribosome.
Sampleco-translational E. coli 70S ribosome-nascent chain complexed with SecYEG
SourceEscherichia coli / bacteria / translocon / エシェリキア・コリ, 大腸菌 /
Unidentified / translocon
Map dataEM map of the E.coli proten-conducting channel bound to a translating ribosome
Methodsingle particle reconstruction, at 14.9 A resolution
AuthorsMitra K / Schaffitzel C / Shaikh T / Tama F / Jenni S / Brooks III CL / Ban N / Frank J
CitationNature, 2005, 438, 318-324

Nature, 2005, 438, 318-324 StrPapers
Structure of the E. coli protein-conducting channel bound to a translating ribosome.
Kakoli Mitra / Christiane Schaffitzel / Tanvir Shaikh / Florence Tama / Simon Jenni / Charles L Brooks / Nenad Ban / Joachim Frank

DateDeposition: Aug 3, 2005 / Header (metadata) release: Aug 3, 2005 / Map release: Jun 13, 2006 / Last update: Aug 3, 2005

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 50
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 50
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1143.map.gz (map file in CCP4 format, 6922 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
121 pix
2.82 A/pix
= 341.22 A
121 pix
2.82 A/pix
= 341.22 A
121 pix
2.82 A/pix
= 341.22 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel size
XYZ
EMDB info.2.822.822.82
CCP4 map header2.822.822.82
EM Navigator Movie #13.593.593.59
Density
Contour Level:46.1, 50 (movie #1):
Minimum - Maximum-299.714 - 454.815
Average (Standard dev.)5.83623 (33.8063)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions121121121
Origin-60-60-60
Limit606060
Spacing121121121
CellA=B=C: 341.22 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.822.822.82
M x/y/z121121121
origin x/y/z0.0000.0000.000
length x/y/z341.220341.220341.220
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-90-90-190
NX/NY/NZ180180380
MAP C/R/S123
start NC/NR/NS-60-60-60
NC/NR/NS121121121
D min/max/mean-299.714454.8155.836

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Supplemental data

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Sample components

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Entire co-translational E. coli 70S ribosome-nascent chain complexed wit...

EntireName: co-translational E. coli 70S ribosome-nascent chain complexed with SecYEG
Number of components: 8

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Component #1: ribosome-prokaryote, 30S

Ribosome-prokaryoteName: 30S / a.k.a: small subunit / Prokaryote: SSU 30S / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: ribosome-prokaryote, 50S

Ribosome-prokaryoteName: 50S / a.k.a: large subunit / Prokaryote: LSU 50S / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #3: nucleic-acid, A-site tRNA

Nucleic-acidName: A-site tRNA / Class: RNA / Structure: DOUBLE HELIX / Synthetic: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #4: nucleic-acid, P-site tRNA

Nucleic-acidName: P-site tRNA / Class: RNA / Structure: DOUBLE HELIX / Synthetic: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #5: nucleic-acid, E-site tRNA

Nucleic-acidName: E-site tRNA / Class: RNA / Structure: DOUBLE HELIX / Synthetic: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #6: nucleic-acid, mRNA

Nucleic-acidName: mRNA / Class: RNA / Structure: SINGLE STRANDED / Synthetic: Yes
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #7: protein, protein-conducting channel

ProteinName: protein-conducting channel / a.k.a: translocon, SecYEG / Oligomeric Details: dimer of heterotrimer / Recombinant expression: Yes / Number of Copies: 2
SourceSpecies: Escherichia coli / bacteria / translocon / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Location in cell: inner membrane

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Component #8: protein, nascent chain

ProteinName: nascent chain / Details: Strep-II-FtsQ-SecM construct / Recombinant expression: Yes
SourceSpecies: Unidentified / translocon

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Experimental details

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Sample preparation

Specimen stateparticle
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 93 K / Humidity: 90 % / Method: Blot for 2 seconds before plunging
Details: Vitrification instrument: two sided blotting plunger

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F30 / Date: Mar 9, 2004
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 11 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 39000 X (nominal), 39000 X (calibrated) / Cs: 2.26 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 4300 nm
Specimen HolderHolder: Cryo stage / Model: OTHER / Temperature: 93 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 385 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 12 / OD range: 1.2

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 53325 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: reference projection / Software: SPIDER package / CTF correction: defocus groups / Resolution: 14.9 A / Resolution method: FSC 0.5 / Euler angles: SPIDER: theta 15 degrees, phi 15 degrees
Details: The falloff of Fourier amplitudes toward higher spatial frequencies was corrected using the x-ray solution scattering intensity distribution of 70S ribosomes from E. coli during each round of refinement

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Target criteria: correlation coefficient / Refinement space: REAL
Details: Protocol: normal mode-based flexible fitting. Fitting of SecYEG atomic model into isolated EM density of protein-conducting channels
Modeling #2Refinement protocol: flexible / Target criteria: correlation coefficient / Refinement space: REAL
Details: Protocol: normal mode-based flexible fitting. Fitting of SecYEG atomic model into isolated EM density of protein-conducting channels
Modeling #3Software: RSR2000 / Refinement protocol: rigid body / Target criteria: R-factor / Refinement space: REAL / Details: Protocol: real space refinement
Modeling #4Software: RSR2000 / Refinement protocol: rigid body / Target criteria: R-factor / Refinement space: REAL / Details: Protocol: real space refinement
Output model

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