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- EMDB-3451: Folding intermediate of spectrin R16 bound to 70s ribosome -

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Basic information

Entry
Database: EMDB / ID: 3451
TitleFolding intermediate of spectrin R16 bound to 70s ribosome
SampleFolding intermediate of spectrin R16 bound to 70s ribosome
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataFolding intermediate of spectrin R16 bound to 70s ribosome
Methodsingle particle reconstruction, at 4.8 A resolution
AuthorsNilsson OB / Nickson AA / Clarke J
CitationNat. Struct. Mol. Biol., 2017

Nat. Struct. Mol. Biol., 2017 StrPapers
Cotranslational folding of spectrin domains via partially structured states.
Ola B Nilsson / Adrian A Nickson / Jeffrey J Hollins / Stephan Wickles / Annette Steward / Roland Beckmann / Gunnar von Heijne / Jane Clarke

DateDeposition: Oct 25, 2016 / Header (metadata) release: Nov 23, 2016 / Map release: Jan 11, 2017 / Last update: Oct 25, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.000296
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.000296
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5m6s
  • Surface level: 0.000296
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_3451.map.gz (map file in CCP4 format, 199345 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
368 pix
1.08 A/pix
= 398.912 A
368 pix
1.08 A/pix
= 398.912 A
368 pix
1.08 A/pix
= 398.912 A

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.084 A
Density
Contour Level:0.000296 (by author), 0.000296 (movie #1):
Minimum - Maximum-0.0007037198 - 0.0017035634
Average (Standard dev.)-3.8463795E-6 (0.000127588)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions368368368
Origin000
Limit367367367
Spacing368368368
CellA=B=C: 398.912 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.0841.0841.084
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z398.912398.912398.912
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS368368368
D min/max/mean-0.0010.002-0.000

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Supplemental data

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Sample components

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Entire Folding intermediate of spectrin R16 bound to 70s ribosome

EntireName: Folding intermediate of spectrin R16 bound to 70s ribosome
Number of components: 1
MassTheoretical: 2.5 MDa

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Component #1: protein, Folding intermediate of spectrin R16 bound to 70s ribosome

ProteinName: Folding intermediate of spectrin R16 bound to 70s ribosome
Recombinant expression: No
MassTheoretical: 2.5 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 solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 278 K / Humidity: 100 %

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2.4 e/A2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: - 2500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 46067
3D reconstructionSoftware: SPIDER
CTF correction: CTF correction was done following 3D reconstruction.
Resolution: 4.8 A / Resolution method: FSC 0.143 CUT-OFF
Details: To exclude potential overfitting, the data were processed using a frequency limited refinement protocol by truncating high frequencies (low-pass filter at 8A)

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Atomic model buiding

Output model

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