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- EMDB-5438: 3D reconstruction of a self-assembling designed oligomer with oct... -

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Basic information

Entry
Database: EMDB / ID: 5438
Title3D reconstruction of a self-assembling designed oligomer with octahedral symmetry
Keywordsoctahedral symmetry / designed
SampleDesigned protein oligomer with octahedral symmetry. The model for the design is PduT from Salmonella enterica with the following mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L
SourceSalmonella enterica / bacteria / サルモネラ・エンテリカ, サルモネラ・コレレスイス, ブタコレラ菌
Map dataReconstruction of designed self-assembling protein oligomer with octahedral symmetry
Methodsingle particle reconstruction, at 20 A resolution
AuthorsVollmar BS / King NP / Baker D / Gonen T
CitationScience, 2012, 336, 1171-1174

Science, 2012, 336, 1171-1174 StrPapers
Computational design of self-assembling protein nanomaterials with atomic level accuracy.
Neil P King / William Sheffler / Michael R Sawaya / Breanna S Vollmar / John P Sumida / Ingemar André / Tamir Gonen / Todd O Yeates / David Baker

DateDeposition: Jun 24, 2012 / Header (metadata) release: Jun 29, 2012 / Map release: Jun 29, 2012 / Last update: Jun 24, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.8
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 1.8
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_5438.map.gz (map file in CCP4 format, 6751 KB)
Projections & slices
Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
120 pix
1.47 A/pix
= 176.88 A
120 pix
1.47 A/pix
= 176.88 A
120 pix
1.47 A/pix
= 176.88 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.474 A
Density
Contour Level:1.8 (by author), 1.8 (movie #1):
Minimum - Maximum-2.47524214 - 4.30226564
Average (Standard dev.)-2E-8 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions120120120
Origin000
Limit119119119
Spacing120120120
CellA=B=C: 176.88 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.4741.4741.474
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z176.880176.880176.880
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120120120
D min/max/mean-2.4754.302-0.000

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Supplemental data

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Sample components

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Entire Designed protein oligomer with octahedral symmetry. The model for...

EntireName: Designed protein oligomer with octahedral symmetry. The model for the design is PduT from Salmonella enterica with the following mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L
Details: Monodisperse sample / Number of components: 1 / Oligomeric State: 24
MassTheoretical: 480 kDa

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Component #1: protein, Propanediol utilization polyhedral body protein PduT

ProteinName: Propanediol utilization polyhedral body protein PduT
Details: Mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L
Recombinant expression: Yes / Number of Copies: 24
SourceSpecies: Salmonella enterica / bacteria / サルモネラ・エンテリカ, サルモネラ・コレレスイス, ブタコレラ菌
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pET29b

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.3 mg/ml / Buffer solution: 25 mM Tris, pH 8.0, 150 mM NaCl, 1 mM DTT / pH: 8
Support filmQuantifoil R1.2/1.3 holey carbon 400 mesh copper grids
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %
Method: Blotted with filter paper and plunged into liquid ethane.

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20 / Date: Jul 12, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
LensMagnification: 100000 X (nominal), 217096 X (calibrated) / Cs: 2.12 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2000 nm
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: TVIPS TEMCAM-F816 (8k x 8k)

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Image acquisition

Image acquisitionNumber of digital images: 565

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 42025
Details: Particles were selected using the automatic selection program Electron Micrograph Utility (cryoem.ucsf.edu).
Applied symmetry: O (octahedral)
3D reconstructionSoftware: FREALIGN / CTF correction: CTFFIND3
Details: Reconstruction was calculated based on 2x binned images yielding a pixel size of 1.474 A/pixel.
Resolution: 20 A / Resolution method: FSC 0.5

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