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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: EMD-5438
Title3D reconstruction of a self-assembling designed oligomer with octahedral symmetry
Map dataReconstruction of designed self-assembling protein oligomer with octahedral symmetry
Sample
  • Sample: 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
  • Protein or peptide: Propanediol utilization polyhedral body protein PduT
Keywordsoctahedral symmetry / designed
Function / homology
Function and homology information


propanediol degradation polyhedral organelle / 1,2-propanediol catabolic process / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Bacterial microcompartment shell protein PduT / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily
Similarity search - Domain/homology
: / Bacterial microcompartment shell protein PduT
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsVollmar BS / King NP / Baker D / Gonen T
CitationJournal: Science / Year: 2012
Title: Computational design of self-assembling protein nanomaterials with atomic level accuracy.
Authors: Neil P King / William Sheffler / Michael R Sawaya / Breanna S Vollmar / John P Sumida / Ingemar André / Tamir Gonen / Todd O Yeates / David Baker /
Abstract: We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify ...We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials.
History
DepositionJun 24, 2012-
Header (metadata) releaseJun 29, 2012-
Map releaseJun 29, 2012-
UpdateDec 19, 2012-
Current statusDec 19, 2012Processing site: RCSB / Status: Released

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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
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5438_1.jpg

emd_5438_2.tif

Downloads & links

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Map

FileDownload / File: emd_5438.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of designed self-assembling protein oligomer with octahedral symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.47 Å/pix.
x 120 pix.
= 176.88 Å		1.47 Å/pix.
x 120 pix.
= 176.88 Å		1.47 Å/pix.
x 120 pix.
= 176.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.474 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.8 / Movie #1: 1.8
Minimum - Maximum-2.47524214 - 4.30226564
Average (Standard dev.)-0.00000002 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 176.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
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
Components
  • Sample: 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
  • Protein or peptide: Propanediol utilization polyhedral body protein PduT

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Supramolecule #1000: Designed protein oligomer with octahedral symmetry. The model for...

SupramoleculeName: 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
type: sample / ID: 1000 / Details: Monodisperse sample / Oligomeric state: 24 / Number unique components: 1
Molecular weightTheoretical: 480 KDa

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Macromolecule #1: Propanediol utilization polyhedral body protein PduT

MacromoleculeName: Propanediol utilization polyhedral body protein PduT / type: protein_or_peptide / ID: 1
Details: Mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L
Number of copies: 24 / Recombinant expression: Yes
Source (natural)Organism: Salmonella enterica (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET29b

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 8 / Details: 25 mM Tris, pH 8.0, 150 mM NaCl, 1 mM DTT
GridDetails: Quantifoil R1.2/1.3 holey carbon 400 mesh copper grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III
Method: Blotted with filter paper and plunged into liquid ethane.

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Electron microscopy

MicroscopeFEI TECNAI F20
DateJul 12, 2011
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Number real images: 565
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 217096 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.12 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsParticles were selected using the automatic selection program Electron Micrograph Utility (cryoem.ucsf.edu).
CTF correctionDetails: CTFFIND3
Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: FREALIGN
Details: Reconstruction was calculated based on 2x binned images yielding a pixel size of 1.474 A/pixel.
Number images used: 42025

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