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- EMDB-20063: Fractal-like assemblies of designed AtzA and AtzC proteins -

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Basic information

Entry
Database: EMDB / ID: EMD-20063
TitleFractal-like assemblies of designed AtzA and AtzC proteins
Map dataSubtomogram of a large AtzA-AtzC assembly.
Sample
  • Complex: Designed proteins AtzA-pY:AtzC-SH2
Biological speciesPseudomonas sp. (bacteria)
Methodelectron tomography / cryo EM
AuthorsDai W / Chen M / Khare S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1330760 United States
CitationJournal: Nat Chem / Year: 2019
Title: Stimulus-responsive self-assembly of protein-based fractals by computational design.
Authors: Nancy E Hernández / William A Hansen / Denzel Zhu / Maria E Shea / Marium Khalid / Viacheslav Manichev / Matthew Putnins / Muyuan Chen / Anthony G Dodge / Lu Yang / Ileana Marrero-Berríos ...Authors: Nancy E Hernández / William A Hansen / Denzel Zhu / Maria E Shea / Marium Khalid / Viacheslav Manichev / Matthew Putnins / Muyuan Chen / Anthony G Dodge / Lu Yang / Ileana Marrero-Berríos / Melissa Banal / Phillip Rechani / Torgny Gustafsson / Leonard C Feldman / Sang-Hyuk Lee / Lawrence P Wackett / Wei Dai / Sagar D Khare /
Abstract: Fractal topologies, which are statistically self-similar over multiple length scales, are pervasive in nature. The recurrence of patterns in fractal-shaped branched objects, such as trees, lungs and ...Fractal topologies, which are statistically self-similar over multiple length scales, are pervasive in nature. The recurrence of patterns in fractal-shaped branched objects, such as trees, lungs and sponges, results in a high surface area to volume ratio, which provides key functional advantages including molecular trapping and exchange. Mimicking these topologies in designed protein-based assemblies could provide access to functional biomaterials. Here we describe a computational design approach for the reversible self-assembly of proteins into tunable supramolecular fractal-like topologies in response to phosphorylation. Guided by atomic-resolution models, we develop fusions of Src homology 2 (SH2) domain or a phosphorylatable SH2-binding peptide, respectively, to two symmetric, homo-oligomeric proteins. Mixing the two designed components resulted in a variety of dendritic, hyperbranched and sponge-like topologies that are phosphorylation-dependent and self-similar over three decades (~10 nm-10 μm) of length scale, in agreement with models from multiscale computational simulations. Designed assemblies perform efficient phosphorylation-dependent capture and release of cargo proteins.
History
DepositionApr 5, 2019-
Header (metadata) releaseMay 1, 2019-
Map releaseJul 10, 2019-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Movie viewer
Supplemental images

emd_20063.png

Downloads & links

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Map

FileDownload / File: emd_20063.map.gz / Format: CCP4 / Size: 17.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram of a large AtzA-AtzC assembly.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
27.9 Å/pix.
x 108 pix.
= 3013.2 Å		27.9 Å/pix.
x 170 pix.
= 4743. Å		27.9 Å/pix.
x 256 pix.
= 7142.4 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 27.9 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-3.9731262 - 3.9711313
Average (Standard dev.)-0.00027300356 (±0.71553123)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions170256108
Spacing256170108
CellA: 7142.4 Å / B: 4743.0 Å / C: 3013.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z27.927.927.9
M x/y/z256170108
origin x/y/z0.0000.0000.000
length x/y/z7142.4004743.0003013.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256170108
D min/max/mean-3.9733.971-0.000

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Supplemental data

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Sample components

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Entire : Designed proteins AtzA-pY:AtzC-SH2

EntireName: Designed proteins AtzA-pY:AtzC-SH2
Components
  • Complex: Designed proteins AtzA-pY:AtzC-SH2

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Supramolecule #1: Designed proteins AtzA-pY:AtzC-SH2

SupramoleculeName: Designed proteins AtzA-pY:AtzC-SH2 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Pseudomonas sp. (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: LEICA EM GP
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: EMS / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
TemperatureMin: 93.0 K / Max: 110.0 K
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average exposure time: 2.0 sec. / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 6.0 µm / Calibrated defocus min: 4.0 µm / Calibrated magnification: 39000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 39000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: EMAN2 / Number images used: 60

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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