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- EMDB-40073: Cryo-EM map of synthetic cage_T3_5 reconstructed without symmetry... -

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Basic information

Entry
Database: EMDB / ID: EMD-40073
TitleCryo-EM map of synthetic cage_T3_5 reconstructed without symmetry (C1), with 1 monomer missing (class 3.0)
Map datacage_T3_5 refined without symmetry (C1)
Sample
  • Complex: Expandable de novo designed complex cage_T3_5
    • Protein or peptide: cage_T3_5
Keywordssynthetic / self-assembling / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsCoudray N / Redler R / Huddy TF / Hsia Y / Baker D / Ekiert D / Bhabha G
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: bioRxiv / Year: 2023
Title: Blueprinting expandable nanomaterials with standardized protein building blocks.
Abstract: A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The ...A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies in comparison has been much more complex, largely due to the irregular shapes of protein structures . Here we describe extendable linear, curved, and angled protein building blocks, as well as inter-block interactions that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight "train track" assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence-structure relationships, it has not been previously possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank 3D canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to "back of an envelope" architectural blueprints.
History
DepositionMar 14, 2023-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40073.png

Downloads & links

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Map

FileDownload / File: emd_40073.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcage_T3_5 refined without symmetry (C1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 296.928 Å		0.82 Å/pix.
x 360 pix.
= 296.928 Å		0.82 Å/pix.
x 360 pix.
= 296.928 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8248 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.062114786 - 0.20798182
Average (Standard dev.)0.0001992038 (±0.0096179005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 296.928 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40073_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cage T3 5 refined without symmetry (C1), half map B

Fileemd_40073_half_map_1.map
Annotationcage_T3_5 refined without symmetry (C1), half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cage T3 5 refined without symmetry (C1), half map A

Fileemd_40073_half_map_2.map
Annotationcage_T3_5 refined without symmetry (C1), half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Expandable de novo designed complex cage_T3_5

EntireName: Expandable de novo designed complex cage_T3_5
Components
  • Complex: Expandable de novo designed complex cage_T3_5
    • Protein or peptide: cage_T3_5

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Supramolecule #1: Expandable de novo designed complex cage_T3_5

SupramoleculeName: Expandable de novo designed complex cage_T3_5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: cage_T3_5

MacromoleculeName: cage_T3_5 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: mGSVELLAVA ALQELNIELA RALLEAVARL QELNIDLVRK TSELTDEKTI REEIRKVKEE SKRIVEEAEE LIRLAKLASE AIARMAEVAA RGAPPEELIK RLEELLKKAQ EAGMSPEIIH LLLELALAIV EARGVPPEQL AEFAERLVEI LREAGGSPEL VFELLRRIME ...String:
mGSVELLAVA ALQELNIELA RALLEAVARL QELNIDLVRK TSELTDEKTI REEIRKVKEE SKRIVEEAEE LIRLAKLASE AIARMAEVAA RGAPPEELIK RLEELLKKAQ EAGMSPEIIH LLLELALAIV EARGVPPEQL AEFAERLVEI LREAGGSPEL VFELLRRIME IIARRGAPPE LLIELLERLL ELAREAGLSP RQIYLLLMLA LIIVYQRGVP PEQLAEFAEK LKEILREAGG SPELQKALKE LIEAIEELRG AGGSlehhhh hh

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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

Concentration0.5 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Slit width: 30 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 5854 / Average exposure time: 2.0 sec. / Average electron dose: 58.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 959145
Startup modelType of model: NONE / Details: Ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final 3D classificationNumber classes: 2 / Avg.num./class: 58462 / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3)
Details: The reported resolution is derived from masked maps.
Number images used: 64560

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Atomic model buiding 1

RefinementSpace: REAL

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Atomic model buiding 2

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: de novo designed model

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