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- EMDB-38931: Cryo-EM structure of artificial protein nanocage mTIP120-Ba -

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Basic information

Entry
Database: EMDB / ID: EMD-38931
TitleCryo-EM structure of artificial protein nanocage mTIP120-Ba
Map datamain map, job066, postprocess, C1, 7.44A resolution
Sample
  • Complex: artificial protein cage, mTIP120-Ba
    • Protein or peptide: CoreN domain of artificial protein nanocage, mTIP120-Ba
    • Protein or peptide: CoreC domain of artificial protein nanocage, mTIP120-Ba
KeywordsArtificial designed protein complex / Protein cage / Protein nanoparticle / Metal-induced protein assembly / Protein metal complex / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.44 Å
AuthorsOhara N / Kawakami N / Arai R / Adachi N / Ikeda A / Senda T / Miyamoto K
Funding support Japan, 8 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101071 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121001 Japan
Japan Society for the Promotion of Science (JSPS)JP18K05324 Japan
Japan Society for the Promotion of Science (JSPS)JP17KK0104 Japan
Japan Society for the Promotion of Science (JSPS)JP19H02522 Japan
Japan Society for the Promotion of Science (JSPS)JP22J13988 Japan
Other privateJapan Association for Chemical Innovation (JACI) 8th Research Encouragement Award
Other privateKeio University Doctorate Student Grant-in-Aid Program from Ushioda Memorial Fund
CitationJournal: Angew Chem Int Ed Engl / Year: 2018
Title: Design of Hollow Protein Nanoparticles with Modifiable Interior and Exterior Surfaces.
Authors: Norifumi Kawakami / Hiroki Kondo / Yuki Matsuzawa / Kaoru Hayasaka / Erika Nasu / Kenji Sasahara / Ryoichi Arai / Kenji Miyamoto /
Abstract: Protein-based nanoparticles hold promise for a broad range of applications. Here, we report the production of a uniform anionic hollow protein nanoparticle, designated TIP60, which spontaneously ...Protein-based nanoparticles hold promise for a broad range of applications. Here, we report the production of a uniform anionic hollow protein nanoparticle, designated TIP60, which spontaneously assembles from a designed fusion protein subunit based on the geometric features of polyhedra. We show that TIP60 tolerates mutation and both its interior and exterior surfaces can be chemically modified. Moreover, TIP60 forms larger structures upon the addition of a cationic protein. Therefore, TIP60 can be used as a modifiable nano-building block for further molecular assembly.
History
DepositionJan 31, 2024-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38931.png

Downloads & links

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Map

FileDownload / File: emd_38931.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map, job066, postprocess, C1, 7.44A resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 540 pix.
= 453.6 Å		0.84 Å/pix.
x 540 pix.
= 453.6 Å		0.84 Å/pix.
x 540 pix.
= 453.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0064
Minimum - Maximum-0.011498429 - 0.020687206
Average (Standard dev.)-0.000008053852 (±0.0012079107)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 453.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38931_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: full map, job053, refine3d, C1, 8.40A resolution

Fileemd_38931_additional_1.map
Annotationfull map, job053, refine3d, C1, 8.40A resolution
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2, job053, refine3d, C1, 8.40A resolution

Fileemd_38931_half_map_1.map
Annotationhalf map 2, job053, refine3d, C1, 8.40A resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1, job053, refine3d, C1, 8.40A resolution

Fileemd_38931_half_map_2.map
Annotationhalf map 1, job053, refine3d, C1, 8.40A resolution
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : artificial protein cage, mTIP120-Ba

EntireName: artificial protein cage, mTIP120-Ba
Components
  • Complex: artificial protein cage, mTIP120-Ba
    • Protein or peptide: CoreN domain of artificial protein nanocage, mTIP120-Ba
    • Protein or peptide: CoreC domain of artificial protein nanocage, mTIP120-Ba

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Supramolecule #1: artificial protein cage, mTIP120-Ba

SupramoleculeName: artificial protein cage, mTIP120-Ba / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: metal-ion induced TIP120 (truncated icosahedral protein composed of 120-mer fusion proteins) complexed with barium ions
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.074 MDa

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Macromolecule #1: CoreN domain of artificial protein nanocage, mTIP120-Ba

MacromoleculeName: CoreN domain of artificial protein nanocage, mTIP120-Ba
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGSSHHHHHH SQDPKNIKIM RLVTGEDIIG NISESQGLIT IKKAFVIIPM QATP

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Macromolecule #2: CoreC domain of artificial protein nanocage, mTIP120-Ba

MacromoleculeName: CoreC domain of artificial protein nanocage, mTIP120-Ba
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGSSHHHHHH SQDPLEVLFQ GPGKPVQLVL SPWQPYTDDK EIVIDDSKVI TITSPKDDII KSYESHTRVL ENKQVEEILR LEKEIEDLQR MKEQQELSLT EASLQKLQER RDQELRRLEE E

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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

Concentration5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMHEPES2-[4-(2-hydroxyethyl)-1-piperazinyl]ethanesulfonic acid
100.0 mMNaClsodium chloride
0.04 mMBaCl2barium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: The grid was washed by acetone prior to use.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting time was 5 seconds (blot force 15).

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 6191 / Average exposure time: 4.66 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 366131
Startup modelType of model: OTHER
Details: An ab initio model was generated using RELION3's own implementation of Stochastic Gradient Descent (SGD) algorithm and low-pass filtered to 60 A for use as an initial model for Refine3D (C1).
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 7.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 81967
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final 3D classificationNumber classes: 4 / Avg.num./class: 26527 / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7xm1


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 582 / Target criteria: Correlation coefficient

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