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- EMDB-64381: Cryo-EM structure of pyrene-modified TIP60 double mutant (G12C/S5... -

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Entry
Database: EMDB / ID: EMD-64381
TitleCryo-EM structure of pyrene-modified TIP60 double mutant (G12C/S50C) with addition of Nile Red
Map dataPostprocess map, I symmetry, 3.8A resolution
Sample
  • Complex: Pyrene-modified TIP60 double mutant (G12C/S50C) with addition of Nile Red
    • Protein or peptide: TIP60 double mutant (G12C/S50C)
  • Ligand: N-(1-pyrenyl)maleimide
KeywordsArtificial designed protein complex / Fusion protein / Protein nanocage / Protein nanoparticle / Pyrene modification / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYamashita M / Kawakami N / Arai R / Ikeda A / Moriya T / Senda T / Miyamoto K
Funding support Japan, 8 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP24ama121001 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)JP24K01267 Japan
Japan Society for the Promotion of Science (JSPS)JP24KJ1946 Japan
Japan Science and TechnologyJPMJSP2123 Japan
Other privateJapan Association for Chemical Innovation (JACI) 8th Research Encouragement Award Japan
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
DepositionApr 26, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64381.png

Downloads & links

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Map

FileDownload / File: emd_64381.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocess map, I symmetry, 3.8A resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 384 pix.
= 425.088 Å		1.11 Å/pix.
x 384 pix.
= 425.088 Å		1.11 Å/pix.
x 384 pix.
= 425.088 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.107 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.014938145 - 0.03736352
Average (Standard dev.)-0.00018053908 (±0.0017764544)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 425.088 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64381_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Full map, Refine3D, I symmetry, 3.8A resolution

Fileemd_64381_additional_1.map
AnnotationFull map, Refine3D, I symmetry, 3.8A resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2, Refine3D, I symmetry, 3.8A resolution

Fileemd_64381_half_map_1.map
AnnotationHalf map 2, Refine3D, I symmetry, 3.8A resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1, Refine3D, I symmetry, 3.8A resolution

Fileemd_64381_half_map_2.map
AnnotationHalf map 1, Refine3D, I symmetry, 3.8A resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pyrene-modified TIP60 double mutant (G12C/S50C) with addition of ...

EntireName: Pyrene-modified TIP60 double mutant (G12C/S50C) with addition of Nile Red
Components
  • Complex: Pyrene-modified TIP60 double mutant (G12C/S50C) with addition of Nile Red
    • Protein or peptide: TIP60 double mutant (G12C/S50C)
  • Ligand: N-(1-pyrenyl)maleimide

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Supramolecule #1: Pyrene-modified TIP60 double mutant (G12C/S50C) with addition of ...

SupramoleculeName: Pyrene-modified TIP60 double mutant (G12C/S50C) with addition of Nile Red
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Pyrene-modified TIP60 (Truncated Icosahedral Protein composed of 60-mer fusion proteins) double mutant (G12C/S50C) with addition of Nile Red
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.108 MDa

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Macromolecule #1: TIP60 double mutant (G12C/S50C)

MacromoleculeName: TIP60 double mutant (G12C/S50C) / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 17.856383 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGSSHHHHHH SQDPKNIKIM RLVTCEDIIG NISESQGLIT IKKAFVIIPM QATPGKPVQL VLCPWQPYTD DKEIVIDDSK VITITSPKD DIIKSYESHT RVLENKQVEE ILRLEKEIED LQRMKEQQEL SLTEASLQKL QERRDQELRR LEEE

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Macromolecule #2: N-(1-pyrenyl)maleimide

MacromoleculeName: N-(1-pyrenyl)maleimide / type: ligand / ID: 2 / Number of copies: 120 / Formula: A1L9F
Molecular weightTheoretical: 297.307 Da

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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

Concentration12.4 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC4H12ClNO3Tris-HCl
1.0 mMC10H16N2O8EDTA

Details: 20 mM Tris-HCl, 1 mM EDTA
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
Details: PIB-10 (Vacuum Device Inc.) was used for glow discharge.
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
TemperatureMin: 77.0 K / Max: 100.0 K
SoftwareName: EPU
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: 2110 / Average exposure time: 6.02 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: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 92000
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

Particle selectionNumber selected: 235783 / Details: Topaz auto-picking
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: An ab initio model was generated using RELION4 with variable-metric gradient descent (VDAM) algorithm.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.2) / Number images used: 22050
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.2)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 4.0.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7eq9


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: Coot
RefinementSpace: REAL / Protocol: OTHER / Target criteria: Correlation coefficient
Output model

PDB-9uol:
Cryo-EM structure of pyrene-modified TIP60 double mutant (G12C/S50C) with addition of Nile Red

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