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- EMDB-31256: Cryo-EM structure of designed protein nanoparticle TIP60 (Truncat... -

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Entry
Database: EMDB / ID: EMD-31256
TitleCryo-EM structure of designed protein nanoparticle TIP60 (Truncated Icosahedral Protein composed of 60-mer fusion proteins)
Map dataSharpened map by auto-sharpen in Phenix, based on locally-filtered and sharpened map by Relion
Sample
  • Complex: 60-meric complex of designed fusion proteins TIP60
    • Protein or peptide: TIP60
KeywordsArtificial designed protein complex / VIRUS LIKE PARTICLE / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsObata J / Kawakami N
Funding support Japan, 5 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19H02522 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)JP16K05841 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101115 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 30, 2021-
Header (metadata) releaseSep 15, 2021-
Map releaseSep 15, 2021-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7eq9
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7eq9
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31256.png

Downloads & links

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Map

FileDownload / File: emd_31256.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map by auto-sharpen in Phenix, based on locally-filtered and sharpened map by Relion
Voxel sizeX=Y=Z: 1.545 Å
Density
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-13.33911 - 23.471050000000002
Average (Standard dev.)0.000000000005809 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 309.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.5451.5451.545
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z309.000309.000309.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-13.33923.4710.000

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Supplemental data

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Mask #1

Fileemd_31256_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Raw full map

Fileemd_31256_additional_1.map
AnnotationRaw full map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_31256_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_31256_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : 60-meric complex of designed fusion proteins TIP60

EntireName: 60-meric complex of designed fusion proteins TIP60
Components
  • Complex: 60-meric complex of designed fusion proteins TIP60
    • Protein or peptide: TIP60

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Supramolecule #1: 60-meric complex of designed fusion proteins TIP60

SupramoleculeName: 60-meric complex of designed fusion proteins TIP60 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: 60-meric complex of designed fusion proteins of a pentameric Sm-like protein (3BY7) and a dimeric MyoX-coil domain (2LW9)
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.066 MDa

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Macromolecule #1: TIP60

MacromoleculeName: TIP60 / type: protein_or_peptide / ID: 1
Details: Designed fusion protein of pentameric Sm-like protein (3BY7) and dimeric MyoX-coil domain (2LW9)
Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 17.794227 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGSSHHHHHH SQDPKNIKIM RLVTGEDIIG NISESQGLIT IKKAFVIIPM QATPGKPVQL VLSPWQPYTD DKEIVIDDSK VITITSPKD DIIKSYESHT RVLENKQVEE ILRLEKEIED LQRMKEQQEL SLTEASLQKL QERRDQELRR LEEE

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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
20.0 mMTristris(hydroxymethyl)aminomethane
300.0 mMNaClSodium chloridesodium chloride
1.0 mMEDTAEthylenediaminetetraacetic acidethylenediaminetetraacetic acid
GridModel: Quantifoil R2/1 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number real images: 1755 / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 175419
Startup modelType of model: OTHER / Details: stochastic gradient descent algorithm
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 1 / Avg.num./class: 115596 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 115596
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3by7

chain_id: A, residue_range: 2-86, source_name: PDB, initial_model_type: experimental model

2lw9

chain_id: A, residue_range: 1-47, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: BACKBONE TRACE / Overall B value: 205.47 / Target criteria: Correlation coefficient
Output model

PDB-7eq9:
Cryo-EM structure of designed protein nanoparticle TIP60 (Truncated Icosahedral Protein composed of 60-mer fusion proteins)

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