[English] 日本語
Yorodumi
- PDB-7xm1: Cryo-EM structure of mTIP60-Ba (metal-ion induced TIP60 (K67E) co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xm1
TitleCryo-EM structure of mTIP60-Ba (metal-ion induced TIP60 (K67E) complex with barium ions
ComponentsTIP60 K67E mutant
KeywordsDE NOVO PROTEIN / Artificial designed protein complex / Protein cage / Protein nanoparticle / Metal-induced protein assembly / Protein metal complex
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.96 Å
AuthorsOhara, N. / Kawakami, N. / Arai, R. / Adachi, N. / Moriya, T. / Kawasaki, M. / Miyamoto, K.
Funding support Japan, 4items
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 Agency for Medical Research and Development (AMED)JP21am0101071 Japan
Citation
Journal: J Am Chem Soc / Year: 2023
Title: Reversible Assembly of an Artificial Protein Nanocage Using Alkaline Earth Metal Ions.
Authors: Naoya Ohara / Norifumi Kawakami / Ryoichi Arai / Naruhiko Adachi / Toshio Moriya / Masato Kawasaki / Kenji Miyamoto /
Abstract: Protein nanocages are of increasing interest for use as drug capsules, but the encapsulation and release of drug molecules at appropriate times require the reversible association and dissociation of ...Protein nanocages are of increasing interest for use as drug capsules, but the encapsulation and release of drug molecules at appropriate times require the reversible association and dissociation of the nanocages. One promising approach to addressing this challenge is the design of metal-dependent associating proteins. Such designed proteins typically have Cys or His residues at the protein surface for connecting the associating proteins through metal-ion coordination. However, Cys and His residues favor interactions with soft and borderline metal ions, such as Au and Zn, classified by the hard and soft acids and bases concept, restricting the types of metal ions available to drive association. Here, we show the alkaline earth (AE) metal-dependent association of the recently designed artificial protein nanocage TIP60, which is composed of 60-mer fusion proteins. The introduction of a Glu (hard base) mutation to the fusion protein (K67E mutant) prevented the formation of the 60-mer but formed the expected cage structure in the presence of Ca, Sr, or Ba ions (hard acids). Cryogenic electron microscopy (cryo-EM) analysis indicated a Ba ion at the interface of the subunits. Furthermore, we demonstrated the encapsulation and release of single-stranded DNA molecules using this system. Our results provide insights into the design of AE metal-dependent association and dissociation mechanisms for proteins.
#1: Journal: 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.
#2: Journal: Chem Commun (Camb) / Year: 2021
Title: Icosahedral 60-meric porous structure of designed supramolecular protein nanoparticle TIP60.
Authors: Junya Obata / Norifumi Kawakami / Akihisa Tsutsumi / Erika Nasu / Kenji Miyamoto / Masahide Kikkawa / Ryoichi Arai /
Abstract: Supramolecular protein nanoparticles and nanocages have potential in a broad range of applications. Recently, we developed a uniform supramolecular protein nanoparticle, TIP60, symmmetrically self- ...Supramolecular protein nanoparticles and nanocages have potential in a broad range of applications. Recently, we developed a uniform supramolecular protein nanoparticle, TIP60, symmmetrically self-assembled from fusion proteins of a pentameric Sm-like protein and a dimeric MyoX-coil domain. Herein, we report the icosahedral 60-meric structure of TIP60 solved using single-particle cryo-electron microscopy. Interestingly, the structure revealed 20 regular-triangle-like pores on the surface. TIP60 and its mutants have many modifiable sites on their exterior and interior surfaces. The TIP60 architecture will be useful in the development of biomedical and biochemical nanoparticles/nanocages for future applications.
History
DepositionApr 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / em_3d_fitting_list
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TIP60 K67E mutant
B: TIP60 K67E mutant
C: TIP60 K67E mutant
D: TIP60 K67E mutant
E: TIP60 K67E mutant
F: TIP60 K67E mutant
G: TIP60 K67E mutant
H: TIP60 K67E mutant
I: TIP60 K67E mutant
J: TIP60 K67E mutant
K: TIP60 K67E mutant
L: TIP60 K67E mutant
M: TIP60 K67E mutant
N: TIP60 K67E mutant
O: TIP60 K67E mutant
P: TIP60 K67E mutant
Q: TIP60 K67E mutant
R: TIP60 K67E mutant
S: TIP60 K67E mutant
T: TIP60 K67E mutant
V: TIP60 K67E mutant
W: TIP60 K67E mutant
X: TIP60 K67E mutant
Y: TIP60 K67E mutant
Z: TIP60 K67E mutant
AA: TIP60 K67E mutant
BA: TIP60 K67E mutant
CA: TIP60 K67E mutant
DA: TIP60 K67E mutant
EA: TIP60 K67E mutant
FA: TIP60 K67E mutant
GA: TIP60 K67E mutant
HA: TIP60 K67E mutant
IA: TIP60 K67E mutant
JA: TIP60 K67E mutant
KA: TIP60 K67E mutant
LA: TIP60 K67E mutant
MA: TIP60 K67E mutant
NA: TIP60 K67E mutant
OA: TIP60 K67E mutant
PA: TIP60 K67E mutant
QA: TIP60 K67E mutant
RA: TIP60 K67E mutant
SA: TIP60 K67E mutant
TA: TIP60 K67E mutant
UA: TIP60 K67E mutant
VA: TIP60 K67E mutant
WA: TIP60 K67E mutant
XA: TIP60 K67E mutant
YA: TIP60 K67E mutant
ZA: TIP60 K67E mutant
AB: TIP60 K67E mutant
BB: TIP60 K67E mutant
CB: TIP60 K67E mutant
DB: TIP60 K67E mutant
EB: TIP60 K67E mutant
FB: TIP60 K67E mutant
GB: TIP60 K67E mutant
HB: TIP60 K67E mutant
IB: TIP60 K67E mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,075,889120
Polymers1,067,65060
Non-polymers8,24060
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, Molecular weight = 1033 kDa, SAXS, Rg = 9.4 nm Dmax = 21.8 nm
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein ...
TIP60 K67E mutant


Mass: 17794.160 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Gene: TIP60 / Variant: K67E / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical...
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: mTIP60-Ba / Type: COMPLEX
Details: metal-ion induced TIP60 (truncated icosahedral protein composed of 60-mer fusion proteins) complexed with barium ions
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 1.074 MDa / Experimental value: YES
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pETDuet-1
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
125 mM2-[4-(2-hydroxyethyl)-1-piperazinyl]ethanesulfonic acidHEPES1
2100 mMsodium chlorideNaClSodium chloride1
30.3 mMbarium chlorideBaCl21
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: The grid was washed by acetone prior to use. / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K / Details: Blotting time was 15 seconds (blot force 5)

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 120000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 66.42 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2206
Image scansWidth: 4096 / Height: 4096

-
Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPUimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
14PHENIX1.19model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 113155
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61251 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 22.77 / Protocol: OTHER / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 7EQ9

7eq9


Pdb chain-ID: A / Accession code: 7EQ9 / Pdb chain residue range: 2-136 / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 22.84 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002460660
ELECTRON MICROSCOPYf_angle_d0.427281540
ELECTRON MICROSCOPYf_chiral_restr0.04339780
ELECTRON MICROSCOPYf_plane_restr0.002210380
ELECTRON MICROSCOPYf_dihedral_angle_d3.17367740

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more