7EQ9

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

PDB DOI: https://doi.org/10.2210/pdb7EQ9/pdb
EM Map EMD-31256: EMDB EMDataResource

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-04-30 Released: 2021-09-15
Deposition Author(s): Obata, J., Kawakami, N., Tsutsumi, A., Miyamoto, K., Kikkawa, M., Arai, R.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Icosahedral 60-meric porous structure of designed supramolecular protein nanoparticle TIP60.

Obata, J., Kawakami, N., Tsutsumi, A., Nasu, E., Miyamoto, K., Kikkawa, M., Arai, R.

(2021) Chem Commun (Camb) 57: 10226-10229

PubMed: 34523636 Search on PubMed
DOI: https://doi.org/10.1039/d1cc03114g
Primary Citation of Related Structures:
7EQ9

PubMed 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-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.

Organizational Affiliation

Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Ueda, Nagano 386-8567, Japan. rarai@shinshu-u.ac.jp.

Macromolecule Content

Total Structure Weight: 1,067.65 kDa
Atom Count: 62,520
Modelled Residue Count: 7,620
Deposited Residue Count: 9,180
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TIP60	A AA [auth BA] AB [auth BB] B BA [auth CA] A, AA [auth BA], AB [auth BB], B, BA [auth CA], BB [auth CB], C, CA [auth DA], CB [auth DB], D, DA [auth EA], DB [auth EB], E, EA [auth FA], EB [auth FB], F, FA [auth GA], FB [auth GB], G, GA [auth HA], GB [auth HB], H, HA [auth IA], HB [auth IB], I, IA [auth JA], J, JA [auth KA], K, KA [auth LA], L, LA [auth MA], M, MA [auth NA], N, NA [auth OA], O, OA [auth PA], P, PA [auth QA], Q, QA [auth RA], R, RA [auth SA], S, SA [auth TA], T, TA [auth UA], U [auth V], UA [auth VA], V [auth W], VA [auth WA], W [auth X], WA [auth XA], X [auth Y], XA [auth YA], Y [auth Z], YA [auth ZA], Z [auth AA], ZA [auth AB]	153	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1.19

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-09-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H02522
Japan Society for the Promotion of Science (JSPS)	Japan	JP18K05324
Japan Society for the Promotion of Science (JSPS)	Japan	JP17KK0104
Japan Society for the Promotion of Science (JSPS)	Japan	JP16K05841
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101115