9UOL | pdb_00009uol

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

misteINK: a protein nanocage-based ink with reversible, stimuli-responsive color shifts.

Yamashita, M.Kawakami, N.Arai, R.Ikeda, A.Moriya, T.Senda, T.Miyamoto, K.

(2025) Biomater Sci 13: 6652-6661

  • DOI: https://doi.org/10.1039/d5bm01052g
  • Primary Citation of Related Structures:  
    9UOL

  • PubMed Abstract: 

    Dyes exhibiting polarity-dependent color changes, known as solvatochromism, have great potential for creating sensors, smart materials, and responsive coatings. However, full-range color shifts require a technique to disperse dyes across a wide range of solvent polarities, which remains a persistent challenge. For example, hydrophobic dyes often aggregate in water, preventing effective color shifts. Although surfactants can assist in dye dispersion, they can also prevent solvent molecules from accessing the dye. To address this, we used a 60-mer protein nanocage, TIP60, with a densely pyrene-modified interior surface. The modification did not induce protein denaturation, as monitored by small-angle X-ray scattering, and greatly increased the aqueous solubility of a hydrophobic solvatochromic dye, Nile Red (NR), while preserving its fluorescence. The NR-loaded solution appeared blue, reflecting the polar environment surrounding NR. Cryogenic electron microscopy suggested that the pyrenes interacted with each other to form a binding site for NR. This interaction also contributed to thermostability of TIP60 (65 °C to 86 °C) and stability against sodium dodecyl sulfate, as observed by electrophoresis experiments. When brushed onto plain copy paper, the NR-loaded nanocage appeared bluish-purple and shifted reversibly to purplish red upon heating, returning on cooling-presumably via nanocage dissociation and reassembly. The color change was also sensitive to humidity. We term this material "misteINK", a protein-based ink with reversible temperature- and humidity-dependent color changes. These findings demonstrate that a single-step interior modification enables the rational design of protein materials for tuning dye photophysics, providing a powerful strategy for designing protein-based functional materials.


  • Organizational Affiliation
    • Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan. norikawakami@bio.keio.ac.jp.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TIP60 double mutant (G12C/S50C)153synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L9F (Subject of Investigation/LOI)
Query on A1L9F

Download Ideal Coordinates CCD File 
AC [auth J]
AD [auth X]
AE [auth KA]
AF [auth XA]
BC [auth J]
AC [auth J],
AD [auth X],
AE [auth KA],
AF [auth XA],
BC [auth J],
BD [auth X],
BE [auth KA],
BF [auth XA],
CC [auth K],
CD [auth Y],
CE [auth LA],
CF [auth YA],
DC [auth K],
DD [auth Y],
DE [auth LA],
DF [auth YA],
EC [auth L],
ED [auth Z],
EE [auth MA],
EF [auth ZA],
FC [auth L],
FD [auth Z],
FE [auth MA],
FF [auth ZA],
GC [auth M],
GD [auth AA],
GE [auth NA],
GF [auth AB],
HC [auth M],
HD [auth AA],
HE [auth NA],
HF [auth AB],
IB [auth A],
IC [auth N],
ID [auth BA],
IE [auth OA],
IF [auth BB],
JB [auth A],
JC [auth N],
JD [auth BA],
JE [auth OA],
JF [auth BB],
KB [auth B],
KC [auth O],
KD [auth CA],
KE [auth PA],
KF [auth CB],
LB [auth B],
LC [auth O],
LD [auth CA],
LE [auth PA],
LF [auth CB],
MB [auth C],
MC [auth P],
MD [auth DA],
ME [auth QA],
MF [auth DB],
NB [auth C],
NC [auth P],
ND [auth DA],
NE [auth QA],
NF [auth DB],
OB [auth D],
OC [auth Q],
OD [auth EA],
OE [auth RA],
OF [auth EB],
PB [auth D],
PC [auth Q],
PD [auth EA],
PE [auth RA],
PF [auth EB],
QB [auth E],
QC [auth R],
QD [auth FA],
QE [auth SA],
QF [auth FB],
RB [auth E],
RC [auth R],
RD [auth FA],
RE [auth SA],
RF [auth FB],
SB [auth F],
SC [auth S],
SD [auth GA],
SE [auth TA],
SF [auth GB],
TB [auth F],
TC [auth S],
TD [auth GA],
TE [auth TA],
TF [auth GB],
UB [auth G],
UC [auth T],
UD [auth HA],
UE [auth UA],
UF [auth HB],
VB [auth G],
VC [auth T],
VD [auth HA],
VE [auth UA],
VF [auth HB],
WB [auth H],
WC [auth V],
WD [auth IA],
WE [auth VA],
WF [auth IB],
XB [auth H],
XC [auth V],
XD [auth IA],
XE [auth VA],
XF [auth IB],
YB [auth I],
YC [auth W],
YD [auth JA],
YE [auth WA],
ZB [auth I],
ZC [auth W],
ZD [auth JA],
ZE [auth WA]
N-(1-pyrenyl)maleimide
C20 H11 N O2
YXKWRQLPBHVBRP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONRELION4.0.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP24ama121001
Japan Society for the Promotion of Science (JSPS)JapanJP18K05324
Japan Society for the Promotion of Science (JSPS)JapanJP17KK0104
Japan Society for the Promotion of Science (JSPS)JapanJP19H02522
Japan Society for the Promotion of Science (JSPS)JapanJP24K01267
Japan Society for the Promotion of Science (JSPS)JapanJP24KJ1946
Japan Science and TechnologyJapanJPMJSP2123
Other privateJapanJapan Association for Chemical Innovation (JACI) 8th Research Encouragement Award

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2025-11-26
    Changes: Data collection, Database references