2025-11-26 REL PDBj INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.page_first _citation.page_last _em_admin.last_update PDBj PDBj 2025-04-26 2025-11-19 2025-11-19 2025-11-26 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 Technology JPMJSP2123 Japan Other private Japan Association for Chemical Innovation (JACI) 8th Research Encouragement Award Japan Cryo-EM structure of pyrene-modified TIP60 double mutant (G12C/S50C) with addition of Nile Red Yamashita M Kawakami N Arai R Ikeda A Moriya T Senda T Miyamoto K Artificial designed protein complex, Fusion protein, Protein nanocage, Protein nanoparticle, Pyrene modification, DE NOVO PROTEIN Yamashita M Kawakami N Arai R Ikeda A Moriya T Senda T Miyamoto K misteINK: a protein nanocage-based ink with reversible, stimuli-responsive color shifts. Biomater Sci 13 6652 6661 2025 41099093 doi:10.1039/d5bm01052g 2047-4849 Yamashita M Kawakami N Miyamoto K Hydrophobization of a TIP60 Protein Nanocage for the Encapsulation of Hydrophobic Compounds. Chempluschem DE 2023 36775805 doi:10.1002/cplu.202200392 2192-650 0353 Obata J Kawakami N Tsutsumi A Nasu E Miyamoto K Kikkawa M Arai R Icosahedral 60-meric porous structure of designed supramolecular protein nanoparticle TIP60. CHEM.COMMUN.(CAMB.) UK 2021 34523636 doi:10.1039/d1cc03114g 1364-548X 0353 Kawakami N Kondo H Matsuzawa Y Hayasaka K Nasu E Sasahara K Arai R Miyamoto K Design of Hollow Protein Nanoparticles with Modifiable Interior and Exterior Surfaces. Angew.Chem.Int.Ed.Engl. GE 2018 30066354 doi:10.1002/anie.201805565 1433-7851 0353 9uol FULLOVERLAP PDB 7EQ9 unspecified
The structure of the original TIP60.
 EMDB EMD-64381 associated EM volume
Cryo-EM structure of pyrene-modified TIP60 double mutant (G12C/S50C) with addition of Nile Red
 Pyrene-modified TIP60 double mutant (G12C/S50C) with addition of Nile Red Pyrene-modified TIP60 double mutant (G12C/S50C) with addition of Nile Red 0 1
Pyrene-modified TIP60 (Truncated Icosahedral Protein composed of 60-mer fusion proteins) double mutant (G12C/S50C) with addition of Nile Red
synthetic construct 1.108 TIP60 double mutant (G12C/S50C) synthetic construct 0.017856383 60 Escherichia coli BL21(DE3) LEVO MGSSHHHHHHSQDPKNIKIMRLVTCEDIIGNISESQGLITIKKAFVIIPMQATPGKPVQLVLCPWQPYTDDKEIVIDDSK VITITSPKDDIIKSYESHTRVLENKQVEEILRLEKEIEDLQRMKEQQELSLTEASLQKLQERRDQELRRLEEE N-(1-pyrenyl)maleimide 0.000297307 120 A1L9F singleParticle particle 12.4 7.4 20.0 C4H12ClNO3 Tris-HCl 1.0 C10H16N2O8 EDTA
20 mM Tris-HCl, 1 mM EDTA
 Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY ARRAY GLOW DISCHARGE
PIB-10 (Vacuum Device Inc.) was used for glow discharge.
 ETHANE 100 291 FEI VITROBOT MARK IV
Blotting time was 5 seconds (blot force 15).
FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 1.0 2.5 92000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 77.0 100.0 EPU FEI FALCON IV (4k x 4k) COUNTING 4096 4096 1 2110 6.02 50.0 1 235783
Topaz auto-picking
 CTFFIND 4.1.14 PHASE FLIPPING AND AMPLITUDE CORRECTION
An ab initio model was generated using RELION4 with variable-metric gradient descent (VDAM) algorithm.
 1 I FOURIER SPACE 3.8 FSC 0.143 CUT-OFF RELION 4.0.2 22050 MAXIMUM LIKELIHOOD RELION 4.0.2 MAXIMUM LIKELIHOOD RELION 4.0.2 4 RELION 4.0.2 emd_64381.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 425.088 425.088 425.088 90.0 90.0 90.0 X Y Z -0.014938145 0.03736352 -0.00018053908 0.0017764544 1.107 1.107 1.107 0.008 AUTHOR Postprocess map, I symmetry, 3.8A resolution 7EQ9 PDB experimental model OTHER Coot Correlation coefficient REAL emd_64381_msk_1.map emd_64381_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 425.088 425.088 425.088 90.0 90.0 90.0 X Y Z -0.0015391919 0.01647052 -0.00018021005 0.0014246115 1.107 1.107 1.107 AUTHOR Full map, Refine3D, I symmetry, 3.8A resolution emd_64381_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 425.088 425.088 425.088 90.0 90.0 90.0 X Y Z -0.0047971997 0.018663142 -0.00019700022 0.0015318181 1.107 1.107 1.107 AUTHOR Half map 1, Refine3D, I symmetry, 3.8A resolution emd_64381_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 425.088 425.088 425.088 90.0 90.0 90.0 X Y Z -0.004858713 0.017524047 -0.00016393936 0.0015341702 1.107 1.107 1.107 AUTHOR Half map 2, Refine3D, I symmetry, 3.8A resolution