Nature Search

Structural Mechanism of Receptor-Triggered MyD88 Oligomeric Assembly in Innate Immune Signaling

MyD88 is an immune adaptor protein that self-assembles via its TIR domain to initiate TLR and inflammatory signaling. Here, authors reveal the cryo-EM structure of MyD88 TIR filaments and show how dimerized receptors directly nucleate this assembly.

Kazuki Kasai
Kayo Imamura
Hidehito Tochio
ResearchOpen Access17 Apr 2026
Nature Communications

P: 1-13
Native flagellar MS ring is formed by 34 subunits with 23-fold and 11-fold subsymmetries

The bacterial flagellar MS ring is a core transmembrane complex within the flagellar basal body. Here, cryoEM analysis suggests that the MS ring is formed by 34 full-length FliF subunits, with 23- and 11-fold subsymmetries in the inner and middle M ring, respectively.

Akihiro Kawamoto
Tomoko Miyata
Keiichi Namba
ResearchOpen Access09 Jul 2021
Nature Communications

Volume: 12, P: 1-10
Clinical characteristics of EYS-associated retinal dystrophy in 291 Japanese patients

Yoshito Koyanagi
Yusuke Murakami
Yasuhiro Ikeda
ResearchOpen Access06 Dec 2025
npj Genomic Medicine

Volume: 11, P: 1-9
Cholesterol-functionalized DNA/RNA heteroduplexes cross the blood–brain barrier and knock down genes in the rodent CNS

Genes in the rodent brain are knocked down by DNA/RNA heteroduplexes injected intravenously.

Tetsuya Nagata
Chrissa A. Dwyer
Takanori Yokota
Research12 Aug 2021
Nature Biotechnology

Volume: 39, P: 1529-1536
Structure of the native supercoiled flagellar hook as a universal joint

The bacterial flagellar hook is a molecular universal joint that connects the rotary motor and long helical propeller of the bacterial flagellum. Here the authors present the 3.6 Å resolution cryo-EM structure of the native supercoiled Salmonella hook that provides insights into the dynamic changes of subunit conformations and intermolecular interactions of the hook protein FlgE.

Takayuki Kato
Fumiaki Makino
Keiichi Namba
ResearchOpen Access22 Nov 2019
Nature Communications

Volume: 10, P: 1-8
The clamp-loading complex for processive DNA replication

Tomoko Miyata
Takuji Oyama
Kosuke Morikawa
Research20 Jun 2004
Nature Structural & Molecular Biology

Volume: 11, P: 632-636
Elevation of serum interleukins 8, 4 and 1β levels in patients with gastrointestinal low-grade B-cell lymphoma

Tomoko Miyata-Takata
Katsuyoshi Takata
Tadashi Yoshino
ResearchOpen Access17 Dec 2015
Scientific Reports

Volume: 5, P: 1-7
Structure of the molecular bushing of the bacterial flagellar motor

In the basal body of the bacterial flagellum, the LP ring acts as a bushing supporting the distal rod for its rapid and stable rotation. Here, Yamaguchi et al. present the electron cryomicroscopy structure of the LP ring around the rod, shedding light into potential mechanisms involved in stability and assembly of the structure.

Tomoko Yamaguchi
Fumiaki Makino
Keiichi Namba
ResearchOpen Access22 Jul 2021
Nature Communications

Volume: 12, P: 1-12
Optical Coherence Tomography Angiography to Estimate Retinal Blood Flow in Eyes with Retinitis Pigmentosa

Masako Sugahara
Manabu Miyata
Nagahisa Yoshimura
ResearchOpen Access13 Apr 2017
Scientific Reports

Volume: 7, P: 1-10
Activation of Hsp70 reduces neurotoxicity by promoting polyglutamine protein degradation

An allosteric activator of Hsp70 mimics Hip and reduces neurotoxicity in a model for spinobulbar muscular atrophy by promoting ubiquitination and degradation of oligomeric polyglutamine-containing clients.

Adrienne M Wang
Yoshinari Miyata
Andrew P Lieberman
Research09 Dec 2012
Nature Chemical Biology

Volume: 9, P: 112-118
Membrane structure-responsive lipid scrambling by TMEM63B to control plasma membrane lipid distribution

By combining genome-wide clustered regularly interspaced short palindromic repeats with Cas9 screening and cryo-electron microscopy structure analysis, the authors identified transmembrane protein 63B as a lipid scramblase that detects structural changes in the lipid bilayer and scrambles lipids to regulate membrane lipid distributions.

Yugo Miyata
Katsuya Takahashi
Katsumori Segawa
ResearchOpen Access18 Oct 2024
Nature Structural & Molecular Biology

Volume: 32, P: 185-198
Common architecture of the flagellar type III protein export apparatus and F- and V-type ATPases

FliJ interacts with many flagellar proteins involved in protein export, but its function was unclear. Now the crystal structure of FliJ shows it is a homolog of the F1-ATPase γ-subunit. Binding of FliI to FliJ promotes FliI hexameric ring formation, suggesting that flagellar type III protein export systems and F1-ATP synthase use a similar mechanism.

Tatsuya Ibuki
Katsumi Imada
Keiichi Namba
Research30 Jan 2011
Nature Structural & Molecular Biology

Volume: 18, P: 277-282
Identical folds used for distinct mechanical functions of the bacterial flagellar rod and hook

The bacterial flagellum is a motile organelle that enables bacterial movement. Here the authors explain how the structurally similar flagellum components FlgG and FlgE can give rise to distinct macrostructures—the rod and hook—through subtle differences in domain orientation attributable to a short N-terminal insertion in FlgG.

Takashi Fujii
Takayuki Kato
Keiichi Namba
ResearchOpen Access25 Jan 2017
Nature Communications

Volume: 8, P: 1-10
Charge transfer emission between π- and 4f-orbitals in a trivalent europium complex

Photoinduced metal-to-ligand (or ligand-to-metal) charge-transfer (CT) states in metal complexes have been extensively studied, but primarily limited to CT transitions between d- and π-orbitals. Here, CT emission from 4f- to π-orbitals is demonstrated using a trivalent europium complex.

Yuichi Kitagawa
Toranosuke Tomikawa
Yasuchika Hasegawa
ResearchOpen Access28 Jan 2025
Communications Chemistry

Volume: 8, P: 1-6
Association between choriocapillaris flow deficit and choroidal neovascularization activity in eyes with myopic choroidal neovascularization

Sato Uematsu
Hirokazu Sakaguchi
Kohji Nishida
ResearchOpen Access09 Nov 2021
Scientific Reports

Volume: 11, P: 1-8
Straight and rigid flagellar hook made by insertion of the FlgG specific sequence into FlgE

Koichi D. Hiraoka
Yusuke V. Morimoto
Keiichi Namba
ResearchOpen Access21 Apr 2017
Scientific Reports

Volume: 7, P: 1-8
Progression of retinitis pigmentosa on static perimetry, optical coherence tomography, and fundus autofluorescence

Yuhei Iga
Tomoko Hasegawa
Akitaka Tsujikawa
ResearchOpen Access12 Dec 2023
Scientific Reports

Volume: 13, P: 1-10
Common and distinct structural features of Salmonella injectisome and flagellar basal body

Akihiro Kawamoto
Yusuke V. Morimoto
Keiichi Namba
ResearchOpen Access28 Nov 2013
Scientific Reports

Volume: 3, P: 1-6
Evaluation of outer nuclear layer overshadowed by retinal vessels in retinitis pigmentosa

Yuki Otsuka
Akio Oishi
Akitaka Tsujikawa
Research11 May 2021
Eye

Volume: 36, P: 1042-1049
Relationship between Ocular Deviation and Visual Function in Retinitis Pigmentosa

Manabu Miyata
Akio Oishi
Akitaka Tsujikawa
ResearchOpen Access05 Oct 2018
Scientific Reports

Volume: 8, P: 1-9
Wavelength of light and photophobia in inherited retinal dystrophy

Yuki Otsuka
Akio Oishi
Akitaka Tsujikawa
ResearchOpen Access09 Sept 2020
Scientific Reports

Volume: 10, P: 1-6
Up-regulation of activation-induced cytidine deaminase and its strong expression in extra-germinal centres in IgG4-related disease

Yuka Gion
Mai Takeuchi
Yasuharu Sato
ResearchOpen Access24 Jan 2019
Scientific Reports

Volume: 9, P: 1-6
Thymic stromal lymphopoietin induces corticosteroid resistance in natural helper cells during airway inflammation

Allergic airway inflammation in asthma can be treated with corticosteroids, but some patients remain unresponsive to this therapy. Here, Kabata et al. show that thymic stromal lymphopoietin contributes to the corticosteroid resistance during airway inflammation through its action on natural helper cells.

Hiroki Kabata
Kazuyo Moro
Koichiro Asano
Research25 Oct 2013
Nature Communications

Volume: 4, P: 1-10
Construction of a system using a deep learning algorithm to count cell numbers in nanoliter wells for viable single-cell experiments

Takashi Kamatani
Koichi Fukunaga
Sotaro Uemura
ResearchOpen Access04 Dec 2017
Scientific Reports

Volume: 7, P: 1-8
A subset of ocular adnexal marginal zone lymphomas may arise in association with IgG4-related disease

Kyotaro Ohno
Yasuharu Sato
Tadashi Yoshino
ResearchOpen Access27 Aug 2015
Scientific Reports

Volume: 5, P: 1-10
Dissection of the polygenic architecture of neuronal Aβ production using a large sample of individual iPSC lines derived from Alzheimer’s disease patients

Using more than 100 independent iPSC lines derived from patients with Alzheimer’s disease, the authors discovered loci associated with the neuronal production of amyloid β and confirmed their influence using RNA interference.

Takayuki Kondo
Norikazu Hara
Haruhisa Inoue
Research17 Feb 2022
Nature Aging

Volume: 2, P: 125-139
DNA/RNA heteroduplex oligonucleotide for highly efficient gene silencing

Antisense oligonucleotides (ASOs) can repress the expression of specific genes. Here, the authors show that a DNA/RNA heteroduplex oligonucleotide (HDO) with a structure different from ASOs is more potent in suppressing target gene expression, and causes a less adverse effect in mouse liver.

Kazutaka Nishina
Wenying Piao
Takanori Yokota
ResearchOpen Access10 Aug 2015
Nature Communications

Volume: 6, P: 1-13
Distinctive and functional pigment arrangements in Lhcp, a prasinophyte-specific photosynthetic light-harvesting complex

The 1.94 Å cryo-EM structure of the Lhcp trimer from a prasinophyte Ostreococcus tauri reveals all pigments, including a unique carotenoid aiding trimer stabilization. Comparison with LHCII links structural differences to enhanced blue light absorption.

Soichiro Seki
Masato Kubota
Ritsuko Fujii
ResearchOpen Access17 Nov 2025
Communications Biology

Volume: 8, P: 1-11
Production of Sry knockout mouse using TALEN via oocyte injection

Tomoko Kato
Kohei Miyata
Shuji Takada
ResearchOpen Access05 Nov 2013
Scientific Reports

Volume: 3, P: 1-8
Development of a 1:1-binding biparatopic anti-TNFR2 antagonist by reducing signaling activity through epitope selection

Biparatopic antibodies binding to two different epitopes of tumor necrosis factor receptor 2 (TNFR2) are developed, and one of them binds TNFR2 in a 1:1 manner, functions as an antagonist without transducing intracellular signal.

Hiroki Akiba
Junso Fujita
Kouhei Tsumoto
ResearchOpen Access27 Sept 2023
Communications Biology

Volume: 6, P: 1-12
Structural basis for assembly and function of the Salmonella flagellar MS-ring with three different symmetries

Kinoshita et. al. demonstrate that the flagellar MS-ring, essential for flagellar assembly, forms through FliF subunits adopting two conformations, generating three distinct symmetries. Using cryoEM and mutational analyses, they identified the conserved DQxGxxL motif as key to this process, enabling precise assembly critical for housing the flagellar protein export complex.

Miki Kinoshita
Fumiaki Makino
Tohru Minamino
ResearchOpen Access16 Jan 2025
Communications Biology

Volume: 8, P: 1-13
A deep learning approach to predict differentiation outcomes in hypothalamic-pituitary organoids

A deep learning model predicts gene expression and subsequent adrenocorticotropic hormone secretory function in the differentiation process of hypothalamic–pituitary organoids.

Tomoyoshi Asano
Hidetaka Suga
Hiroshi Arima
ResearchOpen Access06 Dec 2024
Communications Biology

Volume: 7, P: 1-10
Post hoc analysis of a randomized placebo-controlled trial suggests potential visual benefits of branched-chain amino acids in retinitis pigmentosa

Tomoko Hasegawa
Hanako Ohashi Ikeda
Akitaka Tsujikawa
ResearchOpen Access01 Jul 2025
Scientific Reports

Volume: 15, P: 1-8
Hypoglycemia and hyperinsulinemia induced by phenolic uremic toxins in CKD and DKD patients

Yoshiyasu Tongu
Tomoko Kasahara
Takaaki Abe
ResearchOpen Access17 Feb 2025
Scientific Reports

Volume: 15, P: 1-14
Differentiation of human induced pluripotent stem cells into hypothalamic vasopressin neurons with minimal exogenous signals and partial conversion to the naive state

Hajime Ozaki
Hidetaka Suga
Hiroshi Arima
ResearchOpen Access17 Oct 2022
Scientific Reports

Volume: 12, P: 1-11
Blood pressure during long-term cilostazol-based dual antiplatelet therapy after stroke: a post hoc analysis of the CSPS.com trial

Kazunori Toyoda
Masatoshi Koga
Hiroaki Tanaka
ResearchOpen Access09 Jul 2024
Hypertension Research

Volume: 47, P: 2238-2249
Higher longitudinal brain white matter atrophy rate in aquaporin-4 IgG-positive NMOSD compared with healthy controls

Hiroki Masuda
Masahiro Mori
Satoshi Kuwabara
ResearchOpen Access03 Aug 2023
Scientific Reports

Volume: 13, P: 1-14
Anti-tumor effects of anti-programmed cell death-1 antibody treatment are attenuated in streptozotocin-induced diabetic mice

Masaaki Ito
Shintaro Iwama
Hiroshi Arima
ResearchOpen Access12 Apr 2023
Scientific Reports

Volume: 13, P: 1-11
GABA_B receptor signaling in the caudate putamen is involved in binge-like consumption during a high fat diet in mice

Runan Sun
Taku Tsunekawa
Hiroshi Arima
ResearchOpen Access29 Sept 2021
Scientific Reports

Volume: 11, P: 1-11
EYS is a major gene involved in retinitis pigmentosa in Japan: genetic landscapes revealed by stepwise genetic screening

Shogo Numa
Akio Oishi
Akitaka Tsujikawa
ResearchOpen Access27 Nov 2020
Scientific Reports

Volume: 10, P: 1-9
Endoplasmic reticulum chaperone BiP/GRP78 knockdown leads to autophagy and cell death of arginine vasopressin neurons in mice

Yohei Kawaguchi
Daisuke Hagiwara
Hiroshi Arima
ResearchOpen Access12 Nov 2020
Scientific Reports

Volume: 10, P: 1-13
Interaction of cytokeratin 19 head domain and HER2 in the cytoplasm leads to activation of HER2-Erk pathway

Tomoaki Ohtsuka
Masakiyo Sakaguchi
Shinichi Toyooka
ResearchOpen Access23 Dec 2016
Scientific Reports

Volume: 6, P: 1-13
Serotonin 1A receptor gene and major depressive disorder: an association study and meta-analysis

Taro Kishi
Tomoko Tsunoka
Nakao Iwata
Research04 Sept 2009
Journal of Human Genetics

Volume: 54, P: 629-633
Genetic association study between the detected risk variants based upon type II diabetes GWAS and psychotic disorders in the Japanese population

Yusuke Kajio
Kenji Kondo
Nakao Iwata
Research07 Nov 2013
Journal of Human Genetics

Volume: 59, P: 54-56
Clinical and Genetic Characteristics of 18 Patients from 13 Japanese Families with CRX-associated retinal disorder: Identification of Genotype-phenotype Association

Yu Fujinami-Yokokawa
Kaoru Fujinami
Yasuhiro Murakawa
ResearchOpen Access12 Jun 2020
Scientific Reports

Volume: 10, P: 1-13
The feeding habit of sea turtles influences their reaction to artificial marine debris

Takuya Fukuoka
Misaki Yamane
Katsufumi Sato
ResearchOpen Access16 Jun 2016
Scientific Reports

Volume: 6, P: 1-11
Therapeutic hypothermia for neonatal encephalopathy: a report from the first 3 years of the Baby Cooling Registry of Japan

Kennosuke Tsuda
Takeo Mukai
Kayo Yoshikawa
ResearchOpen Access04 Jan 2017
Scientific Reports

Volume: 7, P: 1-10
Generation of PLASE score for patent ductus arteriosus using the PLASE study database

Satoshi Masutani
Tetsuya Isayama
Shin Kato
ResearchOpen Access08 Feb 2025
Pediatric Research

Volume: 98, P: 152-160

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