Search filters

List of works by Masaki Yamamoto

A large pocket structure surrounding the catalytic center in the BCG protein from Mycobacterium tuberculosis

A large-area CMOS imager as an X-ray detector for synchrotron radiation experiments.

scientific article published on 23 June 2004

A nearly on-axis spectroscopic system for simultaneously measuring UV-visible absorption and X-ray diffraction in the SPring-8 structural genomics beamline

scientific article published on January 2016

A novel allosteric mechanism on protein-DNA interactions underlying the phosphorylation-dependent regulation of Ets1 target gene expressions

scientific article

A temperature-controlled cold-gas humidifier and its application to protein crystals with the humid-air and glue-coating method

scientific article published on 14 June 2019

An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography

scientific article published on 11 September 2015

An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser

scientific article published on 17 October 2019

An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase.

scientific article published in January 2018

An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures

Architecture of the complete oxygen-sensing FixL-FixJ two-component signal transduction system.

scientific article published on 10 April 2018

Beamline Scheduling Software: administration software for automatic operation of the RIKEN structural genomics beamlines at SPring-8.

scientific article published on 14 April 2005

Blue Light-excited Light-Oxygen-Voltage-sensing Domain 2 (LOV2) Triggers a Rearrangement of the Kinase Domain to Induce Phosphorylation Activity in Arabidopsis Phototropin1

scientific article published on 2 August 2016

Blue-light excited LOV1 and LOV2 domains cooperatively regulate the kinase activity of full-length phototropin2 from Arabidopsis

scientific article published in December 2017

Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.

scientific article published on 17 November 2017

Catalytically important damage-free structures of a copper nitrite reductase obtained by femtosecond X-ray laser and room-temperature neutron crystallography

scientific article published on 23 June 2019

Cell-free methods to produce structurally intact mammalian membrane proteins.

scientific article published on 28 July 2016

Channeling and conformational changes in the heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96 ⬇️

scientific article published on July 30, 2010

Coherent X-Ray Diffraction Imaging of Chloroplasts from Cyanidioschyzon merolae by Using X-Ray Free Electron Laser

scientific article published on 5 March 2015

Coherent diffraction imaging analysis of shape-controlled nanoparticles with focused hard X-ray free-electron laser pulses.

scientific article

Common structural features of toxic intermediates from α-synuclein and GroES fibrillogenesis detected using cryogenic coherent X-ray diffraction imaging.

scientific article

Computer-controlled liquid-nitrogen drizzling device for removing frost from cryopreserved crystals

scientific article published on 25 November 2020

Critical Roles of Interactions among Switch I-preceding Residues and between Switch II and Its Neighboring α-Helix in Conformational Dynamics of the GTP-bound Ras Family Small GTPases ⬇️

scientific article published on March 9, 2011

Cryocrystallography of 3-Isopropylmalate dehydrogenase from Thermus thermophilus and its chimeric enzyme

scientific article published on 01 July 1996

Crystal Structure of OXA-58 with the Substrate-Binding Cleft in a Closed State: Insights into the Mobility and Stability of the OXA-58 Structure

scientific article

Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA.

scientific article published on 27 November 2017

Crystal structure of H2-proteinase from the venom of Trimeresurus flavoviridis

scientific article

Crystal structure of M-Ras reveals a GTP-bound "off" state conformation of Ras family small GTPases.

scientific article

Crystal structure of N-carbamyl-D-amino acid amidohydrolase with a novel catalytic framework common to amidohydrolases

scientific article

Crystal structure of a bacterial homologue of SWEET transporters.

scientific article published on 7 November 2014

Crystal structure of a family 80 chitosanase from Mitsuaria chitosanitabida.

scientific article published on 13 January 2017

Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8

scientific article

Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein

scientific article

Crystal structure of rhodopsin: A G protein-coupled receptor

scientific article

Crystal structure of the pyridoxal 5'-phosphate dependent L-methionine gamma-lyase from Pseudomonas putida

scientific article

Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor

scientific article (publication date: 23 May 2003)

Crystal structures of the human adiponectin receptors

scientific article published on 8 April 2015

Crystal structures of the state 1 conformations of the GTP-bound H-Ras protein and its oncogenic G12V and Q61L mutants

scientific article

Crystallization and preliminary X-ray analyses of quaternary, ternary and binary protein-DNA complexes with involvement of AML1/Runx-1/CBFalpha Runt domain, CBFbeta and the C/EBPbeta bZip region

scientific article published on 25 May 2001

Crystallization and preliminary X-ray analysis of the stress-response PPM phosphatase RsbX from Bacillus subtilis

scientific article published on 30 October 2009

Crystallization and preliminary X-ray crystallographic analysis of Thermus thermophilus transcription elongation complex bound to Gfh1.

scientific article published on 25 December 2009

Crystallization and preliminary X-ray diffraction analysis [correction of anaylsis] of the LOV1 domains of phototropin 1 and 2 from Arabidopsis thaliana.

scientific article published on 11 June 2008

Crystals of ternary protein-DNA complexes composed of DNA-binding domains of c-Myb or v-Myb, C/EBPalpha or C/EBPbeta and tom-1A promoter fragment

scientific article published on 25 October 2001

Curved EFC/F-BAR-domain dimers are joined end to end into a filament for membrane invagination in endocytosis

scientific article

DeepCentering: fully automated crystal centering using deep learning for macromolecular crystallography

scientific article published on 03 June 2019

Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL

scientific article

Development of SPACE-II for rapid sample exchange at SPring-8 macromolecular crystallography beamlines

scientific article published on 31 January 2020

Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography

scientific article

Development of a shutterless continuous rotation method using an X-ray CMOS detector for protein crystallography ⬇️

scientific article published on November 17, 2009

Development of an online UV-visible microspectrophotometer for a macromolecular crystallography beamline

scientific article published on 02 October 2013

Diffraction apparatus and procedure in tomography X-ray diffraction imaging for biological cells at cryogenic temperature using synchrotron X-ray radiation

scientific article published on 22 October 2018

Dimeric structures of quinol-dependent nitric oxide reductases (qNORs) revealed by cryo-electron microscopy

scientific article published on 28 August 2019

Dose dependence of radiation damage for protein crystals studied at various X-ray energies.

scientific article

Evaluation of the data-collection strategy for room-temperature micro-crystallography studied by serial synchrotron rotation crystallography combined with the humid air and glue-coating method

scientific article published on 25 February 2021

Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography.

scientific article published on 8 August 2017

Fast microtomography using bright monochromatic x-rays

scientific article published on 01 September 2012

IDATEN and G-SITENNO: GUI-assisted software for coherent X-ray diffraction imaging experiments and data analyses at SACLA.

scientific article

In silico discovery of small-molecule Ras inhibitors that display antitumor activity by blocking the Ras-effector interaction

scientific article

Interaction and stoichiometry of the peripheral stalk subunits NtpE and NtpF and the N-terminal hydrophilic domain of NtpI of Enterococcus hirae V-ATPase.

scientific article published on 6 May 2008

Interleukin-6 deficient mice are protected from bone loss caused by estrogen depletion

scientific article published on March 1994

KAMO: towards automated data processing for microcrystals

scientific article

KOTOBUKI-1 apparatus for cryogenic coherent X-ray diffraction imaging

scientific article

Light-induced conformational changes of LOV1 (light oxygen voltage-sensing domain 1) and LOV2 relative to the kinase domain and regulation of kinase activity in Chlamydomonas phototropin.

scientific article published on 27 November 2013

Long-wavelength native-SAD phasing: opportunities and challenges

scientific article published on 01 April 2019

Low-dose X-ray structure analysis of cytochrome c oxidase utilizing high-energy X-rays

scientific article published on 14 June 2019

Mail-in data collection at SPring-8 protein crystallography beamlines

scientific article

Mapping of the basic amino-acid residues responsible for tubulation and cellular protrusion by the EFC/F-BAR domain of pacsin2/Syndapin II

scientific article

Mechanism of c-Myb-C/EBP beta cooperation from separated sites on a promoter

scientific article

Mechanism of metal activation of human hematopoietic prostaglandin D synthase

scientific article

Micro-crystallography comes of age.

scientific article

Molecular basis of ligand recognition and transport by glucose transporters

scientific article

Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses

scientific article

Post-Transcriptional Regulator Hfq Binds Catalase HPII: Crystal Structure of the Complex

scientific article

Preliminary X-ray crystallographic study of glucose dehydrogenase from Thermus thermophilus HB8

scientific article published on 28 April 2007

Process of accumulation of metal ions on the interior surface of apo-ferritin: crystal structures of a series of apo-ferritins containing variable quantities of Pd(II) ions

scientific article

Protein microcrystallography using synchrotron radiation

scientific article

Purification, crystallization and preliminary X-ray diffraction analysis of the Kelch-like motif region of mouse Keap1

scientific article

SPring-8 BL41XU, a high-flux macromolecular crystallography beamline.

scientific article published on 2 October 2013

Sagittal focusing of synchrotron radiation X-rays using a winged crystal

scientific article published on 23 January 2013

Single-shot three-dimensional structure determination of nanocrystals with femtosecond X-ray free-electron laser pulses

scientific article

Small-angle X-ray scattering analysis reveals the ATP-bound monomeric state of the ATPase domain from the homodimeric MutL endonuclease, a GHKL phosphotransferase superfamily protein

scientific article published on 26 March 2015

Specimen preparation for cryogenic coherent X-ray diffraction imaging of biological cells and cellular organelles by using the X-ray free-electron laser at SACLA

scientific article

Standard Transport Channels of X-ray Beamlines at SPring-8

article

Structural analyses of DNA recognition by the AML1/Runx-1 Runt domain and its allosteric control by CBFbeta

scientific article

Structural basis for disruption of claudin assembly in tight junctions by an enterotoxin.

scientific article published on 20 September 2016

Structural basis for ligand capture and release by the endocytic receptor ApoER2.

scientific article published on 26 April 2017

Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop.

scientific article published on 8 March 2004

Structural basis of the substrate-specific two-step catalysis of long chain fatty acyl-CoA synthetase dimer

scientific article

Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms

scientific article

Structure of the RsbX phosphatase involved in the general stress response of Bacillus subtilis

scientific article

Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling

scientific article published on 15 March 2001

TAKASAGO-6 apparatus for cryogenic coherent X-ray diffraction imaging of biological non-crystalline particles using X-ray free electron laser at SACLA.

scientific article

Taste substance binding elicits conformational change of taste receptor T1r heterodimer extracellular domains

scientific article (publication date: 10 May 2016)

The 1.48 A resolution crystal structure of the homotetrameric cytidine deaminase from mouse.

scientific article published in June 2006

The 1.55 A resolution structure of Nicotiana alata S(F11)-RNase associated with gametophytic self-incompatibility

scientific article

The Catalytic Architecture of Leukotriene C4 Synthase with Two Arginine Residues ⬇️

scientific article published on March 16, 2011

The adoption of a twisted structure of importin-beta is essential for the protein-protein interaction required for nuclear transport

scientific article

The flexible C-terminal region of Aspergillus terreus blasticidin S deaminase: identification of its functional roles with deletion enzymes.

scientific article published in January 2002

The start of a new generation: the present status of the SPring-8 synchrotron and its use in structural biology

Trichromatic Concept Optimizes MAD Experiments in Synchrotron X-Ray Crystallography

scientific article published on 01 September 2002

Trichromatic Concept at SPring-8 RIKEN Beamline I

scientific article published on 01 May 1998

X-ray Crystallographic Structure of Thermophilic Rhodopsin: IMPLICATIONS FOR HIGH THERMAL STABILITY AND OPTOGENETIC FUNCTION

scientific article

X-ray structure of beta-carbonic anhydrase from the red alga, Porphyridium purpureum, reveals a novel catalytic site for CO(2) hydration

scientific article

ZOO: an automatic data-collection system for high-throughput structure analysis in protein microcrystallography

scientific article published on 28 January 2019

Paulina is supported by:

About Paulina

Help