List of works - Eiki Yamashita

A diffraction-quality protein crystal processed as an autophagic cargo

scientific article

A high-resolution structure of the pre-microRNA nuclear export machinery

scientific article

A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase

scientific article

A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump

scientific article

Absolute configuration of the hydroxyfarnesylethyl group of haem A, determined by X-ray structural analysis of bovine heart cytochrome c oxidase using methods applicable at 2.8 Angstrom resolution.

scientific article

Bovine cytochrome c oxidase structures enable O 2 reduction with minimization of reactive oxygens and provide a proton-pumping gate

scientific article

Circadian rhythms. Atomic-scale origins of slowness in the cyanobacterial circadian clock

scientific article

Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode

scientific article published on 15 December 2016

Conformational rearrangements of the C1 ring in KaiC measure the timing of assembly with KaiB.

scientific article

Conservation of Lipid Functions in Cytochrome bc Complexes ⬇️

scientific article published on September 28, 2011

Crystal Structure of the Cytoplasmic Phosphatase and Tensin Homolog (PTEN)-like Region of Ciona intestinalis Voltage-sensing Phosphatase Provides Insight into Substrate Specificity and Redox Regulation of the Phosphoinositide Phosphatase Activity

scientific article

Crystal structure of bacterial multidrug efflux transporter AcrB

scientific article

Crystal structure of human T-protein of glycine cleavage system at 2.0 A resolution and its implication for understanding non-ketotic hyperglycinemia

scientific journal article

Crystal structure of the C-terminal domain of Mu phage central spike and functions of bound calcium ion

scientific article

Crystal structure of the DsbB-DsbA complex reveals a mechanism of disulfide bond generation.

scientific article

Crystal structure of tripartite-type ABC transporter MacB from Acinetobacter baumannii

scientific article published on 6 November 2017

Crystal structures of OprN and OprJ, outer membrane factors of multidrug tripartite efflux pumps of Pseudomonas aeruginosa

scientific article

Crystal structures of a multidrug transporter reveal a functionally rotating mechanism.

scientific article

Crystal structures of the OmpF porin: function in a colicin translocon

scientific article

Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453

scientific article published on 27 March 2006

Crystallization and preliminary X-ray analysis of gene product 44 from bacteriophage Mu.

scientific article published on 24 December 2004

Crystallization and preliminary X-ray crystallographic study of the human MST2 SARAH domain.

scientific article published on 27 October 2011

Crystallization and preliminary X-ray diffraction analysis of human importin β-Snail zinc finger domain complex

scientific article published on 23 August 2013

Crystallization and preliminary X-ray diffraction studies of a β-carbonic anhydrase from the red algaPorphyridium purpureum

scientific article published on 01 February 2000

Crystallization and preliminary crystallographic analysis of rat monoamine oxidase A complexed with clorgyline.

scientific article published on 23 January 2004

Crystallization and preliminary crystallographic analysis of the importin-β–SREBP-2 complex

scientific article published on 19 September 2003

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

scientific article

Distinguishing between Cl- and O2(2-) as the bridging element between Fe3+ and Cu2+ in resting-oxidized cytochrome c oxidase

scientific article

Effects of ethyleneglycol chain length of dodecyl polyethyleneglycol monoether on the crystallization of bovine heart cytochrome c oxidase

scientific article (publication date: 10 March 1995)

Elucidation of master allostery essential for circadian clock oscillation in cyanobacteria

scientific article published on 15 April 2022

Evaluation of transition-state mimics in a superior BACE1 cleavage sequence as peptide-mimetic BACE1 inhibitors

scientific article

Expression and molecular characterization of spherical particles derived from the genome of the hyperthermophilic euryarchaeote Pyrococcus furiosus

scientific article published on 01 August 2005

Fused-ring structure of decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors

scientific article

Intermonomer interactions in dimer of bovine heart cytochromecoxidase

scientific article published on 21 June 2001

Lipid-Induced Conformational Changes within the Cytochrome b 6 f Complex of Oxygenic Photosynthesis

scientific article

Low pH-driven folding of WW45-SARAH domain leads to stabilization of the WW45-Mst2 complex.

scientific article published on 25 March 2015

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

scientific article published on 14 June 2019

Membrane proteins in four acts: function precedes structure determination.

scientific article

Methods for studying interactions of detergents and lipids with α-helical and β-barrel integral membrane proteins

scientific article

Monomeric structure of an active form of bovine cytochrome c oxidase

scientific article published on 18 September 2019

On the structural role of the aromatic residue environment of the chlorophyll a in the cytochrome b6f complex.

scientific article

Optimization of the energy constant of the methionine Sδ—C∊bond forX-PLORrefinement of protein structure

Pathways of colicin import: utilization of BtuB, OmpF porin and the TolC drug-export protein.

scientific article published in December 2012

Phage tail fibre assembly proteins employ a modular structure to drive the correct folding of diverse fibres

scientific article published on 17 June 2019

Plant-specific DUF1110 protein from Oryza sativa: expression, purification and crystallization

scientific article published on 23 May 2016

Redox-Coupled Crystal Structural Changes in Bovine Heart Cytochrome c Oxidase ⬇️

scientific article published on June 12, 1998

Selective nuclear export mechanism of small RNAs.

scientific article published on 07 December 2010

Structural and functional analysis of Hikeshi, a new nuclear transport receptor of Hsp70s

scientific article

Structural basis for the assembly of the Ragulator-Rag GTPase complex ⬇️

scientific article published on 20 November 2017

Structural basis for the development of SARS 3CL protease inhibitors from a peptide mimic to an aza-decaline scaffold.

scientific article published on 17 November 2015

Structural flexibility regulates phosphopeptide-binding activity of the tyrosine kinase binding domain of Cbl-c

scientific article

Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1) ⬇️

scientific article published on April 25, 2011

Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae

scientific article published on 13 September 2021

Structure of bovine cytochrome c oxidase crystallized at a neutral pH using a fluorinated detergent

scientific article published on 20 June 2017

Structure of bovine cytochrome c oxidase in the ligand-free reduced state at neutral pH.

scientific article

Structure of rat monoamine oxidase A and its specific recognitions for substrates and inhibitors

scientific article published in April 2004

Structure of the Central Hub of Bacteriophage Mu Baseplate Determined by X-ray Crystallography of gp44

scientific article published on 01 September 2005

Structure of the complex of the colicin E2 R-domain and its BtuB receptor. The outer membrane colicin translocon

scientific article

Structure of the connexin 26 gap junction channel at 3.5 A resolution

scientific article

Structure of the cytochrome b6f complex: quinone analogue inhibitors as ligands of heme cn

scientific article

Structure of the far-red light utilizing photosystem I of Acaryochloris marina

scientific article published on 20 April 2021

Structure-Function, Stability, and Chemical Modification of the Cyanobacterial Cytochrome b6f Complex from Nostoc sp. PCC 7120

scientific article

Structure-function of the cytochrome b6f complex.

scientific article

Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase

scientific article

Structures of Metal Sites of Oxidized Bovine Heart Cytochrome c Oxidase at 2.8 Å ⬇️

scientific article published on August 25, 1995

Structures of the wild-type MexAB-OprM tripartite pump reveal its complex formation and drug efflux mechanism

scientific article published on 03 April 2019

The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle.

scientific article published on 7 September 2016

The Q cycle of cytochrome bc complexes: A structure perspective ⬇️

scientific article published on February 23, 2011

The asymmetric IscA homodimer with an exposed [2Fe-2S] cluster suggests the structural basis of the Fe-S cluster biosynthetic scaffold.

scientific article

The host-binding domain of the P2 phage tail spike reveals a trimeric iron-binding structure

scientific article

The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process

scientific article

The structure of importin-beta bound to SREBP-2: nuclear import of a transcription factor

scientific article

The structure of melon necrotic spot virus determined at 2.8 Å resolution

scientific article

The structure of rat liver vault at 3.5 angstrom resolution

scientific article

The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A

scientific article

Traffic within the cytochrome b6f lipoprotein complex: gating of the quinone portal

scientific article

Trichromatic Concept Optimizes MAD Experiments in Synchrotron X-Ray Crystallography

scientific article published on 01 September 2002

Ultrafast optical pump-probe studies of the cytochrome b(6)f complex in solution and crystalline states.

scientific article

Utilization of light by fucoxanthin-chlorophyll-binding protein in a marine centric diatom, Chaetoceros gracilis.

scientific article

X-ray crystal structure of voltage-gated proton channel

scientific article published on 2 March 2014

X-ray structure of azide-bound fully oxidized cytochromecoxidase from bovine heart at 2.9 Å resolution

scientific article published on 01 May 2000

X-ray structure of cyanide-bound bovine heart cytochrome c oxidase in the fully oxidized state at 2.0 Å resolution.

scientific article published on 22 May 2015

X-ray structure of the NO-bound CuBin bovine cytochromecoxidase

scientific article

X-ray structures of catalytic intermediates of cytochrome c oxidase provide insights into its O2-activation and unidirectional proton-pump mechanisms

scientific article published on 12 March 2020

List of works by Eiki Yamashita

A diffraction-quality protein crystal processed as an autophagic cargo

A high-resolution structure of the pre-microRNA nuclear export machinery

A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase

A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump

Absolute configuration of the hydroxyfarnesylethyl group of haem A, determined by X-ray structural analysis of bovine heart cytochrome c oxidase using methods applicable at 2.8 Angstrom resolution.

Bovine cytochrome c oxidase structures enable O 2 reduction with minimization of reactive oxygens and provide a proton-pumping gate

Circadian rhythms. Atomic-scale origins of slowness in the cyanobacterial circadian clock

Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode

Conformational rearrangements of the C1 ring in KaiC measure the timing of assembly with KaiB.

Conservation of Lipid Functions in Cytochrome bc Complexes ⬇️

Crystal Structure of the Cytoplasmic Phosphatase and Tensin Homolog (PTEN)-like Region of Ciona intestinalis Voltage-sensing Phosphatase Provides Insight into Substrate Specificity and Redox Regulation of the Phosphoinositide Phosphatase Activity

Crystal structure of bacterial multidrug efflux transporter AcrB

Crystal structure of human T-protein of glycine cleavage system at 2.0 A resolution and its implication for understanding non-ketotic hyperglycinemia

Crystal structure of the C-terminal domain of Mu phage central spike and functions of bound calcium ion

Crystal structure of the DsbB-DsbA complex reveals a mechanism of disulfide bond generation.

Crystal structure of tripartite-type ABC transporter MacB from Acinetobacter baumannii

Crystal structures of OprN and OprJ, outer membrane factors of multidrug tripartite efflux pumps of Pseudomonas aeruginosa

Crystal structures of a multidrug transporter reveal a functionally rotating mechanism.

Crystal structures of the OmpF porin: function in a colicin translocon

Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453

Crystallization and preliminary X-ray analysis of gene product 44 from bacteriophage Mu.

Crystallization and preliminary X-ray crystallographic study of the human MST2 SARAH domain.

Crystallization and preliminary X-ray diffraction analysis of human importin β-Snail zinc finger domain complex

Crystallization and preliminary X-ray diffraction studies of a β-carbonic anhydrase from the red algaPorphyridium purpureum

Crystallization and preliminary crystallographic analysis of rat monoamine oxidase A complexed with clorgyline.

Crystallization and preliminary crystallographic analysis of the importin-β–SREBP-2 complex

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

Distinguishing between Cl- and O2(2-) as the bridging element between Fe3+ and Cu2+ in resting-oxidized cytochrome c oxidase

Effects of ethyleneglycol chain length of dodecyl polyethyleneglycol monoether on the crystallization of bovine heart cytochrome c oxidase

Elucidation of master allostery essential for circadian clock oscillation in cyanobacteria

Evaluation of transition-state mimics in a superior BACE1 cleavage sequence as peptide-mimetic BACE1 inhibitors

Expression and molecular characterization of spherical particles derived from the genome of the hyperthermophilic euryarchaeote Pyrococcus furiosus

Fused-ring structure of decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors

Intermonomer interactions in dimer of bovine heart cytochromecoxidase

Lipid-Induced Conformational Changes within the Cytochrome b 6 f Complex of Oxygenic Photosynthesis

Low pH-driven folding of WW45-SARAH domain leads to stabilization of the WW45-Mst2 complex.

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

Membrane proteins in four acts: function precedes structure determination.

Methods for studying interactions of detergents and lipids with α-helical and β-barrel integral membrane proteins

Monomeric structure of an active form of bovine cytochrome c oxidase

On the structural role of the aromatic residue environment of the chlorophyll a in the cytochrome b6f complex.

Optimization of the energy constant of the methionine Sδ—C∊bond forX-PLORrefinement of protein structure

Pathways of colicin import: utilization of BtuB, OmpF porin and the TolC drug-export protein.

Phage tail fibre assembly proteins employ a modular structure to drive the correct folding of diverse fibres

Plant-specific DUF1110 protein from Oryza sativa: expression, purification and crystallization

Redox-Coupled Crystal Structural Changes in Bovine Heart Cytochrome c Oxidase ⬇️

Selective nuclear export mechanism of small RNAs.

Structural and functional analysis of Hikeshi, a new nuclear transport receptor of Hsp70s

Structural basis for the assembly of the Ragulator-Rag GTPase complex ⬇️

Structural basis for the development of SARS 3CL protease inhibitors from a peptide mimic to an aza-decaline scaffold.

Structural flexibility regulates phosphopeptide-binding activity of the tyrosine kinase binding domain of Cbl-c

Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1) ⬇️

Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae

Structure of bovine cytochrome c oxidase crystallized at a neutral pH using a fluorinated detergent

Structure of bovine cytochrome c oxidase in the ligand-free reduced state at neutral pH.

Structure of rat monoamine oxidase A and its specific recognitions for substrates and inhibitors

Structure of the Central Hub of Bacteriophage Mu Baseplate Determined by X-ray Crystallography of gp44

Structure of the complex of the colicin E2 R-domain and its BtuB receptor. The outer membrane colicin translocon

Structure of the connexin 26 gap junction channel at 3.5 A resolution

Structure of the cytochrome b6f complex: quinone analogue inhibitors as ligands of heme cn

Structure of the far-red light utilizing photosystem I of Acaryochloris marina

Structure-Function, Stability, and Chemical Modification of the Cyanobacterial Cytochrome b6f Complex from Nostoc sp. PCC 7120

Structure-function of the cytochrome b6f complex.

Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase

Structures of Metal Sites of Oxidized Bovine Heart Cytochrome c Oxidase at 2.8 Å ⬇️

Structures of the wild-type MexAB-OprM tripartite pump reveal its complex formation and drug efflux mechanism

The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle.

The Q cycle of cytochrome bc complexes: A structure perspective ⬇️

The asymmetric IscA homodimer with an exposed [2Fe-2S] cluster suggests the structural basis of the Fe-S cluster biosynthetic scaffold.

The host-binding domain of the P2 phage tail spike reveals a trimeric iron-binding structure

The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process

The structure of importin-beta bound to SREBP-2: nuclear import of a transcription factor

The structure of melon necrotic spot virus determined at 2.8 Å resolution

The structure of rat liver vault at 3.5 angstrom resolution

The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A

Traffic within the cytochrome b6f lipoprotein complex: gating of the quinone portal

Trichromatic Concept Optimizes MAD Experiments in Synchrotron X-Ray Crystallography

Ultrafast optical pump-probe studies of the cytochrome b(6)f complex in solution and crystalline states.

Utilization of light by fucoxanthin-chlorophyll-binding protein in a marine centric diatom, Chaetoceros gracilis.