List of works - Atsushi Nakagawa

14-3-3 proteins act as intracellular receptors for rice Hd3a florigen

scientific article

A Structural Determinant for the Control of PIP2 Sensitivity in G Protein-gated Inward Rectifier K+ Channels ⬇️

scientific article published on September 29, 2010

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

scientific article

Ab initio crystal structure determination of spherical viruses that exhibit a centrosymmetric location in the unit cell.

scientific article published on 20 July 2005

Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source

scientific article published in August 2016

Conformation of amyloid fibrils of beta2-microglobulin probed by tryptophan mutagenesis

scientific article published on 10 August 2006

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 1-aminocyclopropane-1-carboxylate deaminase from Hansenula saturnus

scientific article

Crystal structure of a Bombyx mori sigma-class glutathione transferase exhibiting prostaglandin E synthase activity

scientific article

Crystal structure of a ribonuclease from the seeds of bitter gourd (Momordica charantia) at 1.75 A resolution

scientific article

Crystal structure of bovine lipoyltransferase in complex with lipoyl-AMP

scientific article

Crystal structure of human D-dopachrome tautomerase, a homologue of macrophage migration inhibitory factor, at 1.54 A resolution

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 mammalian alpha1,6-fucosyltransferase, FUT8

scientific 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 the hemolytic lectin CEL-III isolated from the marine invertebrate Cucumaria echinata: implications of domain structure for its membrane pore-formation mechanism

scientific article published on 11 June 2004

Crystallization and Preliminary X-Ray Crystallographic Study of a 23S rRNA Binding Domain of the Ribosomal Protein L2 fromBacillus stearothermophilus

scientific article published on 01 December 1998

Crystallization and preliminary X-ray analysis of human D-dopachrome tautomerase

scientific article

Crystallization and preliminary X-ray analysis of hyperthermophilic L-threonine dehydrogenase from the archaeon Pyrococcus horikoshii

scientific article

Crystallization and preliminary X-ray crystallographic study of the ribosomal protein S7 from Bacillus stearothermophilus

scientific article published on 01 October 1997

Crystallization and preliminary X-ray diffraction analysis of recombinant hepatitis E virus-like particle.

scientific article published on 29 March 2008

Crystallization and preliminary X-ray investigation of proteinase A, a non-pepsin-type acid proteinase from Aspergillus niger var. macrosporus.

scientific article published in January 1992

Crystallization and preliminary X-ray studies of two serine proteinase inhibitors, BGIA and BGIT, from the seeds of bitter gourd

scientific article published on 01 November 1997

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

Crystallization of rat liver macrophage migration inhibitory factor for MAD analysis

scientific article published on 01 November 1995

Crystallization, preliminary diffraction and electron paramagnetic resonance studies of a single crystal of cytochrome P450nor

scientific article published on 01 July 1997

Crystallographic Analysis Reveals Octamerization of Viroplasm Matrix Protein P9-1 of Rice Black Streaked Dwarf Virus

scientific article

Design and performance of an imaging plate system for X-ray diffraction study

article by Yoshiyuki Amemiya et al published April 1988 in Nuclear Instruments and Methods in Physics Research

Dynamic nature of disulphide bond formation catalysts revealed by crystal structures of DsbB

scientific article

Entropic stabilization of the tryptophan synthase alpha-subunit from a hyperthermophile, Pyrococcus furiosus. X-ray analysis and calorimetry

scientific article

Escherichia coli positive regulator OmpR has a large loop structure at the putative RNA polymerase interaction site

scientific article

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

Flavocommelin octaacetate

Hierarchical structure assembly model of rice dwarf virus particle formation

scientific article published on 14 December 2017

High-resolution X-ray crystal structure of bovine H-protein at 0.88 A resolution

scientific article

High-resolution crystal structure of beta2-microglobulin formed at pH 7.0

scientific article

High-resolution crystal structure of magnesium (MgII)-iron (FeII) hybrid hemoglobin with liganded beta subunits

scientific article published on 01 February 1996

High-resolution crystals of the HU mutant K38N from Bacillus stearothermophilus

scientific article published on 01 March 1999

Host innate immune receptors and beyond: making sense of microbial infections

scientific article

How coenzyme B12 radicals are generated: the crystal structure of methylmalonyl-coenzyme A mutase at 2 A resolution

scientific article

Identification of a new interaction mode between the Src homology 2 domain of C-terminal Src kinase (Csk) and Csk-binding protein/phosphoprotein associated with glycosphingolipid microdomains.

scientific article

Immunogenicity of whole-parasite vaccines against Plasmodium falciparum involves malarial hemozoin and host TLR9.

scientific article published in January 2010

Inverse agonist-like action of cadmium on G-protein-gated inward-rectifier K(+) channels

scientific article

Lipocalin 2 bolsters innate and adaptive immune responses to blood-stage malaria infection by reinforcing host iron metabolism

scientific article published in November 2012

Magnesium(II) and zinc(II)-protoporphyrin IX's stabilize the lowest oxygen affinity state of human hemoglobin even more strongly than deoxyheme

scientific article

Molecular cloning of human D-dopachrome tautomerase cDNA: N-terminal proline is essential for enzyme activation

scientific article

Ni2+ binds to active site of hen egg-white lysozyme and quenches fluorescence of Trp62 and Trp108.

scientific article published in November 2004

Noncrystallographic symmetry-constrained map obtained by direct density optimization ⬇️

scientific article published on 31 January 2020

Orexin-A is composed of a highly conserved C-terminal and a specific, hydrophilic N-terminal region, revealing the structural basis of specific recognition by the orexin-1 receptor

scientific article published in July 2006

Outer-capsid P8 proteins of phytoreoviruses mediate secretion of assembled virus-like particles from insect cells.

scientific article published on 14 July 2010

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

Preliminary crystallographic analysis of the antibiotic discharge outer membrane lipoprotein OprM of Pseudomonas aeruginosa with an exceptionally long unit cell and complex lattice structure

scientific article published on 24 December 2004

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

scientific article

Recombinant mammalian tubulin polyglutamylase TTLL7 performs both initiation and elongation of polyglutamylation on beta-tubulin through a random sequential pathway

scientific journal article

Ribosomal protein S7: a new RNA-binding motif with structural similarities to a DNA architectural factor

scientific article

SPring-8 BL44XU, a synchrotron radiation beamline for biological macromolecular assemblies, operated by the Institute for Protein Research, Osaka University

scientific article published on 23 July 2019

Samd7 is a cell type-specific PRC1 component essential for establishing retinal rod photoreceptor identity

scientific article published on 12 September 2017

Structural basis for catalytic activity of a silkworm Delta-class glutathione transferase

scientific article

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

scientific article published on 20 November 2017

Structural basis of Gip1 for cytosolic sequestration of G protein in wide-range chemotaxis

scientific article published in Nature Communications

Structural characteristics of the redox-sensing coiled coil in the voltage-gated H+ channel.

scientific article

Structural elements responsible for the transition between closed states of inward rectifier K+ channel

Structural evolution of reoviridae revealed by oryzavirus in acquiring the second capsid shell.

scientific article published on 10 September 2008

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

scientific article

Structural insight into the specific interaction between murine SHPS-1/SIRP alpha and its ligand CD47

scientific article

Structural insights into the electron/proton transfer pathways in the quinol:fumarate reductase from Desulfovibrio gigas

scientific article published in Scientific Reports

Structure and thermodynamics of the extraordinarily stable molten globule state of canine milk lysozyme

scientific article

Structure of human erythrocyte NADH-cytochrome b5 reductase.

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 carboxyl-terminal Src kinase, Csk

scientific article

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

scientific article published on 03 April 2019

Synchrotron radiation protein data collection system using the newly developed Weissenberg camera and imaging plate for crystal structure analysis (abstract)

Targeting AMAP1 and cortactin binding bearing an atypical src homology 3/proline interface for prevention of breast cancer invasion and metastasis

scientific article

The Weissenberg method for the collection of X-ray diffraction data from macromolecular crystals: modifications to the data-processing program WEIS

scholarly article by B. A. Fields et al published 1 December 1992 in Journal of Applied Crystallography

The amino-terminal region of major capsid protein P3 is essential for self-assembly of single-shelled core-like particles of Rice dwarf virus

scientific article published on March 2004

The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins

scientific article

The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism

scientific article published on 20 February 2019

The crystal structures of semi-synthetic aequorins.

scientific article

The cytoplasmic coiled-coil mediates cooperative gating temperature sensitivity in the voltage-gated H(+) channel Hv1

scientific article

The functional organization of the internal components of Rice dwarf virus

scientific article

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

scientific article

The hydrophobic nature of a novel membrane interface regulates the enzyme activity of a voltage-sensing phosphatase

scientific article published on 28 November 2018

The intracellular region of ClC-3 chloride channel is in a partially folded state and a monomer

scientific article published on 01 May 2006

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

scientific article

The tertiary structure of the human Xkr8-Basigin complex that scrambles phospholipids at plasma membranes

scientific article published on 08 October 2021

The three-dimensional structure of aspergilloglutamic peptidase from Aspergillus niger

scientific article published on 01 September 2004

Transcapsidation and the Conserved Interactions of Two Major Structural Proteins of a Pair of Phytoreoviruses Confirm the Mechanism of Assembly of the Outer Capsid Layer

scientific article published on 01 January 2005

Using cryoloops for X-ray data collection from protein crystals at room temperature: A simple applicable method

Viroplasm matrix protein Pns9 from rice gall dwarf virus forms an octameric cylindrical structure

scientific article published on 25 May 2011

X-ray crystal structure of voltage-gated proton channel

scientific article published on 2 March 2014

List of works by Atsushi Nakagawa

14-3-3 proteins act as intracellular receptors for rice Hd3a florigen

A Structural Determinant for the Control of PIP2 Sensitivity in G Protein-gated Inward Rectifier K+ Channels ⬇️

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

Ab initio crystal structure determination of spherical viruses that exhibit a centrosymmetric location in the unit cell.

Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source

Conformation of amyloid fibrils of beta2-microglobulin probed by tryptophan mutagenesis

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 1-aminocyclopropane-1-carboxylate deaminase from Hansenula saturnus

Crystal structure of a Bombyx mori sigma-class glutathione transferase exhibiting prostaglandin E synthase activity

Crystal structure of a ribonuclease from the seeds of bitter gourd (Momordica charantia) at 1.75 A resolution

Crystal structure of bovine lipoyltransferase in complex with lipoyl-AMP

Crystal structure of human D-dopachrome tautomerase, a homologue of macrophage migration inhibitory factor, at 1.54 A resolution

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 mammalian alpha1,6-fucosyltransferase, FUT8

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 the hemolytic lectin CEL-III isolated from the marine invertebrate Cucumaria echinata: implications of domain structure for its membrane pore-formation mechanism

Crystallization and Preliminary X-Ray Crystallographic Study of a 23S rRNA Binding Domain of the Ribosomal Protein L2 fromBacillus stearothermophilus

Crystallization and preliminary X-ray analysis of human D-dopachrome tautomerase

Crystallization and preliminary X-ray analysis of hyperthermophilic L-threonine dehydrogenase from the archaeon Pyrococcus horikoshii

Crystallization and preliminary X-ray crystallographic study of the ribosomal protein S7 from Bacillus stearothermophilus

Crystallization and preliminary X-ray diffraction analysis of recombinant hepatitis E virus-like particle.

Crystallization and preliminary X-ray investigation of proteinase A, a non-pepsin-type acid proteinase from Aspergillus niger var. macrosporus.

Crystallization and preliminary X-ray studies of two serine proteinase inhibitors, BGIA and BGIT, from the seeds of bitter gourd

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

Crystallization of rat liver macrophage migration inhibitory factor for MAD analysis

Crystallization, preliminary diffraction and electron paramagnetic resonance studies of a single crystal of cytochrome P450nor

Crystallographic Analysis Reveals Octamerization of Viroplasm Matrix Protein P9-1 of Rice Black Streaked Dwarf Virus

Design and performance of an imaging plate system for X-ray diffraction study

Dynamic nature of disulphide bond formation catalysts revealed by crystal structures of DsbB

Entropic stabilization of the tryptophan synthase alpha-subunit from a hyperthermophile, Pyrococcus furiosus. X-ray analysis and calorimetry

Escherichia coli positive regulator OmpR has a large loop structure at the putative RNA polymerase interaction site

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

Flavocommelin octaacetate

Hierarchical structure assembly model of rice dwarf virus particle formation

High-resolution X-ray crystal structure of bovine H-protein at 0.88 A resolution

High-resolution crystal structure of beta2-microglobulin formed at pH 7.0

High-resolution crystal structure of magnesium (MgII)-iron (FeII) hybrid hemoglobin with liganded beta subunits

High-resolution crystals of the HU mutant K38N from Bacillus stearothermophilus

Host innate immune receptors and beyond: making sense of microbial infections

How coenzyme B12 radicals are generated: the crystal structure of methylmalonyl-coenzyme A mutase at 2 A resolution

Identification of a new interaction mode between the Src homology 2 domain of C-terminal Src kinase (Csk) and Csk-binding protein/phosphoprotein associated with glycosphingolipid microdomains.

Immunogenicity of whole-parasite vaccines against Plasmodium falciparum involves malarial hemozoin and host TLR9.

Inverse agonist-like action of cadmium on G-protein-gated inward-rectifier K(+) channels

Lipocalin 2 bolsters innate and adaptive immune responses to blood-stage malaria infection by reinforcing host iron metabolism

Magnesium(II) and zinc(II)-protoporphyrin IX's stabilize the lowest oxygen affinity state of human hemoglobin even more strongly than deoxyheme

Molecular cloning of human D-dopachrome tautomerase cDNA: N-terminal proline is essential for enzyme activation

Ni2+ binds to active site of hen egg-white lysozyme and quenches fluorescence of Trp62 and Trp108.

Noncrystallographic symmetry-constrained map obtained by direct density optimization ⬇️

Orexin-A is composed of a highly conserved C-terminal and a specific, hydrophilic N-terminal region, revealing the structural basis of specific recognition by the orexin-1 receptor

Outer-capsid P8 proteins of phytoreoviruses mediate secretion of assembled virus-like particles from insect cells.

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

Preliminary crystallographic analysis of the antibiotic discharge outer membrane lipoprotein OprM of Pseudomonas aeruginosa with an exceptionally long unit cell and complex lattice structure

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

Recombinant mammalian tubulin polyglutamylase TTLL7 performs both initiation and elongation of polyglutamylation on beta-tubulin through a random sequential pathway

Ribosomal protein S7: a new RNA-binding motif with structural similarities to a DNA architectural factor

SPring-8 BL44XU, a synchrotron radiation beamline for biological macromolecular assemblies, operated by the Institute for Protein Research, Osaka University

Samd7 is a cell type-specific PRC1 component essential for establishing retinal rod photoreceptor identity

Structural basis for catalytic activity of a silkworm Delta-class glutathione transferase

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

Structural basis of Gip1 for cytosolic sequestration of G protein in wide-range chemotaxis

Structural characteristics of the redox-sensing coiled coil in the voltage-gated H+ channel.

Structural elements responsible for the transition between closed states of inward rectifier K+ channel

Structural evolution of reoviridae revealed by oryzavirus in acquiring the second capsid shell.

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

Structural insight into the specific interaction between murine SHPS-1/SIRP alpha and its ligand CD47

Structural insights into the electron/proton transfer pathways in the quinol:fumarate reductase from Desulfovibrio gigas

Structure and thermodynamics of the extraordinarily stable molten globule state of canine milk lysozyme

Structure of human erythrocyte NADH-cytochrome b5 reductase.

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

Structure of the carboxyl-terminal Src kinase, Csk

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

Synchrotron radiation protein data collection system using the newly developed Weissenberg camera and imaging plate for crystal structure analysis (abstract)

Targeting AMAP1 and cortactin binding bearing an atypical src homology 3/proline interface for prevention of breast cancer invasion and metastasis

The Weissenberg method for the collection of X-ray diffraction data from macromolecular crystals: modifications to the data-processing program WEIS

The amino-terminal region of major capsid protein P3 is essential for self-assembly of single-shelled core-like particles of Rice dwarf virus