2TMV
 
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1A05
 | | CRYSTAL STRUCTURE OF THE COMPLEX OF 3-ISOPROPYLMALATE DEHYDROGENASE FROM THIOBACILLUS FERROOXIDANS WITH 3-ISOPROPYLMALATE | | Descriptor: | 3-ISOPROPYLMALATE DEHYDROGENASE, 3-ISOPROPYLMALIC ACID, MAGNESIUM ION | | Authors: | Imada, K, Inagaki, K, Matsunami, H, Kawaguchi, H, Tanaka, H, Tanaka, N, Namba, K. | | Deposit date: | 1997-12-09 | | Release date: | 1998-06-17 | | Last modified: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 A resolution: the role of Glu88 in the unique substrate-recognition mechanism.
Structure, 6, 1998
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5H72
 | | Structure of the periplasmic domain of FliP | | Descriptor: | Flagellar biosynthetic protein FliP | | Authors: | Fukumura, T, Kawaguchi, T, Saijo-Hamano, Y, Namba, K, Minamino, T, Imada, K. | | Deposit date: | 2016-11-16 | | Release date: | 2017-08-02 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Assembly and stoichiometry of the core structure of the bacterial flagellar type III export gate complex
PLoS Biol., 15, 2017
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3MFP
 | | Atomic model of F-actin based on a 6.6 angstrom resolution cryoEM map | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Actin, alpha skeletal muscle | | Authors: | Fujii, T, Iwane, A.H, Yanagida, T, Namba, K. | | Deposit date: | 2010-04-03 | | Release date: | 2010-09-29 | | Last modified: | 2019-12-18 | | Method: | ELECTRON MICROSCOPY (6.6 Å) | | Cite: | Direct visualization of secondary structures of F-actin by electron cryomicroscopy
Nature, 467, 2010
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1VGL
 | | Crystal structure of tetrameric KaiB from T.elongatus BP-1 | | Descriptor: | Circadian clock protein kaiB, MERCURY (II) ION | | Authors: | Iwase, R, Imada, K, Hayashi, F, Uzumaki, T, Namba, K, Ishiura, M. | | Deposit date: | 2004-04-27 | | Release date: | 2005-08-16 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Functionally important substructures of circadian clock protein KaiB in a unique tetramer complex.
J.Biol.Chem., 280, 2005
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1UCU
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5B0O
 | | Structure of the FliH-FliI complex | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Flagellar assembly protein FliH, Flagellum-specific ATP synthase | | Authors: | Imada, K, Uchida, Y, Kinoshita, M, Namba, K, Minamino, T. | | Deposit date: | 2015-11-02 | | Release date: | 2016-03-23 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Insight into the flagella type III export revealed by the complex structure of the type III ATPase and its regulator
Proc.Natl.Acad.Sci.USA, 113, 2016
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5WRH
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8K6J
 | | Cryo-EM Structure of Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus variant-H1147A | | Descriptor: | FE3-S4 CLUSTER, FLAVIN-ADENINE DINUCLEOTIDE, Fructose dehydrogenase (H1147A) large subunit, ... | | Authors: | Fukawa, E, Miyata, T, Makino, F, Adachi, T, Suzuki, Y, Tanaka, H, Namba, K, Sowa, K, Kitazumi, Y, Shirai, O. | | Deposit date: | 2023-07-25 | | Release date: | 2024-05-22 | | Method: | ELECTRON MICROSCOPY (2.77 Å) | | Cite: | Structural and electrochemical elucidation of biocatalytic mechanisms in direct electron transfer-type D-fructose dehydrogenase.
Electrochim Acta, 490, 2024
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8K6K
 | | Cryo-EM Structure of Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus variant-N1146A | | Descriptor: | FE3-S4 CLUSTER, FLAVIN-ADENINE DINUCLEOTIDE, Fructose dehydrogenase (N1146A) large subunit, ... | | Authors: | Fukawa, E, Miyata, T, Makino, F, Adachi, T, Suzuki, Y, Tanaka, H, Namba, K, Sowa, K, Kitazumi, Y, Shirai, O. | | Deposit date: | 2023-07-25 | | Release date: | 2024-05-22 | | Method: | ELECTRON MICROSCOPY (2.4 Å) | | Cite: | Structural and electrochemical elucidation of biocatalytic mechanisms in direct electron transfer-type D-fructose dehydrogenase.
Electrochim Acta, 490, 2024
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1WLG
 | | Crystal structure of FlgE31, a major fragment of the hook protein | | Descriptor: | Flagellar hook protein flgE | | Authors: | Samatey, F.A, Matsunami, H, Imada, K, Nagashima, S, Shaikh, T.R, Thomas, D.R, DeRosier, D.J, Kitao, A, Namba, K. | | Deposit date: | 2004-06-25 | | Release date: | 2004-11-02 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism.
Nature, 431, 2004
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3J6P
 | | Pseudo-atomic model of dynein microtubule binding domain-tubulin complex based on a cryoEM map | | Descriptor: | Dynein heavy chain, cytoplasmic, GUANOSINE-5'-DIPHOSPHATE, ... | | Authors: | Uchimura, S, Fujii, T, Takazaki, H, Ayukawa, R, Nishikawa, Y, Minoura, I, Hachikubo, Y, Kurisu, G, Sutoh, K, Kon, T, Namba, K, Muto, E. | | Deposit date: | 2014-03-20 | | Release date: | 2014-12-31 | | Last modified: | 2024-03-20 | | Method: | ELECTRON MICROSCOPY (8.2 Å) | | Cite: | A flipped ion pair at the dynein-microtubule interface is critical for dynein motility and ATPase activation
J.Cell Biol., 208, 2015
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5H53
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5B3D
 | | Structure of a flagellar type III secretion chaperone, FlgN | | Descriptor: | Flagella synthesis protein FlgN | | Authors: | Nakanishi, Y, Kinoshita, M, Namba, K, Minamino, T, Imada, K. | | Deposit date: | 2016-02-15 | | Release date: | 2016-06-01 | | Last modified: | 2020-02-26 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Rearrangements of alpha-helical structures of FlgN chaperone control the binding affinity for its cognate substrates during flagellar type III export
Mol.Microbiol., 101, 2016
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9IWQ
 | | Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292) forming the L-type straight filament | | Descriptor: | Flagellin | | Authors: | Waraich, K, Makino, F, Miyata, T, Kinoshita, M, Minamino, T, Namba, K. | | Deposit date: | 2024-07-25 | | Release date: | 2024-08-07 | | Method: | ELECTRON MICROSCOPY (2.08 Å) | | Cite: | Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292) forming the L-type straight filament
To Be Published
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1IO1
 | | CRYSTAL STRUCTURE OF F41 FRAGMENT OF FLAGELLIN | | Descriptor: | PHASE 1 FLAGELLIN | | Authors: | Samatey, F.A, Imada, K, Nagashima, S, Vondervisz, F, Kumasaka, T, Yamamoto, M, Namba, K. | | Deposit date: | 2000-12-28 | | Release date: | 2001-04-04 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling
Nature, 410, 2001
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1GTT
 | | CRYSTAL STRUCTURE OF HPCE | | Descriptor: | 4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE, CALCIUM ION | | Authors: | Tame, J.R.H, Namba, K, Dodson, E.J, Roper, D.I. | | Deposit date: | 2002-01-18 | | Release date: | 2002-03-08 | | Last modified: | 2019-07-24 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | The Crystal Structure of Hpce, a Bifunctional Decarboxylase/Isomerase with a Multifunctional Fold.
Biochemistry, 41, 2002
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3A5X
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3J0R
 | | Model of a type III secretion system needle based on a 7 Angstrom resolution cryoEM map | | Descriptor: | Protein mxiH | | Authors: | Fujii, T, Cheung, M, Blanco, A, Kato, T, Blocker, A.J, Namba, K. | | Deposit date: | 2011-11-03 | | Release date: | 2012-02-29 | | Last modified: | 2024-02-21 | | Method: | ELECTRON MICROSCOPY (7.7 Å) | | Cite: | Structure of a type III secretion needle at 7-A resolution provides insights into its assembly and signaling mechanisms.
Proc.Natl.Acad.Sci.USA, 109, 2012
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3J82
 | | Electron cryo-microscopy of DNGR-1 in complex with F-actin | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Actin, cytoplasmic 1, ... | | Authors: | Hanc, P, Fujii, T, Yamada, Y, Huotari, J, Schulz, O, Ahrens, S, Kjaer, S, Way, M, Namba, K, Reis e Sousa, C. | | Deposit date: | 2014-09-25 | | Release date: | 2015-05-20 | | Last modified: | 2019-12-18 | | Method: | ELECTRON MICROSCOPY (7.7 Å) | | Cite: | Structure of the Complex of F-Actin and DNGR-1, a C-Type Lectin Receptor Involved in Dendritic Cell Cross-Presentation of Dead Cell-Associated Antigens.
Immunity, 42, 2015
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8W8M
 | | Cryo-EM structure of helical filament of MyD88 TIR | | Descriptor: | Myeloid differentiation primary response protein MyD88 | | Authors: | Kasai, K, Imamura, K, Narita, A, Makino, F, Miyata, T, Kato, T, Namba, K, Onishi, H, Tochio, H. | | Deposit date: | 2023-09-04 | | Release date: | 2024-09-04 | | Method: | ELECTRON MICROSCOPY (3.28 Å) | | Cite: | Signaling adopter protein in a self-assembled form
To Be Published
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7VQ0
 | | Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) bound to neutralizing nanobodies P86 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Maeda, R, Fujita, J, Konishi, Y, Kazuma, Y, Yamazaki, H, Anzai, I, Yamaguchi, K, Kasai, K, Nagata, K, Yamaoka, Y, Miyakawa, K, Ryo, A, Shirakawa, K, Makino, F, Matsuura, Y, Inoue, T, Imura, A, Namba, K, Takaori-Kondo, A. | | Deposit date: | 2021-10-18 | | Release date: | 2022-07-20 | | Method: | ELECTRON MICROSCOPY (3.03 Å) | | Cite: | A panel of nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants including Omicron.
Commun Biol, 5, 2022
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8HLB
 | | Cryo-EM structure of biparatopic antibody Bp109-92 in complex with TNFR2 | | Descriptor: | TR109 heavy chain, TR109 light chain, TR92 heavy chain, ... | | Authors: | Akiba, H, Fujita, J, Ise, T, Nishiyama, K, Miyata, T, Kato, T, Namba, K, Ohno, H, Kamada, H, Nagata, S, Tsumoto, K. | | Deposit date: | 2022-11-29 | | Release date: | 2023-10-04 | | Method: | ELECTRON MICROSCOPY (3.63 Å) | | Cite: | Development of a 1:1-binding biparatopic anti-TNFR2 antagonist by reducing signaling activity through epitope selection.
Commun Biol, 6, 2023
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2BGY
 | | Fit of the x-ray structure of the baterial flagellar hook fragment flge31 into an EM map from the hook of Caulobacter crescentus. | | Descriptor: | FLAGELLAR HOOK PROTEIN FLGE | | Authors: | Shaikh, T.R, Thomas, D.R, Chen, J.Z, Samatey, F.A, Matsunami, H, Imada, K, Namba, K, DeRosier, D.J. | | Deposit date: | 2005-01-06 | | Release date: | 2005-01-27 | | Last modified: | 2024-05-08 | | Method: | ELECTRON MICROSCOPY (9 Å) | | Cite: | A Partial Atomic Structure for the Flagellar Hook of Salmonella Typhimurium.
Proc.Natl.Acad.Sci.USA, 102, 2005
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2BGZ
 | | ATOMIC MODEL OF THE BACTERIAL FLAGELLAR BASED ON DOCKING AN X-RAY DERIVED HOOK STRUCTURE INTO AN EM MAP. | | Descriptor: | FLAGELLAR HOOK PROTEIN FLGE | | Authors: | Shaikh, T.R, Thomas, D.R, Chen, J.Z, Samatey, F.A, Matsunami, H, Imada, K, Namba, K, Derosier, D.J. | | Deposit date: | 2005-01-06 | | Release date: | 2005-01-27 | | Last modified: | 2024-05-08 | | Method: | ELECTRON MICROSCOPY (9 Å) | | Cite: | A Partial Atomic Structure for the Flagellar Hook of Salmonella Typhimurium.
Proc.Natl.Acad.Sci.USA, 102, 2005
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