2TMV
 
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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 | | Last modified: | 2024-10-16 | | 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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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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1UCU
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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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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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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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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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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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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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8ROR
 | | Single-particle cryo-EM of Mycoplasma pneumoniae adhesin P1 complexed with the anti-adhesive Fab fragment. | | Descriptor: | Adhesin P1, Heavy Chain Fab, Light Chain Fab | | Authors: | Vizarraga, D, Kawamoto, A, Marcos-Silva, M, Fita, I, Miyata, M, Pinyol, J, Namba, K, Kenri, T. | | Deposit date: | 2024-01-12 | | Release date: | 2025-03-05 | | Last modified: | 2025-07-09 | | Method: | ELECTRON MICROSCOPY (2.39 Å) | | Cite: | Dynamics of the adhesion complex of the human pathogens Mycoplasma pneumoniae and Mycoplasma genitalium.
Plos Pathog., 21, 2025
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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: | 2025-04-09 | | 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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5WRH
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5H53
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3A5X
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9IO5
 | | Cryo-EM structure of G1-ATPase dimer from Mycoplasma mobile gliding machinery | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, ADENOSINE-5'-TRIPHOSPHATE, G1-ATPase subunit D, ... | | Authors: | Toyonaga, T, Kato, T, Kawamoto, A, Miyata, T, Kawakami, K, Fujita, J, Hamaguchi, T, Namba, K, Miyata, M. | | Deposit date: | 2024-07-08 | | Release date: | 2025-03-12 | | Method: | ELECTRON MICROSCOPY (3.2 Å) | | Cite: | Dimeric assembly of F 1 -like ATPase for the gliding motility of Mycoplasma.
Sci Adv, 11, 2025
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6LY9
 | | The membrane-embedded Vo domain of V/A-ATPase from Thermus thermophilus | | Descriptor: | V-type ATP synthase subunit C, V-type ATP synthase subunit E, V-type ATP synthase subunit I, ... | | Authors: | Kishikawa, J, Nakanishi, A, Furuta, A, Kato, T, Namba, K, Tamakoshi, M, Mitsuoka, K, Yokoyama, K. | | Deposit date: | 2020-02-13 | | Release date: | 2020-09-09 | | Last modified: | 2024-10-16 | | Method: | ELECTRON MICROSCOPY (3.93 Å) | | Cite: | Mechanical inhibition of isolated V o from V/A-ATPase for proton conductance.
Elife, 9, 2020
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6LY8
 | | V/A-ATPase from Thermus thermophilus, the soluble domain, including V1, d, two EG stalks, and N-terminal domain of a-subunit. | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, V-type ATP synthase alpha chain, V-type ATP synthase beta chain, ... | | Authors: | Kishikawa, J, Nakanishi, A, Furuta, A, Kato, T, Namba, K, Tamakoshi, M, Mitsuoka, K, Yokoyama, K. | | Deposit date: | 2020-02-13 | | Release date: | 2020-09-09 | | Last modified: | 2025-04-09 | | Method: | ELECTRON MICROSCOPY (3.5 Å) | | Cite: | Mechanical inhibition of isolated V o from V/A-ATPase for proton conductance.
Elife, 9, 2020
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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: | 2024-10-16 | | 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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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 | | Last modified: | 2025-03-26 | | Method: | ELECTRON MICROSCOPY (3.28 Å) | | Cite: | From Monomers to Oligomers: Structural Mechanism of Receptor-Triggered MyD88 Assembly in Innate Immune Signaling
Biorxiv, 2024
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8XCN
 | | Cryo-EM Structure of Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus variant-N1190A | | Descriptor: | FE3-S4 CLUSTER, FLAVIN-ADENINE DINUCLEOTIDE, Fructose dehydrogenase cytochrome subunit, ... | | Authors: | Fukawa, E, Miyata, T, Makino, F, Adachi, T, Suzuki, Y, Tanaka, H, Namba, K, Sowa, K, Kitazumi, Y, Shirai, O. | | Deposit date: | 2023-12-09 | | Release date: | 2024-05-22 | | Method: | ELECTRON MICROSCOPY (3.02 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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8XCM
 | | Cryo-EM Structure of Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus variant-N1146Q | | Descriptor: | FE3-S4 CLUSTER, FLAVIN-ADENINE DINUCLEOTIDE, Fructose dehydrogenase cytochrome subunit, ... | | Authors: | Fukawa, E, Miyata, T, Makino, F, Adachi, T, Suzuki, Y, Tanaka, H, Namba, K, Sowa, K, Kitazumi, Y, Shirai, O. | | Deposit date: | 2023-12-09 | | Release date: | 2024-05-22 | | Method: | ELECTRON MICROSCOPY (3.08 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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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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8JEK
 | | Cryo-EM Structure of K-ferricyanide Oxidized Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus | | Descriptor: | FE3-S4 CLUSTER, FLAVIN-ADENINE DINUCLEOTIDE, Fructose dehydrogenase cytochrome subunit, ... | | Authors: | Suzuki, Y, Miyata, T, Makino, F, Tanaka, H, Namba, K, Sowa, K, Kitazumi, Y, Shirai, O. | | Deposit date: | 2023-05-16 | | Release date: | 2023-10-25 | | Method: | ELECTRON MICROSCOPY (2.7 Å) | | Cite: | Essential Insight of Direct Electron Transfer-Type Bioelectrocatalysis by Membrane-Bound d-Fructose Dehydrogenase with Structural Bioelectrochemistry.
Acs Catalysis, 13, 2023
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8JEJ
 | | Cryo-EM Structure of Na-dithionite Reduced Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus | | Descriptor: | FE3-S4 CLUSTER, FLAVIN-ADENINE DINUCLEOTIDE, Fructose dehydrogenase cytochrome subunit, ... | | Authors: | Suzuki, Y, Miyata, T, Makino, F, Tanaka, H, Namba, K, Sowa, K, Kitazumi, Y, Shirai, O. | | Deposit date: | 2023-05-16 | | Release date: | 2023-10-25 | | Method: | ELECTRON MICROSCOPY (2.5 Å) | | Cite: | Essential Insight of Direct Electron Transfer-Type Bioelectrocatalysis by Membrane-Bound d-Fructose Dehydrogenase with Structural Bioelectrochemistry.
Acs Catalysis, 13, 2023
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