2MGS
 
 | | Solution structure of CXCL5 | | Descriptor: | C-X-C motif chemokine 5 | | Authors: | Sepuru, K, Rajarathnam, K. | | Deposit date: | 2013-11-04 | | Release date: | 2014-04-02 | | Last modified: | 2016-04-27 | | Method: | SOLUTION NMR | | Cite: | Solution Structure of CXCL5 - A Novel Chemokine and Adipokine Implicated in Inflammation and Obesity.
Plos One, 9, 2014
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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: | 2020-09-30 | | 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: | 2020-09-30 | | 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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7BWM
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7VPY
 | | Crystal structure of the neutralizing nanobody P86 against SARS-CoV-2 | | Descriptor: | 1,2-ETHANEDIOL, Nanobody, SULFATE ION | | 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 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.6 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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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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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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5WRH
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5XL0
 | | met-aquo form of sperm whale myoglobin reconstituted with 7-PF, a heme possesseing CF3 group as side chain | | Descriptor: | Myoglobin, SULFATE ION, fluorinated heme | | Authors: | Kanai, Y, Harada, A, Shibata, T, Nishimura, R, Namiki, K, Watanabe, M, Nakamura, S, Yumoto, F, Senda, T, Suzuki, A, Neya, S, Yamamoto, Y. | | Deposit date: | 2017-05-10 | | Release date: | 2017-08-16 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.25 Å) | | Cite: | Characterization of Heme Orientational Disorder in a Myoglobin Reconstituted with a Trifluoromethyl-Group-Substituted Heme Cofactor
Biochemistry, 56, 2017
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7VW6
 | | Cryo-EM Structure of Formate Dehydrogenase 1 from Methylorubrum extorquens AM1 | | Descriptor: | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE, FE2/S2 (INORGANIC) CLUSTER, FLAVIN MONONUCLEOTIDE, ... | | Authors: | Yoshikawa, T, Makino, F, Miyata, T, Suzuki, Y, Tanaka, H, Namba, K, Sowa, K, Kitazumi, Y, Shirai, O. | | Deposit date: | 2021-11-09 | | Release date: | 2022-06-01 | | Last modified: | 2024-06-26 | | Method: | ELECTRON MICROSCOPY (2.19 Å) | | Cite: | Multiple electron transfer pathways of tungsten-containing formate dehydrogenase in direct electron transfer-type bioelectrocatalysis.
Chem.Commun.(Camb.), 58, 2022
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5H53
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7W2J
 | | Cryo-EM Structure of Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus | | Descriptor: | FE3-S4 CLUSTER, FLAVIN-ADENINE DINUCLEOTIDE, Fructose dehydrogenase cytochrome subunit, ... | | Authors: | Suzuki, Y, Makino, F, Miyata, T, Tanaka, H, Namba, K, Sowa, K, Kitazumi, Y, Shirai, O. | | Deposit date: | 2021-11-24 | | Release date: | 2022-11-30 | | Last modified: | 2023-12-13 | | Method: | ELECTRON MICROSCOPY (3.6 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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7WSQ
 | | Cryo-EM Structure of Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus | | Descriptor: | FE3-S4 CLUSTER, FLAVIN-ADENINE DINUCLEOTIDE, Fructose dehydrogenase cytochrome subunit, ... | | Authors: | Suzuki, Y, Makino, F, Miyata, T, Tanaka, H, Namba, K, Sowa, K, Kitazumi, Y, Shirai, O. | | Deposit date: | 2022-02-01 | | Release date: | 2023-02-08 | | Last modified: | 2023-12-13 | | Method: | ELECTRON MICROSCOPY (3.8 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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5AX2
 | | Crystal structure of S.cerevisiae Kti11p | | Descriptor: | CADMIUM ION, Diphthamide biosynthesis protein 3 | | Authors: | Kumar, A, Nagarathinam, K, Tanabe, M, Balbach, J. | | Deposit date: | 2015-07-13 | | Release date: | 2016-07-20 | | Last modified: | 2019-02-20 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Hyperbolic Pressure-Temperature Phase Diagram of the Zinc-Finger Protein apoKti11 Detected by NMR Spectroscopy.
J Phys Chem B, 123, 2019
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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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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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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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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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6KFK
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6KN7
 | | Structure of human cardiac thin filament in the calcium free state | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Actin, alpha skeletal muscle, ... | | Authors: | Fujii, T, Yamada, Y, Namba, K. | | Deposit date: | 2019-08-03 | | Release date: | 2020-01-15 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (6.6 Å) | | Cite: | Cardiac muscle thin filament structures reveal calcium regulatory mechanism.
Nat Commun, 11, 2020
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2D4Y
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2D4X
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2DPY
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6K9Q
 | | Structure of the native supercoiled hook as a universal joint | | Descriptor: | Flagellar hook protein FlgE | | Authors: | Kato, T, Miyata, T, Makino, F, Horvath, P, Namba, K. | | Deposit date: | 2019-06-17 | | Release date: | 2020-02-12 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (3.1 Å) | | Cite: | Structure of the native supercoiled flagellar hook as a universal joint.
Nat Commun, 10, 2019
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