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2TMV
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BU of 2tmv by Molmil
VISUALIZATION OF PROTEIN-NUCLEIC ACID INTERACTIONS IN A VIRUS. REFINED STRUCTURE OF INTACT TOBACCO MOSAIC VIRUS AT 2.9 ANGSTROMS RESOLUTION BY X-RAY FIBER DIFFRACTION
Descriptor: CALCIUM ION, RNA (5'-R(P*GP*AP*A)-3'), TMV COAT PROTEIN
Authors:Stubbs, G, Pattanayek, R, Namba, K.
Deposit date:1988-09-15
Release date:1989-01-09
Last modified:2024-02-21
Method:FIBER DIFFRACTION (2.9 Å)
Cite:Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction.
J.Mol.Biol., 208, 1989
2BGY
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BU of 2bgy by Molmil
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
8IBN
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BU of 8ibn by Molmil
Cryo-EM structure of KpFtsZ single filament
Descriptor: Cell division protein FtsZ, PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER, POTASSIUM ION
Authors:Fujita, J, Amesaka, H, Yoshizawa, T, Kuroda, N, Kamimura, N, Hibino, K, Konishi, T, Kato, Y, Hara, M, Inoue, T, Namba, K, Tanaka, S, Matsumura, H.
Deposit date:2023-02-10
Release date:2023-08-02
Last modified:2024-05-08
Method:ELECTRON MICROSCOPY (3.03 Å)
Cite:Structures of a FtsZ single protofilament and a double-helical tube in complex with a monobody.
Nat Commun, 14, 2023
8XCN
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BU of 8xcn by Molmil
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
8XCM
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BU of 8xcm by Molmil
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
3VKI
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BU of 3vki by Molmil
Monoclinic Crystal Structure of Salmonella FlgA in closed form
Descriptor: Flagella basal body P-ring formation protein flgA
Authors:Matsunami, H, Samatey, F.A, Namba, K.
Deposit date:2011-11-16
Release date:2012-11-21
Last modified:2016-07-06
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Structural flexibility of the periplasmic protein, FlgA, regulates flagellar P-ring assembly in Salmonella enterica
Sci Rep, 6, 2016
8W8M
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BU of 8w8m by Molmil
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
5B0O
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BU of 5b0o by Molmil
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
5H72
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BU of 5h72 by Molmil
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
9IWQ
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BU of 9iwq by Molmil
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
2BGZ
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BU of 2bgz by Molmil
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
1IO1
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BU of 1io1 by Molmil
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
1VGL
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BU of 1vgl by Molmil
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
3MFP
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BU of 3mfp by Molmil
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
1UCU
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BU of 1ucu by Molmil
R-type straight flagellar filament made of full-length flagellin
Descriptor: phase 1 Flagellin
Authors:Yonekura, K, Maki-Yonekura, S, Namba, K.
Deposit date:2003-04-22
Release date:2003-08-12
Last modified:2024-03-13
Method:ELECTRON MICROSCOPY (4 Å)
Cite:Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy
NATURE, 424, 2003
5WRH
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BU of 5wrh by Molmil
FlgG structure based on the CryoEM map of the bacterial flagellar polyrod
Descriptor: Flagellar basal-body rod protein FlgG
Authors:Fujii, T, Namba, K.
Deposit date:2016-12-02
Release date:2017-02-08
Method:ELECTRON MICROSCOPY (7.4 Å)
Cite:Identical folds used for distinct mechanical functions of the bacterial flagellar rod and hook.
Nat Commun, 8, 2017
4D3E
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BU of 4d3e by Molmil
Tetramer of IpaD, modified from 2J0O, fitted into negative stain electron microscopy reconstruction of the wild type tip complex from the type III secretion system of Shigella flexneri
Descriptor: INVASIN IPAD
Authors:Cheung, M, Shen, D.-K, Makino, F, Kato, T, Roehrich, D, Martinez-Argudo, I, Walker, M.L, Murillo, I, Liu, X, Pain, M, Brown, J, Frazer, G, Mantell, J, Mina, P, Todd, T, Sessions, R.B, Namba, K, Blocker, A.J.
Deposit date:2014-10-21
Release date:2014-12-10
Last modified:2024-05-08
Method:ELECTRON MICROSCOPY (24 Å)
Cite:Three-Dimensional Electron Microscopy Reconstruction and Cysteine-Mediated Crosslinking Provide a Model of the T3Ss Needle Tip Complex.
Mol.Microbiol., 95, 2015
1A05
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BU of 1a05 by Molmil
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
1WLG
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BU of 1wlg by Molmil
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
5B3D
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BU of 5b3d by Molmil
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
7VQ0
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BU of 7vq0 by Molmil
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
3J6P
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BU of 3j6p by Molmil
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
8JEK
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BU of 8jek by Molmil
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
8JEJ
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BU of 8jej by Molmil
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
7VPY
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BU of 7vpy by Molmil
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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