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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
5GKN
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BU of 5gkn by Molmil
Catalase structure determined by electron crystallography of thin 3D crystals
Descriptor: Catalase, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, PROTOPORPHYRIN IX CONTAINING FE
Authors:Yonekura, K.
Deposit date:2016-07-04
Release date:2016-10-26
Last modified:2023-11-08
Method:ELECTRON CRYSTALLOGRAPHY (3.2 Å)
Cite:Refinement of Cryo-EM Structures Using Scattering Factors of Charged Atoms
J.Appl.Crystallogr., 49, 2016
3J7T
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BU of 3j7t by Molmil
Calcium atpase structure with two bound calcium ions determined by electron crystallography of thin 3D crystals
Descriptor: CALCIUM ION, SODIUM ION, Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Authors:Yonekura, K, Kato, K, Ogasawara, M, Tomita, M, Toyoshima, C.
Deposit date:2014-08-07
Release date:2015-02-18
Last modified:2016-09-28
Method:ELECTRON CRYSTALLOGRAPHY (3.4 Å)
Cite:Electron crystallography of ultrathin 3D protein crystals: atomic model with charges
Proc.Natl.Acad.Sci.USA, 112, 2015
6JNU
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BU of 6jnu by Molmil
Catalase structure determined by eEFD (dataset 2)
Descriptor: Catalase, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, PROTOPORPHYRIN IX CONTAINING FE
Authors:Yonekura, K, Maki-Yonekura, S.
Deposit date:2019-03-18
Release date:2019-04-24
Last modified:2024-03-27
Method:ELECTRON CRYSTALLOGRAPHY (3.001 Å)
Cite:A new cryo-EM system for electron 3D crystallography by eEFD.
J.Struct.Biol., 206, 2019
6JNT
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BU of 6jnt by Molmil
Catalase structure determined by eEFD (dataset 1)
Descriptor: Catalase, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, PROTOPORPHYRIN IX CONTAINING FE
Authors:Yonekura, K, Maki-Yonekura, S.
Deposit date:2019-03-18
Release date:2019-04-24
Last modified:2024-03-27
Method:ELECTRON CRYSTALLOGRAPHY (3 Å)
Cite:A new cryo-EM system for electron 3D crystallography by eEFD.
J.Struct.Biol., 206, 2019
3VU3
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BU of 3vu3 by Molmil
Crystal structure of the Hfq and catalase HPII complex
Descriptor: Catalase HPII, PROTOPORPHYRIN IX CONTAINING FE, Protein hfq
Authors:Watanabe, M, Yonekura, K.
Deposit date:2012-06-15
Release date:2013-11-20
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.85 Å)
Cite:Post-Transcriptional Regulator Hfq Binds Catalase HPII: Crystal Structure of the Complex
Plos One, 8, 2013
5ZFU
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BU of 5zfu by Molmil
Structure of the ExbB/ExbD hexameric complex (ExbB6ExbD3TM)
Descriptor: 22-mer peptide from Biopolymer transport protein ExbD, Biopolymer transport protein ExbB
Authors:Yonekura, K, Yamashita, Y, Matsuoka, R, Maki-Yonekura, S.
Deposit date:2018-03-07
Release date:2018-05-09
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (6.7 Å)
Cite:Hexameric and pentameric complexes of the ExbBD energizer in the Ton system.
Elife, 7, 2018
5ZFV
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BU of 5zfv by Molmil
Structure of the ExbB/ExbD pentameric complex (ExbB5ExbD1TM)
Descriptor: 22-mer peptide from Biopolymer transport protein ExbD, Biopolymer transport protein ExbB
Authors:Yonekura, K, Yamashita, Y, Matsuoka, R, Maki-Yonekura, S.
Deposit date:2018-03-07
Release date:2018-05-09
Method:ELECTRON MICROSCOPY (7.1 Å)
Cite:Hexameric and pentameric complexes of the ExbBD energizer in the Ton system.
Elife, 7, 2018
8WEY
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BU of 8wey by Molmil
PSI-LHCI of the red alga Cyanidium caldarium RK-1 (NIES-2137)
Descriptor: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{R} )-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, BETA-CAROTENE, ...
Authors:Kato, K, Hamaguchi, T, Nakajima, Y, Kawakami, K, Yonekura, K, Shen, J.R, Nagao, R.
Deposit date:2023-09-19
Release date:2024-02-14
Last modified:2024-03-13
Method:ELECTRON MICROSCOPY (1.92 Å)
Cite:The structure of PSI-LHCI from Cyanidium caldarium provides evolutionary insights into conservation and diversity of red-lineage LHCs.
Proc.Natl.Acad.Sci.USA, 121, 2024
7CHK
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BU of 7chk by Molmil
Cryo-EM Structure of Apple Latent Spherical Virus (ALSV)
Descriptor: VP20 protein, VP24 protein, VP25 protein
Authors:Naitow, H, Hamaguchi, T, Maki-Yonekura, S, Isogai, M, Yoshikawa, N, Yonekura, K.
Deposit date:2020-07-06
Release date:2020-11-04
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (2.87 Å)
Cite:Apple latent spherical virus structure with stable capsid frame supports quasi-stable protrusions expediting genome release.
Commun Biol, 3, 2020
3A5X
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BU of 3a5x by Molmil
L-type straight flagellar filament made of full-length flagellin
Descriptor: Flagellin
Authors:Maki-Yonekura, S, Yonekura, K, Namba, K.
Deposit date:2009-08-13
Release date:2010-03-16
Last modified:2024-03-13
Method:ELECTRON MICROSCOPY (4 Å)
Cite:Conformational change of flagellin for polymorphic supercoiling of the flagellar filament
Nat.Struct.Mol.Biol., 17, 2010
7VI4
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BU of 7vi4 by Molmil
Electron crystallographic structure of TIA-1 prion-like domain, A381T mutant
Descriptor: TIA-1 prion-like domain
Authors:Takaba, K, Maki-Yonekura, S, Sekiyama, N, Imamura, K, Kodama, T, Tochio, H, Yonekura, K.
Deposit date:2021-09-24
Release date:2022-09-28
Method:ELECTRON CRYSTALLOGRAPHY (0.95 Å)
Cite:ALS mutations in the TIA-1 prion-like domain trigger highly condensed pathogenic structures.
Proc.Natl.Acad.Sci.USA, 119, 2022
7VI5
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BU of 7vi5 by Molmil
Electron crystallographic structure of TIA-1 prion-like domain, wild type sequence
Descriptor: TIA-1 prion-like domain
Authors:Takaba, K, Maki-Yonekura, S, Sekiyama, N, Imamura, K, Kodama, T, Tochio, H, Yonekura, K.
Deposit date:2021-09-24
Release date:2022-09-28
Last modified:2023-11-29
Method:ELECTRON CRYSTALLOGRAPHY (1.761 Å)
Cite:ALS mutations in the TIA-1 prion-like domain trigger highly condensed pathogenic structures.
Proc.Natl.Acad.Sci.USA, 119, 2022
8HH0
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BU of 8hh0 by Molmil
Peroxiredoxin from Thermococcus kodakaraensis (TkPrx) F42C/C46S/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrx*F42C)
Descriptor: 1-naphthalen-2-ylethanone, Peroxiredoxin
Authors:Himiyama, T, Hamaguchi, T, Yonekura, K, Nakamura, T.
Deposit date:2022-11-16
Release date:2023-03-22
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:Unnaturally Distorted Hexagonal Protein Ring Alternatingly Reorganized from Two Distinct Chemically Modified Proteins.
Bioconjug.Chem., 2023
8J5A
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BU of 8j5a by Molmil
Single-particle cryo-EM structure of mouse apoferritin at 1.19 Angstrom resolution (Dataset A)
Descriptor: Ferritin heavy chain, SODIUM ION
Authors:Kawakami, K, Maki-Yonekura, S, Hamaguchi, T, Takaba, K, Yonekura, K.
Deposit date:2023-04-21
Release date:2023-07-12
Method:ELECTRON MICROSCOPY (1.19 Å)
Cite:Measurement of charges and chemical bonding in a cryo-EM structure.
Commun Chem, 6, 2023
5ZFP
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BU of 5zfp by Molmil
Structure of the ExbB/ExbD hexameric complex
Descriptor: Biopolymer transport protein ExbB
Authors:Maki-Yonekura, S, Matsuoka, R, Yonekura, K.
Deposit date:2018-03-06
Release date:2018-05-09
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.84 Å)
Cite:Hexameric and pentameric complexes of the ExbBD energizer in the Ton system.
Elife, 7, 2018
7VEB
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BU of 7veb by Molmil
Phycocyanin rod structure of cyanobacterial phycobilisome
Descriptor: C-phycocyanin alpha subunit, C-phycocyanin beta subunit, PHYCOCYANOBILIN, ...
Authors:Kawakami, K, Hamaguchi, T, Hirose, Y, Kosumi, D, Miyata, M, Kamiya, N, Yonekura, K.
Deposit date:2021-09-08
Release date:2022-06-15
Last modified:2022-08-17
Method:ELECTRON MICROSCOPY (4.2 Å)
Cite:Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome.
Nat Commun, 13, 2022
7VEA
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BU of 7vea by Molmil
Pentacylindrical allophycocyanin core from Thermosynechococcus vulcanus
Descriptor: Allophycocyanin alpha chain, Allophycocyanin beta chain, PHYCOCYANOBILIN, ...
Authors:Kawakami, K, Hamaguchi, T, Hirose, Y, Kosumi, D, Miyata, M, Kamiya, N, Yonekura, K.
Deposit date:2021-09-08
Release date:2022-06-22
Last modified:2022-08-17
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome.
Nat Commun, 13, 2022
7Y3F
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BU of 7y3f by Molmil
Structure of the Anabaena PSI-monomer-IsiA supercomplex
Descriptor: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, BETA-CAROTENE, ...
Authors:Nagao, R, Kato, K, Hamaguchi, T, Kawakami, K, Yonekura, K, Shen, J.R.
Deposit date:2022-06-10
Release date:2023-03-01
Method:ELECTRON MICROSCOPY (2.62 Å)
Cite:Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120
Nat Commun, 14, 2023
7DI8
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BU of 7di8 by Molmil
Electron crystallographic structure of Catalase using a direct electron detector at 300 kV
Descriptor: Catalase, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, PROTOPORPHYRIN IX CONTAINING FE
Authors:Takaba, K, Maki-Yonekura, S, Yonekura, K.
Deposit date:2020-11-18
Release date:2020-12-09
Last modified:2024-03-27
Method:ELECTRON CRYSTALLOGRAPHY (3.2 Å)
Cite:Protein and Organic-Molecular Crystallography With 300kV Electrons on a Direct Electron Detector.
Front Mol Biosci, 7, 2020
7COY
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BU of 7coy by Molmil
Structure of the far-red light utilizing photosystem I of Acaryochloris marina
Descriptor: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, CHLOROPHYLL D, ...
Authors:Kawakami, K, Yonekura, K, Hamaguchi, T, Kashino, Y, Shinzawa-Itoh, K, Inoue-Kashino, N, Itoh, S, Ifuku, K, Yamashita, E.
Deposit date:2020-08-05
Release date:2021-03-31
Last modified:2021-05-05
Method:ELECTRON MICROSCOPY (2.5 Å)
Cite:Structure of the far-red light utilizing photosystem I of Acaryochloris marina.
Nat Commun, 12, 2021
7EBC
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BU of 7ebc by Molmil
Crystal structure of Isocitrate lyase-1 from Saccaromyces cervisiae
Descriptor: Isocitrate lyase, MAGNESIUM ION, TETRAETHYLENE GLYCOL
Authors:Hiragi, K, Nishio, K, Moriyama, S, Hamaguchi, T, Mizoguchi, A, Yonekura, K, Tani, K, Mizushima, T.
Deposit date:2021-03-09
Release date:2021-06-23
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Structural insights into the targeting specificity of ubiquitin ligase for S. cerevisiae isocitrate lyase but not C. albicans isocitrate lyase.
J.Struct.Biol., 213, 2021
7EBE
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BU of 7ebe by Molmil
Crystal structure of Isocitrate lyase-1 from Candida albicans
Descriptor: FORMIC ACID, Isocitrate lyase, MAGNESIUM ION
Authors:Hiragi, K, Nishio, K, Moriyama, S, Hamaguchi, T, Mizoguchi, A, Yonekura, K, Tani, K, Mizushima, T.
Deposit date:2021-03-09
Release date:2021-06-23
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.69 Å)
Cite:Structural insights into the targeting specificity of ubiquitin ligase for S. cerevisiae isocitrate lyase but not C. albicans isocitrate lyase.
J.Struct.Biol., 213, 2021
7EBF
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BU of 7ebf by Molmil
Cryo-EM structure of Isocitrate lyase-1 from Candida albicans
Descriptor: Isocitrate lyase
Authors:Hiragi, K, Nishio, K, Moriyama, S, Hamaguchi, T, Mizoguchi, A, Yonekura, K, Tani, K, Mizushima, T.
Deposit date:2021-03-09
Release date:2021-06-23
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (2.63 Å)
Cite:Structural insights into the targeting specificity of ubiquitin ligase for S. cerevisiae isocitrate lyase but not C. albicans isocitrate lyase.
J.Struct.Biol., 213, 2021
6JJN
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BU of 6jjn by Molmil
Crystal structure of Mumps virus hemagglutinin-neuraminidase bound to sialyl lewisX
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, HN protein, ...
Authors:Kubota, M, Matsuoka, R, Suzuki, T, Yonekura, K, Yanagi, Y, Hashiguchi, T.
Deposit date:2019-02-26
Release date:2019-05-22
Last modified:2020-07-29
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Molecular Mechanism of the Flexible Glycan Receptor Recognition by Mumps Virus.
J.Virol., 93, 2019

 

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