8JNF
 
 | | The cryo-EM structure of the RAD51 filament bound to the nucleosome | | Descriptor: | DNA (153-MER), DNA (156-MER), DNA repair protein RAD51 homolog 1, ... | | Authors: | Shioi, T, Hatazawa, S, Ogasawara, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-06-06 | | Release date: | 2024-03-27 | | Last modified: | 2024-05-08 | | Method: | ELECTRON MICROSCOPY (6.91 Å) | | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site.
Nature, 628, 2024
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8JND
 | | The cryo-EM structure of the nonameric RAD51 ring bound to the nucleosome with the linker DNA binding | | Descriptor: | DNA (153-MER), DNA (156-MER), DNA repair protein RAD51 homolog 1, ... | | Authors: | Shioi, T, Hatazawa, S, Ogasawara, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-06-06 | | Release date: | 2024-03-27 | | Last modified: | 2024-05-08 | | Method: | ELECTRON MICROSCOPY (3.66 Å) | | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site.
Nature, 628, 2024
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6CX1
 | | Cryo-EM structure of Seneca Valley Virus-Anthrax Toxin Receptor 1 complex | | Descriptor: | Anthrax toxin receptor 1, Capsid protein VP1, Capsid protein VP2, ... | | Authors: | Jayawardena, N, Burga, L, Easingwood, R, Takizawa, Y, Wolf, M, Bostina, M. | | Deposit date: | 2018-04-02 | | Release date: | 2018-10-31 | | Last modified: | 2024-03-13 | | Method: | ELECTRON MICROSCOPY (3.8 Å) | | Cite: | Structural basis for anthrax toxin receptor 1 recognition by Seneca Valley Virus.
Proc. Natl. Acad. Sci. U.S.A., 115, 2018
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2RPV
 | | Solution Structure of GB1 with LBT probe | | Descriptor: | Immunoglobulin G-binding protein G, LANTHANUM (III) ION | | Authors: | Saio, T, Ogura, K, Yokochi, M, Kobashigawa, Y, Inagaki, F. | | Deposit date: | 2008-10-28 | | Release date: | 2009-09-15 | | Last modified: | 2024-10-16 | | Method: | SOLUTION NMR | | Cite: | Two-point anchoring of a lanthanide-binding peptide to a target protein enhances the paramagnetic anisotropic effect
J.Biomol.Nmr, 44, 2009
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8H0V
 | | RNA polymerase II transcribing a chromatosome (type I) | | Descriptor: | DNA (261-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | | Authors: | Hirano, R, Ehara, H, Tomoya, K, Takizawa, Y, Sekine, S, Kurumizaka, H. | | Deposit date: | 2022-09-30 | | Release date: | 2022-12-07 | | Last modified: | 2024-07-03 | | Method: | ELECTRON MICROSCOPY (3.8 Å) | | Cite: | Structural basis of RNA polymerase II transcription on the chromatosome containing linker histone H1.
Nat Commun, 13, 2022
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8JL9
 | | Cryo-EM structure of the human nucleosome with scFv | | Descriptor: | DNA (193-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-06-02 | | Release date: | 2023-10-04 | | Last modified: | 2023-11-08 | | Method: | ELECTRON MICROSCOPY (2.65 Å) | | Cite: | Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II.
Nucleic Acids Res., 51, 2023
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8JLD
 | | Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail | | Descriptor: | DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-06-02 | | Release date: | 2023-10-04 | | Last modified: | 2024-10-16 | | Method: | ELECTRON MICROSCOPY (2.48 Å) | | Cite: | Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II.
Nucleic Acids Res., 51, 2023
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8JLA
 | | Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 | | Descriptor: | DNA (193-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-06-02 | | Release date: | 2023-10-04 | | Last modified: | 2023-11-08 | | Method: | ELECTRON MICROSCOPY (3.44 Å) | | Cite: | Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II.
Nucleic Acids Res., 51, 2023
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1Y43
 | | crystal structure of aspergilloglutamic peptidase from Aspergillus niger | | Descriptor: | Aspergillopepsin II heavy chain, Aspergillopepsin II light chain, SULFATE ION | | Authors: | Sasaki, H, Nakagawa, A, Iwata, S, Muramatsu, T, Suganuma, M, Sawano, Y, Kojima, M, Kubota, K, Takahashi, K. | | Deposit date: | 2004-11-30 | | Release date: | 2005-12-13 | | Last modified: | 2013-02-27 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | The three-dimensional structure of aspergilloglutamic peptidase from Aspergillus niger
Proc.Jpn.Acad.,Ser.B, 80, 2004
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1IRR
 | | Solution structure of paralytic peptide of the silkworm, Bombyx mori | | Descriptor: | paralytic peptide | | Authors: | Miura, K, Kamimura, M, Aizawa, T, Kiuchi, M, Hayakawa, Y, Mizuguchi, M, Kawano, K. | | Deposit date: | 2001-10-23 | | Release date: | 2003-02-11 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure of paralytic peptide of silkworm, Bombyx mori
peptides, 23, 2002
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8XBW
 | | The cryo-EM structure of the RAD51 N-terminal lobe domain bound to the histone H4 tail of the nucleosome | | Descriptor: | DNA (5'-D(P*AP*CP*CP*GP*CP*TP*TP*AP*AP*AP*CP*GP*CP*AP*CP*GP*TP*A)-3'), DNA (5'-D(P*TP*AP*CP*GP*TP*GP*CP*GP*TP*TP*TP*AP*AP*GP*CP*GP*GP*T)-3'), DNA repair protein RAD51 homolog 1, ... | | Authors: | Shioi, T, Hatazawa, S, Ogasawara, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-12-07 | | Release date: | 2024-03-27 | | Last modified: | 2024-05-08 | | Method: | ELECTRON MICROSCOPY (2.89 Å) | | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site.
Nature, 628, 2024
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8XBV
 | | The cryo-EM structure of the RAD51 L1 and L2 loops bound to the linker DNA with the sticky end of the nucleosome | | Descriptor: | DNA (5'-D(P*CP*GP*AP*AP*AP*AP*CP*GP*GP*CP*CP*AP*CP*CP*A)-3'), DNA (5'-D(P*TP*GP*GP*CP*CP*GP*TP*TP*TP*TP*CP*G)-3'), DNA repair protein RAD51 homolog 1 | | Authors: | Shioi, T, Hatazawa, S, Ogasawara, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-12-07 | | Release date: | 2024-03-27 | | Last modified: | 2024-05-08 | | Method: | ELECTRON MICROSCOPY (7.61 Å) | | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site.
Nature, 628, 2024
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8XBX
 | | The cryo-EM structure of the RAD51 L2 loop bound to the linker DNA with the blunt end of the nucleosome | | Descriptor: | DNA (5'-D(P*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*GP*CP*CP*AP*CP*CP*AP*CP*G)-3'), DNA (5'-D(P*CP*GP*TP*GP*GP*TP*GP*GP*CP*CP*GP*TP*TP*TP*TP*CP*GP*TP*T)-3'), DNA repair protein RAD51 homolog 1 | | Authors: | Shioi, T, Hatazawa, S, Ogasawara, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-12-07 | | Release date: | 2024-03-27 | | Last modified: | 2024-04-17 | | Method: | ELECTRON MICROSCOPY (4.36 Å) | | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site.
Nature, 628, 2024
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8XBT
 | | The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding | | Descriptor: | DNA (153-MER), DNA (156-MER), DNA repair protein RAD51 homolog 1, ... | | Authors: | Shioi, T, Hatazawa, S, Ogasawara, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-12-07 | | Release date: | 2024-03-27 | | Last modified: | 2024-05-08 | | Method: | ELECTRON MICROSCOPY (4.12 Å) | | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site.
Nature, 628, 2024
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8XBU
 | | The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with the linker DNA binding | | Descriptor: | DNA (153-MER), DNA (156-MER), DNA repair protein RAD51 homolog 1, ... | | Authors: | Shioi, T, Hatazawa, S, Ogasawara, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-12-07 | | Release date: | 2024-03-27 | | Last modified: | 2024-05-08 | | Method: | ELECTRON MICROSCOPY (4.24 Å) | | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site.
Nature, 628, 2024
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8XBY
 | | The cryo-EM structure of the RAD51 L1 and L2 loops bound to the linker DNA with the blunt end of the nucleosome | | Descriptor: | DNA (5'-D(P*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*GP*CP*CP*AP*CP*CP*AP*CP*G)-3'), DNA (5'-D(P*CP*GP*TP*GP*GP*TP*GP*GP*CP*CP*GP*TP*TP*TP*TP*CP*GP*TP*T)-3'), DNA repair protein RAD51 homolog 1 | | Authors: | Shioi, T, Hatazawa, S, Ogasawara, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-12-07 | | Release date: | 2024-03-27 | | Last modified: | 2024-05-08 | | Method: | ELECTRON MICROSCOPY (7.8 Å) | | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site.
Nature, 628, 2024
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6A7X
 | | Rat Xanthine oxidoreductase, D428A variant, NAD bound form | | Descriptor: | BICARBONATE ION, FE2/S2 (INORGANIC) CLUSTER, FLAVIN-ADENINE DINUCLEOTIDE, ... | | Authors: | Okamoto, K, Kawaguchi, Y. | | Deposit date: | 2018-07-05 | | Release date: | 2019-07-24 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Rat Xanthine oxidoreductase, D428A variant, NAD bound form
To Be Published
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6ADJ
 | | Rat Xanthine oxidoreductase, D428E variant | | Descriptor: | CALCIUM ION, FE2/S2 (INORGANIC) CLUSTER, FLAVIN-ADENINE DINUCLEOTIDE, ... | | Authors: | Okamoto, K, Kawaguchi, Y. | | Deposit date: | 2018-08-01 | | Release date: | 2019-08-07 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.18 Å) | | Cite: | Rat Xanthine oxidoreductase, D428A variant, NAD bound form
To Be Published
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6AC1
 | | Rat Xanthine oxidoreductase, NADH bound form | | Descriptor: | 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, BICARBONATE ION, FE2/S2 (INORGANIC) CLUSTER, ... | | Authors: | Okamoto, K, Kawaguchi, Y. | | Deposit date: | 2018-07-24 | | Release date: | 2019-07-31 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.77 Å) | | Cite: | Rat Xanthine oxidoreductase, D428A variant, NAD bound form
To Be Published
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8JLB
 | | Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant | | Descriptor: | DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-06-02 | | Release date: | 2023-10-04 | | Last modified: | 2023-11-08 | | Method: | ELECTRON MICROSCOPY (2.36 Å) | | Cite: | Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II.
Nucleic Acids Res., 51, 2023
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6AC4
 | | Rat Xanthine oxidoreductase, D428N variant | | Descriptor: | FE2/S2 (INORGANIC) CLUSTER, FLAVIN-ADENINE DINUCLEOTIDE, Xanthine dehydrogenase/oxidase | | Authors: | Okamoto, K, Kawaguchi, Y. | | Deposit date: | 2018-07-25 | | Release date: | 2019-08-28 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.19 Å) | | Cite: | Rat Xanthine oxidoreductase, D428A variant, NAD bound form
To Be Published
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8J92
 | | Cryo-EM structure of nucleosome containing Arabidopsis thaliana H2A.W | | Descriptor: | DNA (169-MER), HTA6, HTB9, ... | | Authors: | Osakabe, A, Takizawa, Y, Horikoshi, N, Hatazawa, S, Berger, F, Kurumizaka, H, Kakutani, T. | | Deposit date: | 2023-05-02 | | Release date: | 2024-07-03 | | Last modified: | 2024-07-24 | | Method: | ELECTRON MICROSCOPY (2.9 Å) | | Cite: | Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1.
Nat Commun, 15, 2024
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8J91
 | | Cryo-EM structure of nucleosome containing Arabidopsis thaliana histones | | Descriptor: | DNA (169-MER), HTA13, Histone H2B.6, ... | | Authors: | Osakabe, A, Takizawa, Y, Horikoshi, N, Hatazawa, S, Berger, F, Kurumizaka, H, Kakutani, T. | | Deposit date: | 2023-05-02 | | Release date: | 2024-07-03 | | Last modified: | 2024-07-24 | | Method: | ELECTRON MICROSCOPY (2.9 Å) | | Cite: | Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1.
Nat Commun, 15, 2024
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8J90
 | | Cryo-EM structure of DDM1-nucleosome complex | | Descriptor: | ATP-dependent DNA helicase DDM1, DNA (169-MER), HTA6, ... | | Authors: | Osakabe, A, Takizawa, Y, Horikoshi, N, Hatazawa, S, Berger, F, Kurumizaka, H, Kakutani, T. | | Deposit date: | 2023-05-02 | | Release date: | 2024-07-03 | | Last modified: | 2024-07-24 | | Method: | ELECTRON MICROSCOPY (4.71 Å) | | Cite: | Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1.
Nat Commun, 15, 2024
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5ZP9
 | | Copper amine oxidase from Arthrobacter globiformis anaerobically reduced by ethylamine at pH 6 at 283 K (1) | | Descriptor: | COPPER (II) ION, Phenylethylamine oxidase, SODIUM ION | | Authors: | Murakawa, T, Baba, S, Kawano, Y, Hayashi, H, Yano, T, Tanizawa, K, Kumasaka, T, Yamamoto, M, Okajima, T. | | Deposit date: | 2018-04-16 | | Release date: | 2018-12-19 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | In crystallothermodynamic analysis of conformational change of the topaquinone cofactor in bacterial copper amine oxidase.
Proc. Natl. Acad. Sci. U.S.A., 116, 2019
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