5H0Q
 
 | | Crystal structure of lipid binding protein Nakanori at 1.5A | | Descriptor: | Lipid binding protein | | Authors: | Makino, A, Abe, M, Ishitsuka, R, Murate, M, Kishimoto, T, Sakai, S, Hullin-Matsuda, F, Shimada, Y, Inaba, T, Miyatake, H, Tanaka, H, Kurahashi, A, Pack, C.G, Kasai, R.S, Kubo, S, Schieber, N.L, Dohmae, N, Tochio, N, Hagiwara, K, Sasaki, Y, Aida, Y, Fujimori, F, Kigawa, T, Nishikori, K, Parton, R.G, Kusumi, A, Sako, Y, Anderluh, G, Yamashita, M, Kobayashi, T, Greimel, P, Kobayashi, T. | | Deposit date: | 2016-10-06 | | Release date: | 2016-10-19 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.501 Å) | | Cite: | A novel sphingomyelin/cholesterol domain-specific probe reveals the dynamics of the membrane domains during virus release and in Niemann-Pick type C
FASEB J., 31, 2017
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5B56
 | | Crystal structure of HIV-1 VPR C-Terminal domain and DIBB-M-Importin-Alpha2 complex | | Descriptor: | Importin subunit alpha-1, Protein Vpr | | Authors: | Miyatake, H, Sanjoh, A, Matusda, G, Murakami, T, Murakami, H, Hagiwara, K, Yokoyama, M, Sato, H, Miyamoto, Y, Dohmae, N, Aida, Y. | | Deposit date: | 2016-04-25 | | Release date: | 2016-06-01 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Molecular Mechanism of HIV-1 Vpr for Binding to Importin-alpha
J.Mol.Biol., 428, 2016
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5GLH
 | | Human endothelin receptor type-B in complex with ET-1 | | Descriptor: | Endothelin Receptor Subtype-B, Peptide from Endothelin-1 | | Authors: | Shihoya, W, Nishizawa, T, Okuta, A, Tani, K, Fujiyoshi, Y, Dohmae, N, Nureki, O, Doi, T. | | Deposit date: | 2016-07-11 | | Release date: | 2016-09-07 | | Last modified: | 2020-02-26 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Activation mechanism of endothelin ETB receptor by endothelin-1.
Nature, 537, 2016
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5GLI
 | | Human endothelin receptor type-B in the ligand-free form | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, Endothelin Receptor Subtype-B, OLEIC ACID, ... | | Authors: | Shihoya, W, Nishizawa, T, Okuta, A, Tani, K, Fujiyoshi, Y, Dohmae, N, Nureki, O, Doi, T. | | Deposit date: | 2016-07-11 | | Release date: | 2016-09-07 | | Last modified: | 2020-02-26 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Activation mechanism of endothelin ETB receptor by endothelin-1.
Nature, 537, 2016
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4P79
 | | Crystal structure of mouse claudin-15 | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, Claudin-15 | | Authors: | Suzuki, H, Nishizawa, T, Tani, K, Yamazaki, Y, Tamura, A, Ishitani, R, Dohmae, N, Tsukita, S, Nureki, O, Fujiyoshi, Y. | | Deposit date: | 2014-03-26 | | Release date: | 2014-04-30 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal structure of a claudin provides insight into the architecture of tight junctions.
Science, 344, 2014
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2AHJ
 | | NITRILE HYDRATASE COMPLEXED WITH NITRIC OXIDE | | Descriptor: | 1,4-DIETHYLENE DIOXIDE, FE (III) ION, NITRIC OXIDE, ... | | Authors: | Nagashima, S, Nakasako, M, Dohmae, N, Tsujimura, M, Takio, K, Odaka, M, Yohda, M, Kamiya, N, Endo, I. | | Deposit date: | 1997-12-24 | | Release date: | 1999-01-27 | | Last modified: | 2022-12-21 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Novel non-heme iron center of nitrile hydratase with a claw setting of oxygen atoms.
Nat.Struct.Biol., 5, 1998
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2ZCF
 | | Mutational study on Alpha-Gln90 of Fe-type nitrile hydratase from Rhodococcus sp. N771 | | Descriptor: | FE (III) ION, MAGNESIUM ION, Nitrile hydratase subunit alpha, ... | | Authors: | Takarada, H, Kawano, Y, Hashimoto, K, Nakayama, H, Ueda, S, Yohda, M, Kamiya, N, Dohmae, N, Maeda, M, Odaka, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-11-08 | | Release date: | 2007-11-20 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.43 Å) | | Cite: | Mutational study on alphaGln90 of Fe-type nitrile hydratase from Rhodococcus sp. N771
Biosci.Biotechnol.Biochem., 70, 2006
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2FHO
 | | NMR solution structure of the human spliceosomal protein complex p14-SF3b155 | | Descriptor: | spliceosomal protein SF3b155, spliceosomal protein p14 | | Authors: | Kuwasako, K, Dohmae, N, Inoue, M, Shirouzu, M, Guntert, P, Seraphin, B, Muto, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-12-26 | | Release date: | 2006-12-26 | | Last modified: | 2022-03-09 | | Method: | SOLUTION NMR | | Cite: | NMR solution structure of the human spliceosomal protein complex p14-SF3b155
To be Published
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7Y3F
 | | 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
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7VD5
 | | Structure of C2S2M2-type PSII-FCPII supercomplex from diatom | | Descriptor: | (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol, (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, ... | | Authors: | Nagao, R, Kato, K, Akita, F, Miyazaki, N, Shen, J.R. | | Deposit date: | 2021-09-06 | | Release date: | 2022-03-02 | | Last modified: | 2022-09-14 | | Method: | ELECTRON MICROSCOPY (2.5 Å) | | Cite: | Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex
Nat Commun, 13, 2022
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7VD6
 | | Structure of S1M1-type FCPII complex from diatom | | Descriptor: | (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol, (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, ... | | Authors: | Nagao, R, Kato, K, Akita, F, Miyazaki, N, Shen, J.R. | | Deposit date: | 2021-09-06 | | Release date: | 2022-03-02 | | Last modified: | 2022-09-14 | | Method: | ELECTRON MICROSCOPY (2.8 Å) | | Cite: | Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex
Nat Commun, 13, 2022
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8WEY
 | | 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
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5I20
 | | Crystal structure of protein | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, SULFATE ION, Uncharacterized protein | | Authors: | Ishitani, R, Nureki, O. | | Deposit date: | 2016-02-08 | | Release date: | 2016-06-01 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural basis for amino acid export by DMT superfamily transporter YddG.
Nature, 534, 2016
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4YBG
 | | Crystal structure of the MAEL domain of Drosophila melanogaster Maelstrom | | Descriptor: | 1,2-ETHANEDIOL, ACETATE ION, Protein maelstrom, ... | | Authors: | Matsumoto, N, Ishitani, R, Nishimasu, H, Nureki, O. | | Deposit date: | 2015-02-18 | | Release date: | 2015-04-29 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.602 Å) | | Cite: | Crystal Structure and Activity of the Endoribonuclease Domain of the piRNA Pathway Factor Maelstrom
Cell Rep, 11, 2015
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7DR2
 | | Structure of GraFix PSI tetramer from Cyanophora paradoxa | | Descriptor: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, BETA-CAROTENE, ... | | Authors: | Kato, K, Nagao, R, Akita, F, Miyazaki, N, Shen, J.R. | | Deposit date: | 2020-12-25 | | Release date: | 2022-02-16 | | Method: | ELECTRON MICROSCOPY (3.8 Å) | | Cite: | Structural insights into an evolutionary turning-point of photosystem I from prokaryotes to eukaryotes
Biorxiv, 2022
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7DR1
 | | Structure of Wild-type PSI monomer2 from Cyanophora paradoxa | | Descriptor: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, BETA-CAROTENE, ... | | Authors: | Kato, K, Nagao, R, Akita, F, Miyazaki, N, Shen, J.R. | | Deposit date: | 2020-12-25 | | Release date: | 2022-02-16 | | Method: | ELECTRON MICROSCOPY (3.2 Å) | | Cite: | Structural insights into an evolutionary turning-point of photosystem I from prokaryotes to eukaryotes
Biorxiv, 2022
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7DR0
 | | Structure of Wild-type PSI monomer1 from Cyanophora paradoxa | | Descriptor: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, BETA-CAROTENE, ... | | Authors: | Kato, K, Nagao, R, Akita, F, Miyazaki, N, Shen, J.R. | | Deposit date: | 2020-12-25 | | Release date: | 2022-02-16 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Structural insights into an evolutionary turning-point of photosystem I from prokaryotes to eukaryotes
Biorxiv, 2022
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4KPP
 | | Crystal Structure of H+/Ca2+ Exchanger CAX | | Descriptor: | (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, CALCIUM ION, OLEIC ACID, ... | | Authors: | Nishizawa, T, Ishitani, R, Nureki, O. | | Deposit date: | 2013-05-14 | | Release date: | 2013-06-26 | | Last modified: | 2022-08-24 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural basis for the counter-transport mechanism of a H+/Ca2+ exchanger.
Science, 341, 2013
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4L3O
 | | Crystal Structure of SIRT2 in complex with the macrocyclic peptide S2iL5 | | Descriptor: | 1,2-ETHANEDIOL, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, NAD-dependent protein deacetylase sirtuin-2, ... | | Authors: | Yamagata, K, Nishimasu, H, Ishitani, R, Nureki, O. | | Deposit date: | 2013-06-06 | | Release date: | 2014-02-19 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.518 Å) | | Cite: | Structural Basis for Potent Inhibition of SIRT2 Deacetylase by a Macrocyclic Peptide Inducing Dynamic Structural Change
Structure, 22, 2013
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5YY9
 | | Crystal structure of Tandem Tudor Domain of human UHRF1 in complex with LIG1-K126me3 | | Descriptor: | E3 ubiquitin-protein ligase UHRF1, Ligase 1 | | Authors: | Kori, S, Defossez, P.A, Arita, K. | | Deposit date: | 2017-12-08 | | Release date: | 2018-12-12 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.653 Å) | | Cite: | Structure of the UHRF1 Tandem Tudor Domain Bound to a Methylated Non-histone Protein, LIG1, Reveals Rules for Binding and Regulation.
Structure, 27, 2019
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5YYA
 | | Crystal structure of Tandem Tudor Domain of human UHRF1 | | Descriptor: | 1,2-ETHANEDIOL, E3 ubiquitin-protein ligase UHRF1, SULFATE ION | | Authors: | Kori, S, Defossez, P.A, Arita, K. | | Deposit date: | 2017-12-08 | | Release date: | 2018-12-12 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Structure of the UHRF1 Tandem Tudor Domain Bound to a Methylated Non-histone Protein, LIG1, Reveals Rules for Binding and Regulation.
Structure, 27, 2019
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5F1C
 | | Crystal structure of an invertebrate P2X receptor from the Gulf Coast tick in the presence of ATP and Zn2+ ion at 2.9 Angstroms | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, ADENOSINE-5'-TRIPHOSPHATE, Putative uncharacterized protein, ... | | Authors: | Kasuya, G, Hattori, M, Ishitani, R, Nureki, O. | | Deposit date: | 2015-11-30 | | Release date: | 2016-03-16 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Structural Insights into Divalent Cation Modulations of ATP-Gated P2X Receptor Channels
Cell Rep, 14, 2016
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4OO8
 | | Crystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNA | | Descriptor: | CRISPR-associated endonuclease Cas9/Csn1, DNA (5'-D(*CP*CP*AP*GP*CP*CP*AP*AP*GP*CP*GP*CP*AP*CP*CP*TP*AP*AP*TP*TP*TP*CP*C)-3'), RNA (97-MER) | | Authors: | Nishimasu, H, Ishitani, R, Nureki, O. | | Deposit date: | 2014-01-31 | | Release date: | 2014-02-26 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal structure of Cas9 in complex with guide RNA and target DNA
Cell(Cambridge,Mass.), 156, 2014
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6KR6
 | | Crystal structure of Drosophila Piwi | | Descriptor: | MERCURY (II) ION, Protein piwi, ZINC ION, ... | | Authors: | Yamaguchi, S, Oe, A, Yamashita, K, Hirano, S, Mastumoto, N, Ishitani, R, Nishimasu, H, Nureki, O. | | Deposit date: | 2019-08-21 | | Release date: | 2020-02-19 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Crystal structure of Drosophila Piwi.
Nat Commun, 11, 2020
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5ZHS
 | | Crystal structure of OsD14 in complex with covalently bound KK052 | | Descriptor: | (4-phenylpiperazin-1-yl)(1H-1,2,3-triazol-1-yl)methanone, Strigolactone esterase D14 | | Authors: | Hirabayashi, K, Miyakawa, T, Tanokura, M. | | Deposit date: | 2018-03-13 | | Release date: | 2018-11-21 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.49 Å) | | Cite: | Triazole Ureas Covalently Bind to Strigolactone Receptor and Antagonize Strigolactone Responses.
Mol Plant, 12, 2019
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