2F87
 
 | | Solution structure of a GAAG tetraloop in SRP RNA from Pyrococcus furiosus | | Descriptor: | SRP RNA | | Authors: | Okada, K, Takahashi, M, Sakamoto, T, Nakamura, K, Kanai, A, Kawai, G | | Deposit date: | 2005-12-02 | | Release date: | 2006-08-08 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | Solution structure of a GAAG tetraloop in helix 6 of SRP RNA from Pyrococcus furiosus
Nucleosides Nucleotides Nucleic Acids, 25, 2006
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2D17
 | | Solution RNA structure of stem-bulge-stem region of the HIV-1 dimerization initiation site | | Descriptor: | 5'-R(*CP*GP*GP*CP*AP*AP*GP*AP*GP*GP*CP*GP*AP*CP*CP*C)-3', 5'-R(*GP*GP*GP*UP*CP*GP*GP*CP*UP*UP*GP*CP*UP*G)-3' | | Authors: | Baba, S, Takahashi, K, Noguchi, S, Takaku, H, Koyanagi, Y, Yamamoto, N, Kawai, G. | | Deposit date: | 2005-08-15 | | Release date: | 2005-11-01 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers.
J.Biochem.(Tokyo), 138, 2005
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2D18
 | | Solution RNA structure of loop region of the HIV-1 dimerization initiation site in the extended-duplex dimer | | Descriptor: | 5'-R(*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*GP*GP*C)-3' | | Authors: | Baba, S, Takahashi, K, Noguchi, S, Takaku, H, Koyanagi, Y, Yamamoto, N, Kawai, G. | | Deposit date: | 2005-08-15 | | Release date: | 2005-11-01 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers.
J.Biochem.(Tokyo), 138, 2005
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2CYX
 | | Structure of human ubiquitin-conjugating enzyme E2 G2 (UBE2G2/UBC7) | | Descriptor: | Ubiquitin-conjugating enzyme E2 G2 | | Authors: | Yoshikawa, S, Arai, R, Murayama, K, Imai, Y, Takahashi, R, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-07-08 | | Release date: | 2006-04-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.56 Å) | | Cite: | Structure of human ubiquitin-conjugating enzyme E2 G2 (UBE2G2/UBC7)
Acta Crystallogr.,Sect.F, 62, 2006
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2D1B
 | | Solution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimer | | Descriptor: | RNA | | Authors: | Baba, S, Takahashi, K, Noguchi, S, Takaku, H, Koyanagi, Y, Yamamoto, N, Kawai, G. | | Deposit date: | 2005-08-15 | | Release date: | 2005-11-01 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers.
J.Biochem.(Tokyo), 138, 2005
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2D1A
 | | Solution RNA structure model of the HIV-1 dimerization initiation site in the extended-duplex dimer | | Descriptor: | RNA | | Authors: | Baba, S, Takahashi, K, Noguchi, S, Takaku, H, Koyanagi, Y, Yamamoto, N, Kawai, G. | | Deposit date: | 2005-08-15 | | Release date: | 2005-11-01 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers.
J.Biochem.(Tokyo), 138, 2005
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2CYC
 | | Crystal structure of Tyrosyl-tRNA Synthetase complexed with L-tyrosine from Pyrococcus horikoshii | | Descriptor: | TYROSINE, tyrosyl-tRNA synthetase | | Authors: | Kuratani, M, Sakai, H, Takahashi, M, Yanagisawa, T, Kobayashi, T, Sakamoto, K, Terada, T, Shirouzu, M, Sekine, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-07-06 | | Release date: | 2005-11-22 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal Structures of Tyrosyl-tRNA Synthetases from Archaea
J.Mol.Biol., 355, 2006
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2CYA
 | | Crystal structure of tyrosyl-tRNA synthetase from Aeropyrum pernix | | Descriptor: | SULFATE ION, Tyrosyl-tRNA synthetase | | Authors: | Kuratani, M, Sakai, H, Takahashi, M, Yanagisawa, T, Kobayashi, T, Murayama, K, Chen, L, Liu, Z.J, Wang, B.C, Kuroishi, C, Kuramitsu, S, Terada, T, Bessho, Y, Shirouzu, M, Sekine, S.I, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-07-06 | | Release date: | 2005-11-22 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal Structures of Tyrosyl-tRNA Synthetases from Archaea
J.Mol.Biol., 355, 2005
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7VPC
 | | Neryl diphosphate synthase from Solanum lycopersicum | | Descriptor: | 1,2-ETHANEDIOL, D-MALATE, Neryl-diphosphate synthase 1 | | Authors: | Imaizumi, R, Misawa, S, Takeshita, K, Sakai, N, Yamamoto, M, Kataoka, K, Nakayama, T, Takahashi, S, Yamashita, S. | | Deposit date: | 2021-10-15 | | Release date: | 2022-05-18 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.94 Å) | | Cite: | Structure-based engineering of a short-chain cis-prenyltransferase to biosynthesize nonnatural all-cis-polyisoprenoids: molecular mechanisms for primer substrate recognition and ultimate product chain-length determination.
Febs J., 289, 2022
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7WAB
 | | Crystal structure of the prolyl endoprotease, PEP, from Aspergillus niger | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, COMPASS (Complex proteins associated with Set1p) component shg1 family protein, ... | | Authors: | Miyazono, K, Kubota, K, Takahashi, K, Tanokura, M. | | Deposit date: | 2021-12-14 | | Release date: | 2022-01-12 | | Last modified: | 2022-02-16 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Crystal structure and substrate recognition mechanism of the prolyl endoprotease PEP from Aspergillus niger.
Biochem.Biophys.Res.Commun., 591, 2022
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6J5L
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7WMC
 | | Crystal structure of macrocyclic peptide 1 bound to human Nicotinamide N-methyltransferase | | Descriptor: | Nicotinamide N-methyltransferase, Peptide1 | | Authors: | Yoshida, S, Uehara, S, Kondo, N, Takahashi, Y, Yamamoto, S, Kameda, A, Kawagoe, S, Inoue, N, Yamada, M, Yoshimura, N, Tachibana, Y. | | Deposit date: | 2022-01-14 | | Release date: | 2022-08-31 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.55 Å) | | Cite: | Peptide-to-Small Molecule: A Pharmacophore-Guided Small Molecule Lead Generation Strategy from High-Affinity Macrocyclic Peptides.
J.Med.Chem., 65, 2022
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7WMT
 | | Crystal structure of small molecule 13 bound to human Nicotinamide N-methyltransferase | | Descriptor: | Nicotinamide N-methyltransferase, [(2~{R},4~{S})-4-[2-(aminomethyl)imidazol-1-yl]-2-[1-[(4-chlorophenyl)methyl]-5-methyl-indol-2-yl]pyrrolidin-1-yl]-(1~{H}-pyrrolo[2,3-b]pyridin-5-yl)methanone | | Authors: | Yoshida, S, Uehara, S, Kondo, N, Takahashi, Y, Yamamoto, S, Kameda, A, Kawagoe, S, Inoue, N, Yamada, M, Yoshimura, N, Tachibana, Y. | | Deposit date: | 2022-01-17 | | Release date: | 2022-08-31 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.77 Å) | | Cite: | Peptide-to-Small Molecule: A Pharmacophore-Guided Small Molecule Lead Generation Strategy from High-Affinity Macrocyclic Peptides.
J.Med.Chem., 65, 2022
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7VUS
 | | Crystal structure of AlleyCat9 with 5-nitro-benzotriazole | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 5-nitro-1H-benzotriazole, AlleyCat, ... | | Authors: | Tame, J.R.H, Korendovych, I.V, Margheritis, E, Takahashi, K. | | Deposit date: | 2021-11-04 | | Release date: | 2022-07-27 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | NMR-guided directed evolution.
Nature, 610, 2022
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7VUR
 | | Crystal structure of AlleyCat9 with calcium but no inhibitor | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, AlleyCat, CALCIUM ION | | Authors: | Margheritis, E, Takahashi, K, Korendovych, I.V, Tame, J.R.H. | | Deposit date: | 2021-11-04 | | Release date: | 2022-07-27 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | NMR-guided directed evolution.
Nature, 610, 2022
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7VUU
 | | Crystal structure of AlleyCat10 with inhibitor | | Descriptor: | 5-nitro-1H-benzotriazole, AlleyCat, CALCIUM ION | | Authors: | Tame, J.R.H, Korendovych, I.V, Margheritis, E, Takahashi, K. | | Deposit date: | 2021-11-04 | | Release date: | 2022-07-27 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | NMR-guided directed evolution.
Nature, 610, 2022
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7VUT
 | | Crystal structure of AlleyCat10 | | Descriptor: | AlleyCat10, CALCIUM ION | | Authors: | Tame, J.R.H, Korendovych, I.V, Margheritis, E, Takahashi, K. | | Deposit date: | 2021-11-04 | | Release date: | 2022-07-27 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | NMR-guided directed evolution.
Nature, 610, 2022
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7VY3
 | | STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER SPHAEROIDES LACKING PROTEIN-U | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, Antenna pigment protein alpha chain, Antenna pigment protein beta chain, ... | | Authors: | Tani, K, Kanno, R, Kawamura, S, Kikuchi, R, Nagashima, K.V.P, Hall, M, Takahashi, A, Yu, L.-J, Kimura, Y, Madigan, M.T, Mizoguchi, A, Humbel, B.M, Wang-Otomo, Z.-Y. | | Deposit date: | 2021-11-13 | | Release date: | 2022-04-27 | | Method: | ELECTRON MICROSCOPY (2.63 Å) | | Cite: | Asymmetric structure of the native Rhodobacter sphaeroides dimeric LH1-RC complex.
Nat Commun, 13, 2022
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7VY2
 | | STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER SPHAEROIDES DIMER | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, Antenna pigment protein alpha chain, Antenna pigment protein beta chain, ... | | Authors: | Tani, K, Kanno, R, Kawamura, S, Kikuchi, R, Nagashima, K.V.P, Hall, M, Takahashi, A, Yu, L.-J, Kimura, Y, Madigan, M.T, Mizoguchi, A, Humbel, B.M, Wang-Otomo, Z.-Y. | | Deposit date: | 2021-11-13 | | Release date: | 2022-04-27 | | Method: | ELECTRON MICROSCOPY (2.75 Å) | | Cite: | Asymmetric structure of the native Rhodobacter sphaeroides dimeric LH1-RC complex.
Nat Commun, 13, 2022
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7Y8P
 | | Crystal structure of 4'-selenoRNA duplex | | Descriptor: | COBALT HEXAMMINE(III), RNA (5'-R(*GP*GP*AP*(IKS)P*(ILK)P*(IKS)P*GP*AP*GP*UP*CP*C)-3') | | Authors: | Kondo, J, Minakawa, N, Ohta, M, Takahashi, H, Tarashima, N. | | Deposit date: | 2022-06-24 | | Release date: | 2023-05-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Synthesis and properties of fully-modified 4'-selenoRNA, an endonuclease-resistant RNA analog.
Bioorg.Med.Chem., 76, 2022
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7WCI
 | | The 0.85 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with two molecules of pelargonic acid | | Descriptor: | Fatty acid-binding protein, heart, HEXAETHYLENE GLYCOL, ... | | Authors: | Sugiyama, S, Kakinouchi, K, Takahashi, J, Matsuoka, S, Tsuchikawa, H, Sonoyama, M, Inoue, Y, Hayashi, F, Murata, M. | | Deposit date: | 2021-12-20 | | Release date: | 2022-12-21 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (0.85 Å) | | Cite: | The 0.85 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with two molecules of pelargonic acid
To Be Published
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6KBI
 | | Crystal structure of ErbB3 N418Q mutant | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Receptor tyrosine-protein kinase erbB-3 | | Authors: | Kato, K, Yao, M. | | Deposit date: | 2019-06-25 | | Release date: | 2020-07-01 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Crystal structure of ErbB3 N418Q mutant
To Be Published
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7X9U
 | | Type-II KH motif of human mitochondrial RbfA | | Descriptor: | Putative ribosome-binding factor A, mitochondrial | | Authors: | Kuwasako, K, Suzuki, S, Furue, M, Takizawa, M, Takahashi, M, Tsuda, K, Nagata, T, Watanabe, S, Tanaka, A, Kobayashi, N, Kigawa, T, Guntert, P, Shirouzu, M, Yokoyama, S, Muto, Y, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2022-03-16 | | Release date: | 2023-01-25 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | 1 H, 13 C, and 15 N resonance assignments and solution structures of the KH domain of human ribosome binding factor A, mtRbfA, involved in mitochondrial ribosome biogenesis.
Biomol.Nmr Assign., 16, 2022
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7YH6
 | | Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-8 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-8 Fab heavy chain, NIV-8 Fab light chain, ... | | Authors: | Moriyama, S, Anraku, Y, Muranishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y. | | Deposit date: | 2022-07-12 | | Release date: | 2023-07-19 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
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7YH7
 | | SARS-CoV-2 spike in complex with neutralizing antibody NIV-8 (state 2) | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-8 Fab heavy chain, ... | | Authors: | Moriyama, S, Anraku, Y, Muranishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y. | | Deposit date: | 2022-07-13 | | Release date: | 2023-07-19 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
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