2DVI
| Complex structure of CCA-adding enzyme, mini-DCC and CTP | Descriptor: | CCA-adding enzyme, CYTIDINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... | Authors: | Tomita, K, Ishitani, R, Fukai, S, Nureki, O. | Deposit date: | 2006-07-31 | Release date: | 2006-11-14 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.61 Å) | Cite: | Complete crystallographic analysis of the dynamics of CCA sequence addition Nature, 443, 2006
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2EQB
| Crystal structure of the Rab GTPase Sec4p, the Sec2p GEF domain, and phosphate complex | Descriptor: | PHOSPHATE ION, Rab guanine nucleotide exchange factor SEC2, Ras-related protein SEC4 | Authors: | Sato, Y, Fukai, S, Ishitani, R, Nureki, O. | Deposit date: | 2007-03-30 | Release date: | 2007-05-22 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Crystal structure of the Sec4p{middle dot}Sec2p complex in the nucleotide exchanging intermediate state Proc.Natl.Acad.Sci.Usa, 104, 2007
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3NKM
| Crystal structure of mouse autotaxin | Descriptor: | (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate, 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Nishimasu, H, Ishitani, R, Mihara, E, Takagi, J, Aoki, J, Nureki, O. | Deposit date: | 2010-06-20 | Release date: | 2011-01-19 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (2.002 Å) | Cite: | Crystal structure of autotaxin and insight into GPCR activation by lipid mediators Nat.Struct.Mol.Biol., 18, 2011
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1IRX
| Crystal structure of class I lysyl-tRNA synthetase | Descriptor: | ZINC ION, lysyl-tRNA synthetase | Authors: | Nureki, O, Terada, T, Ishitani, R, Ambrogelly, A, Ibba, M, Soll, D, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2001-10-25 | Release date: | 2002-04-17 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Functional convergence of two lysyl-tRNA synthetases with unrelated topologies. Nat.Struct.Biol., 9, 2002
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3NKN
| Crystal structure of mouse autotaxin in complex with 14:0-LPA | Descriptor: | (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate, 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Nishimasu, H, Ishitani, R, Mihara, E, Takagi, J, Aoki, J, Nureki, O. | Deposit date: | 2010-06-20 | Release date: | 2011-01-19 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Crystal structure of autotaxin and insight into GPCR activation by lipid mediators Nat.Struct.Mol.Biol., 18, 2011
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1IVO
| Crystal Structure of the Complex of Human Epidermal Growth Factor and Receptor Extracellular Domains. | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Epidermal Growth Factor Receptor, ... | Authors: | Ogiso, H, Ishitani, R, Nureki, O, Fukai, S, Yamanaka, M, Kim, J.H, Saito, K, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2002-03-28 | Release date: | 2002-10-16 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (3.3 Å) | Cite: | Crystal Structure of the Complex of Human Epidermal Growth Factor and Receptor Extracellular Domains. Cell(Cambridge,Mass.), 110, 2002
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1IPA
| CRYSTAL STRUCTURE OF RNA 2'-O RIBOSE METHYLTRANSFERASE | Descriptor: | RNA 2'-O-RIBOSE METHYLTRANSFERASE | Authors: | Nureki, O, Shirouzu, M, Hashimoto, K, Ishitani, R, Terada, T, Tamakoshi, M, Oshima, T, Chijimatsu, M, Takio, K, Vassylyev, D.G, Shibata, T, Inoue, Y, Kuramitsu, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2001-05-02 | Release date: | 2002-07-10 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | An enzyme with a deep trefoil knot for the active-site architecture. Acta Crystallogr.,Sect.D, 58, 2002
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3NKQ
| Crystal structure of mouse autotaxin in complex with 18:3-LPA | Descriptor: | (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E,12Z,15Z)-octadeca-9,12,15-trienoate, 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Nishimasu, H, Ishitani, R, Mihara, E, Takagi, J, Aoki, J, Nureki, O. | Deposit date: | 2010-06-20 | Release date: | 2011-01-19 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Crystal structure of autotaxin and insight into GPCR activation by lipid mediators Nat.Struct.Mol.Biol., 18, 2011
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3NKO
| Crystal structure of mouse autotaxin in complex with 16:0-LPA | Descriptor: | (2R)-2-hydroxy-3-(phosphonooxy)propyl hexadecanoate, 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Nishimasu, H, Ishitani, R, Mihara, E, Takagi, J, Aoki, J, Nureki, O. | Deposit date: | 2010-06-20 | Release date: | 2011-01-19 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Crystal structure of autotaxin and insight into GPCR activation by lipid mediators Nat.Struct.Mol.Biol., 18, 2011
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3NKP
| Crystal structure of mouse autotaxin in complex with 18:1-LPA | Descriptor: | (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate, 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Nishimasu, H, Ishitani, R, Mihara, E, Takagi, J, Aoki, J, Nureki, O. | Deposit date: | 2010-06-20 | Release date: | 2011-01-19 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.751 Å) | Cite: | Crystal structure of autotaxin and insight into GPCR activation by lipid mediators Nat.Struct.Mol.Biol., 18, 2011
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3NKR
| Crystal structure of mouse autotaxin in complex with 22:6-LPA | Descriptor: | (2R)-2-hydroxy-3-(phosphonooxy)propyl (4Z,7E,10E,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoate, 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Nishimasu, H, Ishitani, R, Mihara, E, Takagi, J, Aoki, J, Nureki, O. | Deposit date: | 2010-06-20 | Release date: | 2011-01-19 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.704 Å) | Cite: | Crystal structure of autotaxin and insight into GPCR activation by lipid mediators Nat.Struct.Mol.Biol., 18, 2011
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1J1U
| Crystal structure of archaeal tyrosyl-tRNA synthetase complexed with tRNA(Tyr) and L-tyrosine | Descriptor: | MAGNESIUM ION, TYROSINE, Tyrosyl-tRNA synthetase, ... | Authors: | Kobayashi, T, Nureki, O, Ishitani, R, Tukalo, M, Cusack, S, Sakamoto, K, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2002-12-17 | Release date: | 2003-06-03 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion NAT.STRUCT.BIOL., 10, 2003
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5Y78
| Crystal structure of the triose-phosphate/phosphate translocator in complex with inorganic phosphate | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, PHOSPHATE ION, Putative hexose phosphate translocator | Authors: | Lee, Y, Nishizawa, T, Takemoto, M, Kumazaki, K, Yamashita, K, Hirata, K, Minoda, A, Nagatoishi, S, Tsumoto, K, Ishitani, R, Nureki, O. | Deposit date: | 2017-08-16 | Release date: | 2017-10-04 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity Nat Plants, 3, 2017
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5Y79
| Crystal structure of the triose-phosphate/phosphate translocator in complex with 3-phosphoglycerate | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 3-PHOSPHOGLYCERIC ACID, CITRATE ANION, ... | Authors: | Lee, Y, Nishizawa, T, Takemoto, M, Kumazaki, K, Yamashita, K, Hirata, K, Minoda, A, Nagatoishi, S, Tsumoto, K, Ishitani, R, Nureki, O. | Deposit date: | 2017-08-16 | Release date: | 2017-10-04 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity Nat Plants, 3, 2017
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4GTW
| Crystal structure of mouse Enpp1 in complex with AMP | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ADENOSINE MONOPHOSPHATE, ... | Authors: | Kato, K, Nishimasu, H, Ishitani, R, Nureki, O. | Deposit date: | 2012-08-29 | Release date: | 2012-11-07 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Crystal structure of Enpp1, an extracellular glycoprotein involved in bone mineralization and insulin signaling. Proc.Natl.Acad.Sci.USA, 109, 2012
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4IKY
| Crystal structure of peptide transporter POT (E310Q mutant) in complex with sulfate | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, Di-tripeptide ABC transporter (Permease), OLEIC ACID, ... | Authors: | Doki, S, Kato, H.E, Ishitani, R, Nureki, O. | Deposit date: | 2012-12-28 | Release date: | 2013-07-10 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT. Proc.Natl.Acad.Sci.USA, 110, 2013
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5GUH
| Crystal structure of silkworm PIWI-clade Argonaute Siwi bound to piRNA | Descriptor: | MAGNESIUM ION, PIWI, RNA (28-MER) | Authors: | Matsumoto, N, Nishimasu, H, Ishitani, R, Nureki, O. | Deposit date: | 2016-08-29 | Release date: | 2016-10-19 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Crystal Structure of Silkworm PIWI-Clade Argonaute Siwi Bound to piRNA Cell, 167, 2016
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5AYN
| Crystal structure of a bacterial homologue of iron transporter ferroportin in outward-facing state | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, POTASSIUM ION, Solute carrier family 39 (Iron-regulated transporter) | Authors: | Taniguchi, R, Kato, H.E, Font, J, Deshpande, C.N, Ishitani, R, Jormakka, M, Nureki, O. | Deposit date: | 2015-08-25 | Release date: | 2015-11-04 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.202 Å) | Cite: | Outward- and inward-facing structures of a putative bacterial transition-metal transporter with homology to ferroportin Nat Commun, 6, 2015
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5AYO
| Crystal structure of a bacterial homologue of iron transporter ferroportin in inward-facing state | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, POTASSIUM ION, Solute carrier family 39 (Iron-regulated transporter), ... | Authors: | Taniguchi, R, Kato, H.E, Font, J, Deshpande, C.N, Ishitani, R, Jormakka, M, Nureki, O. | Deposit date: | 2015-08-25 | Release date: | 2015-11-04 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (3.3 Å) | Cite: | Outward- and inward-facing structures of a putative bacterial transition-metal transporter with homology to ferroportin Nat Commun, 6, 2015
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5GIJ
| Crystal structure of TDR-TDIF complex | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Leucine-rich repeat receptor-like protein kinase TDR, ... | Authors: | Morita, J, Kato, K, Ishitani, R, Nishimasu, H, Nureki, O. | Deposit date: | 2016-06-23 | Release date: | 2016-08-24 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Crystal structure of the plant receptor-like kinase TDR in complex with the TDIF peptide Nat Commun, 7, 2016
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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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5XH7
| Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RR variant in complex with crRNA and target DNA (TCCA PAM) | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, CRISPR-associated endonuclease Cpf1, ... | Authors: | Nishimasu, H, Yamano, T, Ishitani, R, Nureki, O. | Deposit date: | 2017-04-19 | Release date: | 2017-06-14 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1 Mol. Cell, 67, 2017
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5XUZ
| Crystal structure of Lachnospiraceae bacterium ND2006 Cpf1 in complex with crRNA and target DNA (CCCA PAM) | Descriptor: | 1,2-ETHANEDIOL, DNA (29-MER), DNA (5'-D(*CP*GP*TP*CP*CP*CP*CP*CP*A)-3'), ... | Authors: | Yamano, T, Nishimasu, H, Ishitani, R, Nureki, O. | Deposit date: | 2017-06-26 | Release date: | 2017-08-09 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1. Mol. Cell, 67, 2017
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5XH6
| Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RVR variant in complex with crRNA and target DNA (TATA PAM) | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, CRISPR-associated endonuclease Cpf1, ... | Authors: | Nishimasu, H, Yamano, T, Ishitani, R, Nureki, O. | Deposit date: | 2017-04-19 | Release date: | 2017-06-14 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1 Mol. Cell, 67, 2017
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5AYM
| Crystal structure of a bacterial homologue of iron transporter ferroportin in outward-facing state with soaked iron | Descriptor: | FE (II) ION, Solute carrier family 39 (Iron-regulated transporter) | Authors: | Taniguchi, R, Kato, H.E, Font, J, Deshpande, C.N, Ishitani, R, Jormakka, M, Nureki, O. | Deposit date: | 2015-08-25 | Release date: | 2015-11-04 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Outward- and inward-facing structures of a putative bacterial transition-metal transporter with homology to ferroportin Nat Commun, 6, 2015
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