7BWI
 
 | | Solution structure of recombinant APETx1 | | Descriptor: | Kappa-actitoxin-Ael2a | | Authors: | Matsumura, K, Kobayashi, N, Kurita, J, Nishimura, Y, Yokogawa, M, Imai, S, Shimada, I, Osawa, M. | | Deposit date: | 2020-04-14 | | Release date: | 2020-12-23 | | Last modified: | 2021-07-14 | | Method: | SOLUTION NMR | | Cite: | Mechanism of hERG inhibition by gating-modifier toxin, APETx1, deduced by functional characterization.
Bmc Mol Cell Biol, 22, 2021
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1DLF
 | | HIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI-DANSYL SWITCH VARIANT ANTIBODY IGG2A(S) CRYSTALLIZED AT PH 5.25 | | Descriptor: | ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S), SULFATE ION | | Authors: | Nakasako, M, Takahashi, H, Shimada, I, Arata, Y. | | Deposit date: | 1998-07-14 | | Release date: | 1999-07-26 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | The pH-dependent structural variation of complementarity-determining region H3 in the crystal structures of the Fv fragment from an anti-dansyl monoclonal antibody.
J.Mol.Biol., 291, 1999
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1BDD
 | | STAPHYLOCOCCUS AUREUS PROTEIN A, IMMUNOGLOBULIN-BINDING B DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE | | Descriptor: | STAPHYLOCOCCUS AUREUS PROTEIN A | | Authors: | Gouda, H, Torigoe, H, Saito, A, Sato, M, Arata, Y, Shimada, I. | | Deposit date: | 1996-06-28 | | Release date: | 1997-01-11 | | Last modified: | 2022-02-16 | | Method: | SOLUTION NMR | | Cite: | Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures.
Biochemistry, 31, 1992
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1BDC
 | | STAPHYLOCOCCUS AUREUS PROTEIN A, IMMUNOGLOBULIN-BINDING B DOMAIN, NMR, 10 STRUCTURES | | Descriptor: | STAPHYLOCOCCUS AUREUS PROTEIN A | | Authors: | Gouda, H, Torigoe, H, Saito, A, Sato, M, Arata, Y, Shimada, I. | | Deposit date: | 1996-06-28 | | Release date: | 1997-01-11 | | Last modified: | 2022-02-16 | | Method: | SOLUTION NMR | | Cite: | Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures.
Biochemistry, 31, 1992
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2I83
 | | hyaluronan-binding domain of CD44 in its ligand-bound form | | Descriptor: | CD44 antigen | | Authors: | Takeda, M, Ogino, S, Umemoto, R, Sakakura, M, Kajiwara, M, Sugahara, K.N, Hayasaka, H, Miyasaka, M, Terasawa, H, Shimada, I. | | Deposit date: | 2006-09-01 | | Release date: | 2006-11-21 | | Last modified: | 2022-03-09 | | Method: | SOLUTION NMR | | Cite: | Ligand-induced Structural Changes of the CD44 Hyaluronan-binding Domain Revealed by NMR
J.Biol.Chem., 281, 2006
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2DLF
 | | HIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI-DANSYL SWITCH VARIANT ANTIBODY IGG2A(S) CRYSTALLIZED AT PH 6.75 | | Descriptor: | PROTEIN (ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S) (HEAVY CHAIN)), PROTEIN (ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S)-KAPPA (LIGHT CHAIN)), SULFATE ION | | Authors: | Nakasako, M, Takahashi, H, Shimada, I, Arata, Y. | | Deposit date: | 1998-12-17 | | Release date: | 1999-12-17 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | The pH-dependent structural variation of complementarity-determining region H3 in the crystal structures of the Fv fragment from an anti-dansyl monoclonal antibody.
J.Mol.Biol., 291, 1999
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8HUJ
 | | Cryo-EM structure of the J-K-St region of EMCV IRES in complex with eIF4G-HEAT1 and eIF4A | | Descriptor: | Eukaryotic initiation factor 4A-I, Eukaryotic translation initiation factor 4 gamma 1, IRES RNA (J-K-St), ... | | Authors: | Suzuki, H, Fujiyoshi, Y, Imai, S, Shimada, I. | | Deposit date: | 2022-12-24 | | Release date: | 2023-08-02 | | Last modified: | 2023-09-13 | | Method: | ELECTRON MICROSCOPY (3.76 Å) | | Cite: | Dynamically regulated two-site interaction of viral RNA to capture host translation initiation factor.
Nat Commun, 14, 2023
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8J7R
 | | Cryo-EM structure of the J-K-St region of EMCV IRES in complex with eIF4G-HEAT1 and eIF4A (J-K-St/eIF4G focused) | | Descriptor: | Eukaryotic translation initiation factor 4 gamma 1, IRES RNA (J-K-St), MAGNESIUM ION | | Authors: | Suzuki, H, Fujiyoshi, Y, Imai, S, Shimada, I. | | Deposit date: | 2023-04-28 | | Release date: | 2023-08-02 | | Last modified: | 2023-09-13 | | Method: | ELECTRON MICROSCOPY (3.7 Å) | | Cite: | Dynamically regulated two-site interaction of viral RNA to capture host translation initiation factor.
Nat Commun, 14, 2023
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2RQH
 | | Structure of GSPT1/ERF3A-PABC | | Descriptor: | G1 to S phase transition 1, Polyadenylate-binding protein 1 | | Authors: | Osawa, M, Nakanishi, T, Hosoda, N, Uchida, S, Hoshino, T, Katada, I, Shimada, I. | | Deposit date: | 2009-05-08 | | Release date: | 2010-05-26 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Eukaryotic Translation Termination Factor Gspt/Erf3 Recognizes Pabp with Chemical Exchange Using Two Overlapping Motifs
To be Published
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2RQG
 | | Structure of GSPT1/ERF3A-PABC | | Descriptor: | G1 to S phase transition 1, Polyadenylate-binding protein 1 | | Authors: | Osawa, M, Nakanishi, T, Hosoda, N, Uchida, S, Hoshino, T, Katada, I, Shimada, I. | | Deposit date: | 2009-05-08 | | Release date: | 2010-05-26 | | Last modified: | 2023-06-14 | | Method: | SOLUTION NMR | | Cite: | Eukaryotic Translation Termination Factor Gspt/Erf3 Recognizes Pabp with Chemical Exchange Using Two Overlapping Motifs
To be Published
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1WZ1
 | | Crystal structure of the Fv fragment complexed with dansyl-lysine | | Descriptor: | Ig heavy chain, Ig light chain, N~6~-{[5-(DIMETHYLAMINO)-1-NAPHTHYL]SULFONYL}-L-LYSINE | | Authors: | Nakasako, M, Oka, T, Mashumo, M, Takahashi, H, Shimada, I, Yamaguchi, Y, Kato, K, Arata, Y. | | Deposit date: | 2005-02-21 | | Release date: | 2006-01-31 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Conformational dynamics of complementarity-determining region H3 of an anti-dansyl Fv fragment in the presence of its hapten
J.Mol.Biol., 351, 2005
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7EN4
 | | Multi-state structure determination and dynamics analysis elucidate a new ubiquitin-recognition mechanism of yeast ubiquitin C-terminal hydrolase. | | Descriptor: | Ubiquitin carboxyl-terminal hydrolase YUH1 | | Authors: | Okada, M, Tateishi, Y, Nojiri, E, Mikawa, T, Rajesh, S, Ogasawa, H, Ueda, T, Yagi, H, Kohno, T, Kigawa, T, Shimada, I, Guentert, P, Yutaka, I, Ikeya, T. | | Deposit date: | 2021-04-15 | | Release date: | 2022-04-20 | | Last modified: | 2023-06-14 | | Method: | SOLUTION NMR | | Cite: | Multi-state structure determination and dynamics analysis elucidate a new ubiquitin-recognition mechanism of yeast ubiquitin C-terminal hydrolase.
To Be Published
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2RSG
 | | Solution structure of the CERT PH domain | | Descriptor: | Collagen type IV alpha-3-binding protein | | Authors: | Sugiki, T, Takeuchi, K, Tokunaga, Y, Kumagai, K, Kawano, M, Nishijima, M, Hanada, K, Takahashi, H, Shimada, I. | | Deposit date: | 2012-02-25 | | Release date: | 2012-08-15 | | Last modified: | 2023-06-14 | | Method: | SOLUTION NMR | | Cite: | Structural basis for the Golgi association by the pleckstrin homology domain of the ceramide trafficking protein (CERT)
J.Biol.Chem., 287, 2012
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2RR8
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6AGP
 | | Structure of Rac1 in the low-affinity state for Mg2+ | | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, Ras-related C3 botulinum toxin substrate 1 | | Authors: | Toyama, Y, Kontani, K, Katada, T, Shimada, I. | | Deposit date: | 2018-08-13 | | Release date: | 2019-03-20 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Conformational landscape alternations promote oncogenic activities of Ras-related C3 botulinum toxin substrate 1 as revealed by NMR.
Sci Adv, 5, 2019
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1OAV
 | | OMEGA-AGATOXIN IVA | | Descriptor: | OMEGA-AGATOXIN IVA | | Authors: | Kim, J.I, Konishi, S, Iwai, H, Kohno, T, Gouda, H, Shimada, I, Sato, K, Arata, Y. | | Deposit date: | 1995-06-28 | | Release date: | 1995-10-15 | | Last modified: | 2017-11-29 | | Method: | SOLUTION NMR | | Cite: | Three-dimensional solution structure of the calcium channel antagonist omega-agatoxin IVA: consensus molecular folding of calcium channel blockers.
J.Mol.Biol., 250, 1995
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1OAW
 | | OMEGA-AGATOXIN IVA | | Descriptor: | OMEGA-AGATOXIN IVA | | Authors: | Kim, J.I, Konishi, S, Iwai, H, Kohno, T, Gouda, H, Shimada, I, Sato, K, Arata, Y. | | Deposit date: | 1995-06-28 | | Release date: | 1995-10-15 | | Last modified: | 2017-11-29 | | Method: | SOLUTION NMR | | Cite: | Three-dimensional solution structure of the calcium channel antagonist omega-agatoxin IVA: consensus molecular folding of calcium channel blockers.
J.Mol.Biol., 250, 1995
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1D1H
 | | SOLUTION STRUCTURE OF HANATOXIN 1 | | Descriptor: | HANATOXIN TYPE 1 | | Authors: | Takahashi, H, Kim, J.I, Sato, K, Swartz, K.J, Shimada, I. | | Deposit date: | 1999-09-16 | | Release date: | 2000-09-20 | | Last modified: | 2022-02-16 | | Method: | SOLUTION NMR | | Cite: | Solution structure of hanatoxin1, a gating modifier of voltage-dependent K(+) channels: common surface features of gating modifier toxins.
J.Mol.Biol., 297, 2000
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6KJO
 | | The microtubule-binding domains of yeast cytoplasmic dynein in the low affinity state | | Descriptor: | Dynein heavy chain, cytoplasmic | | Authors: | Nishida, N, Komori, Y, Takarada, O, Watanabe, A, Tamura, S, Kubo, S, Shimada, I, Kikkawa, M. | | Deposit date: | 2019-07-22 | | Release date: | 2020-03-18 | | Last modified: | 2023-06-14 | | Method: | SOLUTION NMR | | Cite: | Structural basis for two-way communication between dynein and microtubules.
Nat Commun, 11, 2020
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6KIQ
 | | Complex of yeast cytoplasmic dynein MTBD-High and MT with DTT | | Descriptor: | Alpha tubulin, Dynein heavy chain, cytoplasmic, ... | | Authors: | Komori, Y, Nishida, N, Shimada, I, Kikkawa, M. | | Deposit date: | 2019-07-19 | | Release date: | 2020-03-04 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (3.62 Å) | | Cite: | Structural basis for two-way communication between dynein and microtubules.
Nat Commun, 11, 2020
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6KJN
 | | The microtubule-binding domains of yeast cytoplasmic dynein in the high affinity state | | Descriptor: | Dynein heavy chain, cytoplasmic | | Authors: | Nishida, N, Komori, Y, Takarada, O, Watanabe, A, Tamura, S, Kubo, S, Shimada, I, Kikkawa, M. | | Deposit date: | 2019-07-22 | | Release date: | 2020-03-18 | | Last modified: | 2023-06-14 | | Method: | SOLUTION NMR | | Cite: | Structural basis for two-way communication between dynein and microtubules.
Nat Commun, 11, 2020
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6KIO
 | | Complex of yeast cytoplasmic dynein MTBD-High and MT without DTT | | Descriptor: | Dynein heavy chain, cytoplasmic, Tubulin alpha-1A chain, ... | | Authors: | Komori, Y, Nishida, N, Shimada, I, Kikkawa, M. | | Deposit date: | 2019-07-19 | | Release date: | 2020-03-04 | | Last modified: | 2020-03-11 | | Method: | ELECTRON MICROSCOPY (3.94 Å) | | Cite: | Structural basis for two-way communication between dynein and microtubules.
Nat Commun, 11, 2020
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6KR8
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2MLO
 | | Human CCR2 Membrane-Proximal C-Terminal Region (PRO-C) in a Membrane bound form | | Descriptor: | MCP-1 receptor | | Authors: | Esaki, K, Yoshinaga, S, Tsuji, T, Toda, E, Terashima, Y, Saitoh, T, Kohda, D, Kohno, T, Osawa, M, Ueda, T, Shimada, I, Matsushima, K, Terasawa, H. | | Deposit date: | 2014-03-04 | | Release date: | 2014-10-08 | | Last modified: | 2023-06-14 | | Method: | SOLUTION NMR | | Cite: | Structural basis for the binding of the membrane-proximal C-terminal region of chemokine receptor CCR2 with the cytosolic regulator FROUNT.
Febs J., 281, 2014
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2NOO
 | | Crystal Structure of Mutant NikA | | Descriptor: | IODIDE ION, NICKEL (II) ION, Nickel-binding periplasmic protein | | Authors: | Addy, C, Ohara, M, Kawai, F, Kidera, A, Ikeguchi, M, Fuchigami, S, Osawa, M, Shimada, I, Park, S.Y, Tame, J.R.H, Heddle, J.G. | | Deposit date: | 2006-10-26 | | Release date: | 2007-01-23 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography.
Acta Crystallogr.,Sect.D, 63, 2007
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