4X42
 
 | | Crystal structure of DEN4 ED3 mutant with epitope two residues substituted from DEN3 ED3 | | Descriptor: | Envelope protein E, SULFATE ION | | Authors: | Kulkarni, M.R, Islam, M.M, Numoto, N, Elahi, M.M, Ito, N, Kuroda, Y. | | Deposit date: | 2014-12-02 | | Release date: | 2015-09-09 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.78 Å) | | Cite: | Structural and biophysical analysis of sero-specific immune responses using epitope grafted Dengue ED3 mutants.
Biochim.Biophys.Acta, 1854, 2015
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3CI7
 | | Crystal structure of a simplified BPTI containing 20 alanines | | Descriptor: | SULFATE ION, bovine pancreatic trypsin inhibitor | | Authors: | Islam, M.M, Sohya, S, Noguchi, K, Yohda, M, Kuroda, Y. | | Deposit date: | 2008-03-11 | | Release date: | 2008-10-21 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Crystal structure of an extensively simplified variant of bovine pancreatic trypsin inhibitor in which over one-third of the residues are alanines
Proc.Natl.Acad.Sci.Usa, 105, 2008
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5B1C
 | | Crystal structure of DEN4 ED3 mutant with L387I | | Descriptor: | Envelope protein E, SULFATE ION | | Authors: | Kulkarni, M.R, Numoto, N, Ito, N, Kuroda, Y. | | Deposit date: | 2015-12-02 | | Release date: | 2016-02-24 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.003 Å) | | Cite: | Modeling and experimental assessment of a buried Leu-Ile mutation in dengue envelope domain III
Biochem.Biophys.Res.Commun., 471, 2016
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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, 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: | 2023-10-25 | | 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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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, 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: | 2023-10-25 | | 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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8HGL
 | | SARS-CoV-2 spike in complex with neutralizing antibody NIV-11 | | 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-11 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, 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: | 2022-11-15 | | Release date: | 2023-10-25 | | Method: | ELECTRON MICROSCOPY (2.9 Å) | | Cite: | Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
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8HGM
 | | Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-11 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-11 Fab heavy chain, NIV-11 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, 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: | 2022-11-15 | | Release date: | 2023-10-25 | | 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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8HES
 | | Crystal structure of SARS-CoV-2 RBD and NIV-10 complex | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-10 Fab H-chain, NIV-10 Fab L-chain, ... | | Authors: | Moriyama, S, Anraku, Y, Taminishi, 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: | 2022-11-08 | | Release date: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
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1WOT
 | | Structure of putative minimal nucleotidyltransferase | | Descriptor: | PUTATIVE MINIMAL NUCLEOTIDYLTRANSFERASE | | Authors: | Suzuki, S, Hatanaka, H, Hondoh, T, Okumura, A, Kuroda, Y, Kuramitsu, S, Shibata, T, Inoue, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-08-25 | | Release date: | 2004-09-07 | | Last modified: | 2022-03-02 | | Method: | SOLUTION NMR | | Cite: | Structure of Putative Minimal Nucleotidyltransferase
To be Published
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1IYR
 | | NMR Structure Ensemble Of Dff-C Domain | | Descriptor: | DNA FRAGMENTATION FACTOR ALPHA SUBUNIT | | Authors: | Fukushima, K, Kikuchi, J, Koshiba, S, Kigawa, T, Kuroda, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-09-05 | | Release date: | 2002-09-25 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution Structure of the Dff-C Domain of Dff45/Icad. A Structural Basis for the Regulation of Apoptotic DNA Fragmentation
J.Mol.Biol., 321, 2002
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1KOY
 | | NMR structure of DFF-C domain | | Descriptor: | DNA fragmentation factor alpha subunit | | Authors: | Fukushima, K, Kikuchi, J, Koshiba, S, Kigawa, T, Kuroda, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2001-12-25 | | Release date: | 2002-09-04 | | Last modified: | 2022-02-23 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the DFF-C domain of DFF45/ICAD. A structural basis for the regulation of apoptotic DNA fragmentation.
J.Mol.Biol., 321, 2002
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7D2O
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2ZJX
 | | Bovine pancreatic trypsin inhibitor (BPTI) containing only the [5,55] disulfide bond | | Descriptor: | Pancreatic trypsin inhibitor, SULFATE ION | | Authors: | Islam, M.M, Sohya, S, Noguchi, K, Yohda, M, Kuroda, Y. | | Deposit date: | 2008-03-11 | | Release date: | 2008-10-21 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (1.09 Å) | | Cite: | Crystal structure of an extensively simplified variant of bovine pancreatic trypsin inhibitor in which over one-third of the residues are alanines
Proc.Natl.Acad.Sci.Usa, 105, 2008
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2ZVX
 | | Structure of a BPTI-[5,55] variant containing Gly/Val at the 14/38th positions | | Descriptor: | Pancreatic trypsin inhibitor, SULFATE ION | | Authors: | Islam, M.M, Sohya, S, Noguchi, K, Yohda, M, Kuroda, Y. | | Deposit date: | 2008-11-24 | | Release date: | 2009-10-13 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.09 Å) | | Cite: | Thermodynamic and structural analysis of highly stabilized BPTIs by single and double mutations
Proteins, 77, 2009
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3AUG
 | | A simplified BPTI variant with poly Pro amino acid tag (C5P) at the C-terminus | | Descriptor: | Bovine pancreatic trypsin inhibitor, SULFATE ION | | Authors: | Islam, M.M, Kato, A, Khan, M.M.A, Noguchi, K, Yohda, M, Kidokoro, S.I, Kuroda, Y. | | Deposit date: | 2011-02-03 | | Release date: | 2012-02-08 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.398 Å) | | Cite: | Effect of amino acid mutations of protein's solubility, function and structure characterized using short poly amino acid peptide tags
To be Published
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3AUD
 | | Simplified BPTI variant with poly Asn amino acid tag (C5N) at the C-terminus | | Descriptor: | Bovine pancreatic trypsin inhibitor | | Authors: | Islam, M.M, Kato, A, Khan, M.M.A, Noguchi, K, Yohda, M, Kidokoro, S.I, Kuroda, Y. | | Deposit date: | 2011-02-03 | | Release date: | 2012-02-08 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.943 Å) | | Cite: | Effect of amino acid mutations on protein's solubility, function and structure characterized using short poly amino acid peptide tags
To be Published
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3AUB
 | | A simplified BPTI variant stabilized by the A14G and A38V substitutions | | Descriptor: | Bovine Pancreatic trypsin inhibitor | | Authors: | Islam, M.M, Kato, A, Khan, M.M.A, Noguchi, K, Yohda, M, Kidokoro, S.I, Kuroda, Y. | | Deposit date: | 2011-02-03 | | Release date: | 2012-02-08 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1 Å) | | Cite: | Effect of amino acid mutations of protein's solubility, function and structure characterized using short poly amino acid peptide tags
To be Published
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3AUI
 | | A simplified BPTI variant with poly Glu amino acid tag (C3E) at the C-terminus | | Descriptor: | Bovine pancreatic trypsin inhibitor, SULFATE ION | | Authors: | Islam, M.M, Kato, A, Khan, M.M.A, Noguchi, K, Yohda, M, Kidokoro, S.I, Kuroda, Y. | | Deposit date: | 2011-02-03 | | Release date: | 2012-02-08 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.851 Å) | | Cite: | Effect of amino acid mutations on protein's solubility, function and structure characterized using short poly amino acid peptide tags
To be Published
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3AUH
 | | A simplified BPTI variant with poly Arg amino acid tag (C3R) at the C-terminus | | Descriptor: | Bovine pancreatic trypsin inhibitor, SULFATE ION | | Authors: | Islam, M.M, Kato, A, Khan, M.M.A, Noguchi, K, Yohda, M, Kidokoro, S.I, Kuroda, Y. | | Deposit date: | 2011-02-03 | | Release date: | 2012-02-08 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.2 Å) | | Cite: | Effect of amino acid mutations on protein's solubility, function and structure characterized using short poly amino acid peptide tags
To be Published
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3AUC
 | | A simplified BPTI variant with poly SER (C5S) amino acid tag at the c-terminus | | Descriptor: | Bovine pancreatic trypsin inhibitor, SULFATE ION | | Authors: | Islam, M.M, Kato, A, Khan, M.M.A, Noguchi, K, Yohda, M, Kidokoro, S.I, Kuroda, Y. | | Deposit date: | 2011-02-03 | | Release date: | 2012-02-08 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.91 Å) | | Cite: | Effect of amino acid mutations on protein's solubility, function and structure characterized using short poly amino acid peptide tags
To be Published
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3AUE
 | | A simplified BPTI variant with poly His amino acid tag (C5H) at the C-terminus | | Descriptor: | Bovine pancreatic trypsin inhibitor, SULFATE ION | | Authors: | Islam, M.M, Kato, A, Khan, M.M.A, Noguchi, K, Yohda, M, Kidokoro, S.I, Kuroda, Y. | | Deposit date: | 2011-02-03 | | Release date: | 2012-02-08 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.28 Å) | | Cite: | Effect of amino acid mutations on protein's solubility, function and structure characterized using short poly amino acid peptide tags
To be Published
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3VTT
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3WE1
 | | Crystal structure of Dengue 4 Envelope protein domain III (ED3) | | Descriptor: | Envelope protein E | | Authors: | Elahi, M, Islam, M.M, Noguchi, K, Yohda, M, Toh, H, Kuroda, Y. | | Deposit date: | 2013-06-27 | | Release date: | 2014-01-22 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.278 Å) | | Cite: | Computational prediction and experimental characterization of a "size switch type repacking" during the evolution of dengue envelope protein domain III (ED3).
Biochim.Biophys.Acta, 1844, 2014
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7N82
 | | NMR Solution structure of Se0862 | | Descriptor: | Biofilm-related protein | | Authors: | Zhang, N, LiWang, A.L. | | Deposit date: | 2021-06-11 | | Release date: | 2021-07-14 | | Last modified: | 2023-06-14 | | Method: | SOLUTION NMR | | Cite: | Assessment of prediction methods for protein structures determined by NMR in CASP14: Impact of AlphaFold2.
Proteins, 89, 2021
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5JB6
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