2Z3L
 
 | | complex structure of LF-transferase and peptide A | | Descriptor: | D(-)-TARTARIC ACID, Leucyl/phenylalanyl-tRNA-protein transferase, peptide (PHE)(ARG)(TYR)(LEU)(GLY) | | Authors: | Watanabe, K, Toh, Y, Tomita, K. | | Deposit date: | 2007-06-04 | | Release date: | 2007-10-23 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.75 Å) | | Cite: | Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase
Nature, 449, 2007
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2Z3P
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2Z3O
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2Z3N
 | | complex structure of LF-transferase and peptide B | | Descriptor: | D(-)-TARTARIC ACID, Leucyl/phenylalanyl-tRNA-protein transferase, peptide (PHE)(ARG)(TYR)(LEU)(GLY) | | Authors: | Watanabe, K, Toh, Y, Tomita, K. | | Deposit date: | 2007-06-04 | | Release date: | 2007-10-23 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase
Nature, 449, 2007
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7QI4
 | | Human mitochondrial ribosome at 2.2 A resolution (bound to partly built tRNAs and mRNA) | | Descriptor: | 1,4-DIAMINOBUTANE, 12S mitochondrial rRNA, 16S mitochondrial rRNA, ... | | Authors: | Singh, V, Itoh, Y, Amunts, A. | | Deposit date: | 2021-12-14 | | Release date: | 2022-07-13 | | Last modified: | 2024-07-31 | | Method: | ELECTRON MICROSCOPY (2.21 Å) | | Cite: | Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk.
Nat Commun, 15, 2024
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7QI6
 | | Human mitochondrial ribosome in complex with mRNA, A/P- and P/E-tRNAs at 2.98 A resolution | | Descriptor: | 1,4-DIAMINOBUTANE, 12S mitochondrial rRNA, 16S mitochondrial rRNA, ... | | Authors: | Singh, V, Itoh, Y, Amunts, A. | | Deposit date: | 2021-12-14 | | Release date: | 2023-05-17 | | Last modified: | 2024-07-31 | | Method: | ELECTRON MICROSCOPY (2.98 Å) | | Cite: | Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk.
Nat Commun, 15, 2024
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7QI5
 | | Human mitochondrial ribosome in complex with mRNA, A/A-, P/P- and E/E-tRNAs at 2.63 A resolution | | Descriptor: | 1,4-DIAMINOBUTANE, 12S mitochondrial rRNA, 16S mitochondrial rRNA, ... | | Authors: | Singh, V, Itoh, Y, Amunts, A. | | Deposit date: | 2021-12-14 | | Release date: | 2023-07-05 | | Last modified: | 2024-07-31 | | Method: | ELECTRON MICROSCOPY (2.63 Å) | | Cite: | Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk.
Nat Commun, 15, 2024
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8ANY
 | | Human mitochondrial ribosome in complex with LRPPRC, SLIRP, A-site, P-site, E-site tRNAs and mRNA | | Descriptor: | 1,4-DIAMINOBUTANE, 12S mitochondrial rRNA, 16S mitochondrial rRNA, ... | | Authors: | Singh, V, Itoh, Y, Amunts, A. | | Deposit date: | 2022-08-06 | | Release date: | 2023-08-16 | | Last modified: | 2024-09-04 | | Method: | ELECTRON MICROSCOPY (2.85 Å) | | Cite: | Structural basis of LRPPRC-SLIRP-dependent translation by the mitoribosome.
Nat.Struct.Mol.Biol., 2024
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8YGJ
 | | SpCas9-MMLV RT-pegRNA-target DNA complex (elongation 28-nt) | | Descriptor: | CRISPR-associated endonuclease Cas9/Csn1, DNA (5'-D(P*TP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*TP*AP*CP*TP*AP*G)-3'), DNA (51-MER), ... | | Authors: | Shuto, Y, Nakagawa, R, Hoki, M, Omura, S.N, Hirano, H, Itoh, Y, Nureki, O. | | Deposit date: | 2024-02-26 | | Release date: | 2024-06-05 | | Last modified: | 2024-09-11 | | Method: | ELECTRON MICROSCOPY (3.2 Å) | | Cite: | Structural basis for pegRNA-guided reverse transcription by a prime editor.
Nature, 631, 2024
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7QIW
 | | Specific features and methylation sites of a plant ribosome. 60S ribosomal subunit. | | Descriptor: | 25S rRNA, 5.8S rRNA, 50S ribosomal protein L22, ... | | Authors: | Cottilli, P, Itoh, Y, Amunts, A. | | Deposit date: | 2021-12-16 | | Release date: | 2022-07-13 | | Last modified: | 2023-11-15 | | Method: | ELECTRON MICROSCOPY (2.35 Å) | | Cite: | Cryo-EM structure and rRNA modification sites of a plant ribosome.
Plant Commun., 3, 2022
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7QIZ
 | | Specific features and methylation sites of a plant 80S ribosome | | Descriptor: | 1,4-DIAMINOBUTANE, 18S, 25S rRNA, ... | | Authors: | Cottilli, P, Itoh, Y, Amunts, A. | | Deposit date: | 2021-12-16 | | Release date: | 2022-08-03 | | Last modified: | 2024-04-24 | | Method: | ELECTRON MICROSCOPY (2.38 Å) | | Cite: | Cryo-EM structure and rRNA modification sites of a plant ribosome.
Plant Commun., 3, 2022
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7QIY
 | | Specific features and methylation sites of a plant ribosome. 40S head ribosomal subunit. | | Descriptor: | 1,4-DIAMINOBUTANE, 18S rRNA head, 40S head ribosomal protein eS19, ... | | Authors: | Cottilli, P, Itoh, Y, Amunts, A. | | Deposit date: | 2021-12-16 | | Release date: | 2022-06-15 | | Last modified: | 2024-04-24 | | Method: | ELECTRON MICROSCOPY (2.58 Å) | | Cite: | Cryo-EM structure and rRNA modification sites of a plant ribosome.
Plant Commun., 3, 2022
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7QIX
 | | Specific features and methylation sites of a plant ribosome. 40S body ribosomal subunit. | | Descriptor: | 18S rRNA body, 30S ribosomal protein S15, chloroplastic, ... | | Authors: | Cottilli, P, Itoh, Y, Amunts, A. | | Deposit date: | 2021-12-16 | | Release date: | 2022-06-15 | | Last modified: | 2024-04-24 | | Method: | ELECTRON MICROSCOPY (2.53 Å) | | Cite: | Cryo-EM structure and rRNA modification sites of a plant ribosome.
Plant Commun., 3, 2022
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2N37
 | | Solution structure of AVR-Pia | | Descriptor: | AVR-Pia protein | | Authors: | Ose, T, Oikawa, A, Nakamura, Y, Maenaka, K, Higuchi, Y, Satoh, Y, Fujiwara, S, Demura, M, Sone, T. | | Deposit date: | 2015-05-25 | | Release date: | 2015-10-14 | | Last modified: | 2023-06-14 | | Method: | SOLUTION NMR | | Cite: | Solution structure of an avirulence protein, AVR-Pia, from Magnaporthe oryzae
J.Biomol.Nmr, 63, 2015
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6J7C
 | | Crystal structure of proline racemase-like protein from Thermococcus litoralis in complex with proline | | Descriptor: | PROLINE, Proline racemase | | Authors: | Watanabe, Y, Watanabe, S, Itoh, Y, Watanabe, Y. | | Deposit date: | 2019-01-17 | | Release date: | 2019-02-27 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Crystal structure of substrate-bound bifunctional proline racemase/hydroxyproline epimerase from a hyperthermophilic archaeon.
Biochem. Biophys. Res. Commun., 511, 2019
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8HIO
 | | Cryo-EM structure of the Cas12m2-crRNA binary complex | | Descriptor: | Cas12m2, MAGNESIUM ION, RNA (56-MER), ... | | Authors: | Omura, N.S, Nakagawa, R, Wu, Y.W, Sudfeld, C, Warren, V.R, Hirano, H, Kusakizako, T, Kise, Y, Lebbink, H.G.J, Itoh, Y, Oost, V.D.J, Nureki, O. | | Deposit date: | 2022-11-21 | | Release date: | 2023-04-12 | | Last modified: | 2023-08-30 | | Method: | ELECTRON MICROSCOPY (3.73 Å) | | Cite: | Mechanistic and evolutionary insights into a type V-M CRISPR-Cas effector enzyme.
Nat.Struct.Mol.Biol., 30, 2023
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8HHM
 | | Cryo-EM structure of the Cas12m2-crRNA-target DNA ternary complex intermediate state | | Descriptor: | Cas12m2, DNA (36-MER), MAGNESIUM ION, ... | | Authors: | Omura, N.S, Nakagawa, R, Wu, Y.W, Sudfeld, C, Warren, V.R, Hirano, H, Kusakizako, T, Kise, Y, Lebbink, H.G.J, Itoh, Y, Oost, V.D.J, Nureki, O. | | Deposit date: | 2022-11-16 | | Release date: | 2023-04-12 | | Last modified: | 2024-05-22 | | Method: | ELECTRON MICROSCOPY (3.08 Å) | | Cite: | Mechanistic and evolutionary insights into a type V-M CRISPR-Cas effector enzyme.
Nat.Struct.Mol.Biol., 30, 2023
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8HHL
 | | Cryo-EM structure of the Cas12m2-crRNA-target DNA full R-loop complex | | Descriptor: | Cas12m2, MAGNESIUM ION, NTS (36-MER), ... | | Authors: | Omura, N.S, Nakagawa, R, Wu, Y.W, Sudfeld, C, Warren, V.R, Hirano, H, Kusakizako, T, Kise, Y, Lebbink, H.G.J, Itoh, Y, Oost, V.D.J, Nureki, O. | | Deposit date: | 2022-11-16 | | Release date: | 2023-04-12 | | Last modified: | 2023-08-30 | | Method: | ELECTRON MICROSCOPY (2.87 Å) | | Cite: | Mechanistic and evolutionary insights into a type V-M CRISPR-Cas effector enzyme.
Nat.Struct.Mol.Biol., 30, 2023
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8WUS
 | | SpCas9-MMLV RT-pegRNA-target DNA complex (termination) | | Descriptor: | CRISPR-associated endonuclease Cas9/Csn1, DNA (40-MER), DNA (5'-D(*TP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*TP*AP*CP*TP*AP*G)-3'), ... | | Authors: | Shuto, Y, Nakagawa, R, Hoki, M, Omura, S.N, Hirano, H, Itoh, Y, Nureki, O. | | Deposit date: | 2023-10-21 | | Release date: | 2024-06-05 | | Last modified: | 2024-09-11 | | Method: | ELECTRON MICROSCOPY (2.9 Å) | | Cite: | Structural basis for pegRNA-guided reverse transcription by a prime editor.
Nature, 631, 2024
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8WUV
 | | SpCas9-MMLV RT-pegRNA-target DNA complex (elongation 16-nt) | | Descriptor: | CRISPR-associated endonuclease Cas9/Csn1, DNA (5'-D(*TP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*TP*AP*CP*TP*AP*G)-3'), DNA (50-MER), ... | | Authors: | Shuto, Y, Nakagawa, R, Hoki, M, Omura, S.N, Hirano, H, Itoh, Y, Nureki, O. | | Deposit date: | 2023-10-21 | | Release date: | 2024-06-05 | | Last modified: | 2024-09-11 | | Method: | ELECTRON MICROSCOPY (3 Å) | | Cite: | Structural basis for pegRNA-guided reverse transcription by a prime editor.
Nature, 631, 2024
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8WUU
 | | SpCas9-pegRNA-target DNA complex (pre-initiation) | | Descriptor: | CRISPR-associated endonuclease Cas9/Csn1, DNA (34-MER), DNA (5'-D(*TP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*TP*AP*CP*TP*AP*G)-3'), ... | | Authors: | Shuto, Y, Nakagawa, R, Hoki, M, Omura, S.N, Hirano, H, Itoh, Y, Nureki, O. | | Deposit date: | 2023-10-21 | | Release date: | 2024-06-05 | | Last modified: | 2024-09-11 | | Method: | ELECTRON MICROSCOPY (3.2 Å) | | Cite: | Structural basis for pegRNA-guided reverse transcription by a prime editor.
Nature, 631, 2024
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8WUT
 | | SpCas9-MMLV RT-pegRNA-target DNA complex (initiation) | | Descriptor: | CRISPR-associated endonuclease Cas9/Csn1, DNA (5'-D(*TP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*TP*AP*CP*TP*AP*G)-3'), DNA (51-MER), ... | | Authors: | Shuto, Y, Nakagawa, R, Hoki, M, Omura, S.N, Hirano, H, Itoh, Y, Nureki, O. | | Deposit date: | 2023-10-21 | | Release date: | 2024-06-05 | | Last modified: | 2024-09-11 | | Method: | ELECTRON MICROSCOPY (3 Å) | | Cite: | Structural basis for pegRNA-guided reverse transcription by a prime editor.
Nature, 631, 2024
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8J1J
 | | Cryo-EM structure of the AsCas12f-YHAM-sgRNAS3-5v7-target DNA | | Descriptor: | DNA (38-MER), MAGNESIUM ION, RNA (118-MER), ... | | Authors: | Hino, T, Omura, N.S, Nakagawa, R, Togashi, T, Takeda, N.S, Hiramoto, T, Tasaka, S, Hirano, H, Tokuyama, T, Uosaki, H, Ishiguro, H, Yamano, H, Ozaki, Y, Motooka, D, Mori, H, Kirita, Y, Kise, Y, Itoh, Y, Matoba, S, Aburatani, H, Yachie, N, Siksnys, V, Ohmori, T, Hoshino, A, Nureki, O. | | Deposit date: | 2023-04-13 | | Release date: | 2023-09-27 | | Method: | ELECTRON MICROSCOPY (2.91 Å) | | Cite: | Minimal and most efficient genome editing Cas enzyme
To Be Published
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8J3R
 | | Cryo-EM structure of the AsCas12f-HKRA-sgRNAS3-5v7-target DNA | | Descriptor: | DNA (37-MER), DNA (38-MER), MAGNESIUM ION, ... | | Authors: | Hino, T, Omura, N.S, Nakagawa, R, Togashi, T, Takeda, N.S, Hiramoto, T, Tasaka, S, Hirano, H, Tokuyama, T, Uosaki, H, Ishiguro, H, Yamano, H, Ozaki, Y, Motooka, D, Mori, H, Kirita, Y, Kise, Y, Itoh, Y, Matoba, S, Aburatani, H, Yachie, N, Siksnys, V, Ohmori, T, Hoshino, A, Nureki, O. | | Deposit date: | 2023-04-18 | | Release date: | 2023-09-27 | | Method: | ELECTRON MICROSCOPY (2.95 Å) | | Cite: | Minimal and most efficient genome editing Cas enzyme
To Be Published
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8J12
 | | Cryo-EM structure of the AsCas12f-sgRNA-target DNA ternary complex | | Descriptor: | DNA (38-MER), MAGNESIUM ION, RNA (247-MER), ... | | Authors: | Hino, T, Omura, N.S, Nakagawa, R, Togashi, T, Takeda, N.S, Hiramoto, T, Tasaka, S, Hirano, H, Tokuyama, T, Uosaki, H, Ishiguro, H, Yamano, H, Ozaki, Y, Motooka, D, Mori, H, Kirita, Y, Kise, Y, Itoh, Y, Matoba, S, Aburatani, H, Yachie, N, Siksnys, V, Ohmori, T, Hoshino, A, Nureki, O. | | Deposit date: | 2023-04-12 | | Release date: | 2023-09-27 | | Method: | ELECTRON MICROSCOPY (3.08 Å) | | Cite: | Minimal and most efficient genome editing Cas enzyme
To Be Published
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