8UPT
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![BU of 8upt by Molmil](/molmil-images/mine/8upt) | Candidatus Methanomethylophilus alvus tRNAPyl in A-site of ribosome | Descriptor: | RNA (71-MER) | Authors: | Krahn, N, Zhang, J, Melnikov, S.V, Tharp, J.M, Villa, A, Patel, A, Howard, R.J, Gabir, H, Patel, T.R, Stetefeld, J, Puglisi, J, Soll, D. | Deposit date: | 2023-10-23 | Release date: | 2024-01-10 | Last modified: | 2024-02-07 | Method: | ELECTRON MICROSCOPY (2.8 Å) | Cite: | tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut. Nucleic Acids Res., 52, 2024
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1IRX
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![BU of 1irx by Molmil](/molmil-images/mine/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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6N9F
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![BU of 6n9f by Molmil](/molmil-images/mine/6n9f) | Crystal structure of the Thermus thermophilus 70S ribosome in complex with a short substrate mimic ACCA-DPhe and bound to mRNA and P-site tRNA at 3.7A resolution | Descriptor: | 16S Ribosomal RNA, 23S Ribosomal RNA, 30S Ribosomal Protein S19, ... | Authors: | Melnikov, S.V, Khabibullina, N.F, Mairhofer, E, Vargas-Rodriguez, O, Reynolds, N.M, Micura, R, Soll, D, Polikanov, Y.S. | Deposit date: | 2018-12-03 | Release date: | 2018-12-12 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (3.7 Å) | Cite: | Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site. Nucleic Acids Res., 47, 2019
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6N9E
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![BU of 6n9e by Molmil](/molmil-images/mine/6n9e) | Crystal structure of the Thermus thermophilus 70S ribosome in complex with a short substrate mimic CC-Pmn and bound to mRNA and P-site tRNA at 3.7A resolution | Descriptor: | 16S Ribosomal RNA, 23S Ribosomal RNA, 30S Ribosomal Protein S19, ... | Authors: | Melnikov, S.V, Khabibullina, N.F, Mairhofer, E, Vargas-Rodriguez, O, Reynolds, N.M, Micura, R, Soll, D, Polikanov, Y.S. | Deposit date: | 2018-12-03 | Release date: | 2018-12-12 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (3.7 Å) | Cite: | Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site. Nucleic Acids Res., 47, 2019
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7UR5
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![BU of 7ur5 by Molmil](/molmil-images/mine/7ur5) | allo-tRNAUTu1 in the A, P, and E sites of the E. coli ribosome | Descriptor: | allo-tRNAUTu1 | Authors: | Zhang, J, Krahn, N, Prabhakar, A, Vargas-Rodriguez, O, Krupkin, M, Fu, Z, Acosta-Reyes, F.J, Ge, X, Choi, J, Crnkovic, A, Ehrenberg, M, Viani Puglisi, E, Soll, D, Puglisi, J. | Deposit date: | 2022-04-21 | Release date: | 2022-08-10 | Last modified: | 2024-06-12 | Method: | ELECTRON MICROSCOPY (2.6 Å) | Cite: | Uncovering translation roadblocks during the development of a synthetic tRNA. Nucleic Acids Res., 50, 2022
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7URI
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![BU of 7uri by Molmil](/molmil-images/mine/7uri) | allo-tRNAUTu1A in the A site of the E. coli ribosome | Descriptor: | Allo-tRNAUTu1A | Authors: | Zhang, J, Prabhakar, A, Krahn, N, Vargas-Rodriguez, O, Krupkin, M, Fu, Z, Acosta-Reyes, F.J, Ge, X, Choi, J, Crnkovic, A, Ehrenberg, M, Viani Puglisi, E, Soll, D, Puglisi, J. | Deposit date: | 2022-04-22 | Release date: | 2022-08-10 | Last modified: | 2024-06-12 | Method: | ELECTRON MICROSCOPY (2.6 Å) | Cite: | Uncovering translation roadblocks during the development of a synthetic tRNA. Nucleic Acids Res., 50, 2022
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7URM
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![BU of 7urm by Molmil](/molmil-images/mine/7urm) | allo-tRNAUTu1A in the P site of the E. coli ribosome | Descriptor: | allo-tRNAUTU1A | Authors: | Zhang, J, Prabhakar, A, Krahn, N, Vargas-Rodriguez, O, Krupkin, M, Fu, Z, Acosta-Reyes, F.J, Ge, X, Choi, J, Crnkovic, A, Ehrenberg, M, Viani Puglisi, E, Soll, D, Puglisi, J. | Deposit date: | 2022-04-22 | Release date: | 2022-08-10 | Last modified: | 2024-06-12 | Method: | ELECTRON MICROSCOPY (3 Å) | Cite: | Uncovering translation roadblocks during the development of a synthetic tRNA. Nucleic Acids Res., 50, 2022
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3UH0
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![BU of 3uh0 by Molmil](/molmil-images/mine/3uh0) | Crystal structure of the yeast mitochondrial threonyl-tRNA synthetase (MST1) in complex with threonyl sulfamoyl adenylate | Descriptor: | 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE, SULFATE ION, Threonyl-tRNA synthetase, ... | Authors: | Peterson, K.M, Ling, J, Simonovic, I, Cho, C, Soll, D, Simonovic, M. | Deposit date: | 2011-11-03 | Release date: | 2012-02-22 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment. Proc.Natl.Acad.Sci.USA, 109, 2012
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4ZIB
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![BU of 4zib by Molmil](/molmil-images/mine/4zib) | Crystal Structure of the C-terminal domain of PylRS mutant bound with 3-benzothienyl-l-alanine and ATP | Descriptor: | 1,2-ETHANEDIOL, 3-(1-benzothiophen-3-yl)-L-alanine, ADENOSINE-5'-TRIPHOSPHATE, ... | Authors: | Nakamura, A, Guo, L.T, Wang, Y.S, Soll, D. | Deposit date: | 2015-04-28 | Release date: | 2016-03-02 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.054 Å) | Cite: | Probing the active site tryptophan of Staphylococcus aureus thioredoxin with an analog. Nucleic Acids Res., 43, 2015
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2CJB
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![BU of 2cjb by Molmil](/molmil-images/mine/2cjb) | Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with serine | Descriptor: | CHLORIDE ION, SERINE, SERYL-TRNA SYNTHETASE, ... | Authors: | Bilokapic, S, Maier, T, Ahel, D, Gruic-Sovulj, I, Soll, D, Weygand-Durasevic, I, Ban, N. | Deposit date: | 2006-03-30 | Release date: | 2006-06-26 | Last modified: | 2024-05-08 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Structure of the Unusual Seryl-tRNA Synthetase Reveals a Distinct Zinc-Dependent Mode of Substrate Recognition Embo J., 25, 2006
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2CJA
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![BU of 2cja by Molmil](/molmil-images/mine/2cja) | Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with ATP | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, MAGNESIUM ION, ... | Authors: | Bilokapic, S, Maier, T, Ahel, D, Gruic-Sovulj, I, Soll, D, Weygand-Durasevic, I, Ban, N. | Deposit date: | 2006-03-30 | Release date: | 2006-06-26 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Structure of the Unusual Seryl-tRNA Synthetase Reveals a Distinct Zinc-Dependent Mode of Substrate Recognition Embo J., 25, 2006
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2CJ9
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![BU of 2cj9 by Molmil](/molmil-images/mine/2cj9) | Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with an analog of seryladenylate | Descriptor: | 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE, CHLORIDE ION, SERYL-TRNA SYNTHETASE, ... | Authors: | Bilokapic, S, Maier, T, Ahel, D, Gruic-Sovulj, I, Soll, D, Weygand-Durasevic, I, Ban, N. | Deposit date: | 2006-03-29 | Release date: | 2006-06-26 | Last modified: | 2024-05-08 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structure of the Unusual Seryl-tRNA Synthetase Reveals a Distinct Zinc-Dependent Mode of Substrate Recognition Embo J., 25, 2006
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2CIM
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![BU of 2cim by Molmil](/molmil-images/mine/2cim) | Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase | Descriptor: | CHLORIDE ION, PLATINUM (II) ION, SERYL-TRNA SYNTHETASE, ... | Authors: | Bilokapic, S, Maier, T, Ahel, D, Gruic-Sovulj, I, Soll, D, Weygand-Durasevic, I, Ban, N. | Deposit date: | 2006-03-24 | Release date: | 2006-06-26 | Last modified: | 2024-05-08 | Method: | X-RAY DIFFRACTION (2.51 Å) | Cite: | Structure of the Unusual Seryl-tRNA Synthetase Reveals a Distinct Zinc-Dependent Mode of Substrate Recognition Embo J., 25, 2006
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4TQD
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![BU of 4tqd by Molmil](/molmil-images/mine/4tqd) | Crystal Structure of the C-terminal domain of IFRS bound with 3-iodo-L-Phe and ATP | Descriptor: | 1,2-ETHANEDIOL, 3-iodo-L-phenylalanine, ADENOSINE-5'-TRIPHOSPHATE, ... | Authors: | Nakamura, A, O'Donoghue, P, Soll, D. | Deposit date: | 2014-06-11 | Release date: | 2014-11-12 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.1429 Å) | Cite: | Polyspecific pyrrolysyl-tRNA synthetases from directed evolution. Proc.Natl.Acad.Sci.USA, 111, 2014
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4TQF
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![BU of 4tqf by Molmil](/molmil-images/mine/4tqf) | Crystal Structure of the C-terminal domain of IFRS bound with 2-(5-bromothienyl)-L-Ala and ATP | Descriptor: | 1,2-ETHANEDIOL, 3-(5-bromothiophen-2-yl)-L-alanine, ADENOSINE-5'-TRIPHOSPHATE, ... | Authors: | Nakamura, A, O'Donoghue, P, Soll, D. | Deposit date: | 2014-06-11 | Release date: | 2014-11-12 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (2.7143 Å) | Cite: | Polyspecific pyrrolysyl-tRNA synthetases from directed evolution. Proc.Natl.Acad.Sci.USA, 111, 2014
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5UD5
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![BU of 5ud5 by Molmil](/molmil-images/mine/5ud5) | |
3HL2
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![BU of 3hl2 by Molmil](/molmil-images/mine/3hl2) | The crystal structure of the human SepSecS-tRNASec complex | Descriptor: | (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE, Monothiophosphate, O-phosphoseryl-tRNA(Sec) selenium transferase, ... | Authors: | Palioura, S, Steitz, T.A, Soll, D, Simonovic, M. | Deposit date: | 2009-05-26 | Release date: | 2009-10-06 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (2.81 Å) | Cite: | The human SepSecS-tRNASec complex reveals the mechanism of selenocysteine formation. Science, 325, 2009
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4Y4P
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![BU of 4y4p by Molmil](/molmil-images/mine/4y4p) | Crystal structure of the Thermus thermophilus 70S ribosome with rRNA modifications and bound to mRNA and A-, P- and E-site tRNAs at 2.5A resolution | Descriptor: | 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ... | Authors: | Polikanov, Y.S, Melnikov, S.V, Soll, D, Steitz, T.A. | Deposit date: | 2015-02-10 | Release date: | 2015-03-18 | Last modified: | 2019-12-25 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly. Nat.Struct.Mol.Biol., 22, 2015
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4Y4O
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![BU of 4y4o by Molmil](/molmil-images/mine/4y4o) | Crystal structure of the Thermus thermophilus 70S ribosome with rRNA modifications and bound to protein Y (YfiA) at 2.3A resolution | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 16S Ribosomal RNA, 23S Ribosomal RNA, ... | Authors: | Polikanov, Y.S, Melnikov, S.V, Soll, D, Steitz, T.A. | Deposit date: | 2015-02-10 | Release date: | 2015-03-18 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly. Nat.Struct.Mol.Biol., 22, 2015
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5V6X
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![BU of 5v6x by Molmil](/molmil-images/mine/5v6x) | |
4DWR
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![BU of 4dwr by Molmil](/molmil-images/mine/4dwr) | RNA ligase RtcB/Mn2+ complex | Descriptor: | MANGANESE (II) ION, SULFATE ION, beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose, ... | Authors: | Xia, S, Englert, M, Soll, D, Wang, J. | Deposit date: | 2012-02-26 | Release date: | 2012-09-05 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.48 Å) | Cite: | Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3'-terminal phosphate and 5'-OH. Proc.Natl.Acad.Sci.USA, 109, 2012
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4EO4
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![BU of 4eo4 by Molmil](/molmil-images/mine/4eo4) | Crystal structure of the yeast mitochondrial threonyl-tRNA synthetase (MST1) in complex with seryl sulfamoyl adenylate | Descriptor: | 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE, Threonine--tRNA ligase, mitochondrial, ... | Authors: | Peterson, K.M, Ling, J, Simonovic, I, Soll, D, Simonovic, M. | Deposit date: | 2012-04-13 | Release date: | 2012-07-11 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (2.87 Å) | Cite: | The mechanism of pre-transfer editing in yeast mitochondrial threonyl-tRNA synthetase. J.Biol.Chem., 287, 2012
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4DWQ
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![BU of 4dwq by Molmil](/molmil-images/mine/4dwq) | RNA ligase RtcB-GMP/Mn(2+) complex | Descriptor: | GLYCEROL, GUANOSINE-5'-MONOPHOSPHATE, MALONATE ION, ... | Authors: | Okada, C, Xia, S, Englert, M, Yao, M, Soll, D, Wang, J. | Deposit date: | 2012-02-26 | Release date: | 2012-09-05 | Last modified: | 2017-08-02 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3'-terminal phosphate and 5'-OH. Proc.Natl.Acad.Sci.USA, 109, 2012
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3H0R
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![BU of 3h0r by Molmil](/molmil-images/mine/3h0r) | Structure of trna-dependent amidotransferase gatcab from aquifex aeolicus | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, ADENOSINE-5'-TRIPHOSPHATE, ASPARAGINE, ... | Authors: | Wu, J, Bu, W, Sheppard, K, Kitabatake, M, Soll, D, Smith, J.L. | Deposit date: | 2009-04-10 | Release date: | 2009-07-21 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Insights into tRNA-Dependent Amidotransferase Evolution and Catalysis from the Structure of the Aquifex aeolicus Enzyme J.Mol.Biol., 391, 2009
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3H0M
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![BU of 3h0m by Molmil](/molmil-images/mine/3h0m) | Structure of trna-dependent amidotransferase gatcab from aquifex aeolicus | Descriptor: | Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B, GLUTAMINE, Glutamyl-tRNA(Gln) amidotransferase subunit A, ... | Authors: | Wu, J, Bu, W, Sheppard, K, Kitabatake, M, Soll, D, Smith, J.L. | Deposit date: | 2009-04-09 | Release date: | 2009-07-21 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Insights into tRNA-Dependent Amidotransferase Evolution and Catalysis from the Structure of the Aquifex aeolicus Enzyme J.Mol.Biol., 391, 2009
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