8IFE
 
 | | Arbekacin-added human 80S ribosome | | Descriptor: | 18S ribosomal RNA, 28S ribosomal RNA, 40S ribosomal protein S10, ... | | Authors: | Tomono, J, Asano, K, Chiashi, T, Tanaka, Y, Yokoyama, T. | | Deposit date: | 2023-02-17 | | Release date: | 2024-02-14 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (2.57 Å) | | Cite: | Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside.
J.Biochem., 175, 2024
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8IFD
 | | Dibekacin-added human 80S ribosome | | Descriptor: | 18S ribosomal RNA, 28S ribosomal RNA, 40S ribosomal protein S10, ... | | Authors: | Tomono, J, Asano, K, Chiashi, T, Tanaka, Y, Yokoyama, T. | | Deposit date: | 2023-02-17 | | Release date: | 2024-02-14 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (2.59 Å) | | Cite: | Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside.
J.Biochem., 175, 2024
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7D0J
 | | Photosystem I-LHCI-LHCII of Chlamydomonas reinhardtii | | Descriptor: | (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL, (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL, (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL, ... | | Authors: | Wang, W.D, Shen, L.L, Huang, Z.H, Han, G.Y, Zhang, X, Shen, J.R. | | Deposit date: | 2020-09-10 | | Release date: | 2021-03-03 | | Method: | ELECTRON MICROSCOPY (3.42 Å) | | Cite: | Structure of photosystem I-LHCI-LHCII from the green alga Chlamydomonas reinhardtii in State 2.
Nat Commun, 12, 2021
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8IFB
 | | Dibekacin-bound E.coli 70S ribosome in the PURE system | | Descriptor: | 16S ribosomal RNA, 23S ribosomal RNA, 30S ribosomal protein S10, ... | | Authors: | Tomono, J, Asano, K, Chiashi, T, Tanaka, Y, Yokoyama, T. | | Deposit date: | 2023-02-17 | | Release date: | 2024-02-14 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (2.43 Å) | | Cite: | Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside.
J.Biochem., 175, 2024
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7F9O
 | | PSI-NDH supercomplex of Barley | | Descriptor: | (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL, (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, ... | | Authors: | Wang, W.D, Shen, L, Tang, K, Han, G.Y, Shen, J.R, Zhang, X. | | Deposit date: | 2021-07-04 | | Release date: | 2021-12-22 | | Last modified: | 2022-02-09 | | Method: | ELECTRON MICROSCOPY (4.5 Å) | | Cite: | Architecture of the chloroplast PSI-NDH supercomplex in Hordeum vulgare.
Nature, 601, 2022
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7EXT
 | | Cryo-EM structure of cyanobacterial phycobilisome from Synechococcus sp. PCC 7002 | | Descriptor: | Allophycocyanin alpha subunit, Allophycocyanin beta subunit, Allophycocyanin subunit alpha-B, ... | | Authors: | Zheng, L, Zheng, Z, Li, X, Wang, G, Zhang, K, Wei, P, Zhao, J, Gao, N. | | Deposit date: | 2021-05-28 | | Release date: | 2021-10-06 | | Method: | ELECTRON MICROSCOPY (3.5 Å) | | Cite: | Structural insight into the mechanism of energy transfer in cyanobacterial phycobilisomes.
Nat Commun, 12, 2021
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7EYD
 | | Cryo-EM structure of cyanobacterial phycobilisome from Anabaena sp. PCC 7120 | | Descriptor: | Allophycocyanin subunit alpha 1, Allophycocyanin subunit alpha-B, Allophycocyanin subunit beta, ... | | Authors: | Zheng, L, Zheng, Z, Li, X, Wang, G, Zhang, K, Wei, P, Zhao, J, Gao, N. | | Deposit date: | 2021-05-30 | | Release date: | 2021-10-06 | | Method: | ELECTRON MICROSCOPY (3.9 Å) | | Cite: | Structural insight into the mechanism of energy transfer in cyanobacterial phycobilisomes.
Nat Commun, 12, 2021
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7F4V
 | | Cryo-EM structure of a primordial cyanobacterial photosystem I | | Descriptor: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, BETA-CAROTENE, ... | | Authors: | Kato, K, Hamaguchi, T, Nagao, R, Kawakami, K, Yonekura, K, Shen, J.R. | | Deposit date: | 2021-06-21 | | Release date: | 2022-04-06 | | Method: | ELECTRON MICROSCOPY (2.04 Å) | | Cite: | Structural basis for the absence of low-energy chlorophylls responsible for photoprotection from a primitive cyanobacterial PSI
Biorxiv, 2022
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7COH
 | | Dimeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Oxidized State | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, 1,2-ETHANEDIOL, ... | | Authors: | Shinzawa-Itoh, K, Muramoto, K. | | Deposit date: | 2020-08-04 | | Release date: | 2021-04-07 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | The 1.3-A Resolution structure of bovine cytochrome c oxidase suggests a dimerization mechanism
Biochim.Biophys.Acta, 2021
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7DR2
 | | Structure of GraFix PSI tetramer from Cyanophora paradoxa | | Descriptor: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, BETA-CAROTENE, ... | | Authors: | Kato, K, Nagao, R, Akita, F, Miyazaki, N, Shen, J.R. | | Deposit date: | 2020-12-25 | | Release date: | 2022-02-16 | | Method: | ELECTRON MICROSCOPY (3.8 Å) | | Cite: | Structural insights into an evolutionary turning-point of photosystem I from prokaryotes to eukaryotes
Biorxiv, 2022
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7FIX
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7DZ7
 | | State transition supercomplex PSI-LHCI-LHCII from double phosphatase mutant pph1;pbcp of green alga Chlamydomonas reinhardtii | | Descriptor: | (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL, (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL, (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL, ... | | Authors: | Pan, X.W, Li, A.J, Liu, Z.F, Li, M. | | Deposit date: | 2021-01-23 | | Release date: | 2021-06-30 | | Last modified: | 2021-09-01 | | Method: | ELECTRON MICROSCOPY (2.84 Å) | | Cite: | Structural basis of LhcbM5-mediated state transitions in green algae.
Nat.Plants, 7, 2021
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8EKC
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8EKB
 | | Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, deacylated P-site tRNAmet, and thermorubin at 2.70A resolution | | Descriptor: | 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ... | | Authors: | Paranjpe, M.N, Polikanov, Y.S. | | Deposit date: | 2022-09-20 | | Release date: | 2022-12-21 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Insights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin.
Nucleic Acids Res., 51, 2023
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8EIU
 | | E. coli 70S ribosome with A-loop mutations U2554C and U2555C | | Descriptor: | 16S rRNA, 23S rRNA, 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate), ... | | Authors: | Nissley, A.J, Penev, P.I, Watson, Z.L, Banfield, J.F, Cate, J.H.D. | | Deposit date: | 2022-09-15 | | Release date: | 2023-02-01 | | Last modified: | 2023-11-15 | | Method: | ELECTRON MICROSCOPY (2.24 Å) | | Cite: | Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome.
Nucleic Acids Res., 51, 2023
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2FRZ
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8EMM
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8EV6
 | | Crystal structure of the Thermus thermophilus 70S ribosome in complex with amikacin, mRNA, and A-, P-, and E-site tRNAs | | Descriptor: | (2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S ,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide, 16S Ribosomal RNA, 23S Ribosomal RNA, ... | | Authors: | Seely, S.M, Gagnon, M.G. | | Deposit date: | 2022-10-19 | | Release date: | 2023-08-09 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.946 Å) | | Cite: | Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome.
Nat Commun, 14, 2023
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8EV7
 | | Crystal structure of the Thermus thermophilus 70S ribosome in complex with kanamycin, mRNA, and A-, P-, and E-site tRNAs | | Descriptor: | 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ... | | Authors: | Seely, S.M, Gagnon, M.G. | | Deposit date: | 2022-10-19 | | Release date: | 2023-08-09 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.89 Å) | | Cite: | Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome.
Nat Commun, 14, 2023
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8FON
 | | Crystal structure of tRNA^Lys(SUU) bound to AUA codon in the ribosomal P site | | Descriptor: | 16S rRNA, 23S rRNA, 30S ribosomal protein S10, ... | | Authors: | Nguyen, H.A, Hoffer, E.D, Maehigashi, T, Fagan, C.E, Dunham, C.M. | | Deposit date: | 2023-01-02 | | Release date: | 2023-03-29 | | Last modified: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (3.64 Å) | | Cite: | Structural basis for reduced ribosomal A-site fidelity in response to P-site codon-anticodon mismatches.
J.Biol.Chem., 299, 2023
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8FOM
 | | Crystal structure of tRNA^Lys(SUU) bound to UAA codon in the ribosomal P site | | Descriptor: | 16S rRNA, 23S rRNA, 30S ribosomal protein S10, ... | | Authors: | Nguyen, H.A, Hoffer, E.D, Maehigashi, T, Fagan, C.E, Dunham, C.M. | | Deposit date: | 2023-01-02 | | Release date: | 2023-03-29 | | Last modified: | 2023-04-26 | | Method: | X-RAY DIFFRACTION (3.58 Å) | | Cite: | Structural basis for reduced ribosomal A-site fidelity in response to P-site codon-anticodon mismatches.
J.Biol.Chem., 299, 2023
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8G2B
 | | Crystal structure of the A2503-C2,C8-dimethylated Thermus thermophilus 70S ribosome in complex with iboxamycin, mRNA, deacylated A- and E-site tRNAphe, and aminoacylated P-site fMet-tRNAmet at 2.55A resolution | | Descriptor: | 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ... | | Authors: | Aleksandrova, E.V, Wu, K.J.Y, Tresco, B.I.C, Syroegin, E.A, Killeavy, E.E, Balasanyants, S.M, Svetlov, M.S, Gregory, S.T, Atkinson, G.C, Myers, A.G, Polikanov, Y.S. | | Deposit date: | 2023-02-03 | | Release date: | 2023-12-27 | | Last modified: | 2024-07-10 | | Method: | X-RAY DIFFRACTION (2.55 Å) | | Cite: | Structural basis of Cfr-mediated antimicrobial resistance and mechanisms to evade it.
Nat.Chem.Biol., 20, 2024
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8G2A
 | | Crystal structure of the A2503-C2,C8-dimethylated Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-tRNAphe, peptidyl P-site fMTHSMRC-tRNAmet, and deacylated E-site tRNAphe at 2.45A resolution | | Descriptor: | 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ... | | Authors: | Aleksandrova, E.V, Wu, K.J.Y, Tresco, B.I.C, Syroegin, E.A, Killeavy, E.E, Balasanyants, S.M, Svetlov, M.S, Gregory, S.T, Atkinson, G.C, Myers, A.G, Polikanov, Y.S. | | Deposit date: | 2023-02-03 | | Release date: | 2023-12-27 | | Last modified: | 2024-07-10 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | Structural basis of Cfr-mediated antimicrobial resistance and mechanisms to evade it.
Nat.Chem.Biol., 20, 2024
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8G29
 | | Crystal structure of the A2503-C2,C8-dimethylated Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.55A resolution | | Descriptor: | 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ... | | Authors: | Aleksandrova, E.V, Wu, K.J.Y, Tresco, B.I.C, Syroegin, E.A, Killeavy, E.E, Balasanyants, S.M, Svetlov, M.S, Gregory, S.T, Atkinson, G.C, Myers, A.G, Polikanov, Y.S. | | Deposit date: | 2023-02-03 | | Release date: | 2023-12-27 | | Last modified: | 2024-07-10 | | Method: | X-RAY DIFFRACTION (2.55 Å) | | Cite: | Structural basis of Cfr-mediated antimicrobial resistance and mechanisms to evade it.
Nat.Chem.Biol., 20, 2024
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8G2D
 | | Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with tylosin, mRNA, deacylated A- and E-site tRNAphe, and deacylated P-site tRNAmet at 2.70A resolution | | Descriptor: | 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ... | | Authors: | Aleksandrova, E.V, Wu, K.J.Y, Tresco, B.I.C, Syroegin, E.A, Killeavy, E.E, Balasanyants, S.M, Svetlov, M.S, Gregory, S.T, Atkinson, G.C, Myers, A.G, Polikanov, Y.S. | | Deposit date: | 2023-02-03 | | Release date: | 2023-12-27 | | Last modified: | 2024-07-10 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Structural basis of Cfr-mediated antimicrobial resistance and mechanisms to evade it.
Nat.Chem.Biol., 20, 2024
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