2DIN
 
 | | Solution structure of the Myb_DNA-binding domain of human Cell division cycle 5-like protein | | Descriptor: | Cell division cycle 5-like protein | | Authors: | Yoneyama, M, Tochio, N, Koshiba, S, Inoue, M, Kigawa, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2006-03-30 | | Release date: | 2007-04-03 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the Myb_DNA-binding domain of human Cell division cycle 5-like protein
To be Published
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8VTW
 | | Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with macrolone MCX-128 and protein Y at 2.35A resolution | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 1-cyclopropyl-7-(4-{4-[({[(3aR,4R,7R,8S,9S,10R,11R,13R,14E,15S,15aR)-10-{[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy}-4-ethyl-11-methoxy-14-(methoxyimino)-3a,7,9,11,13,15-hexamethyl-2,6-dioxododecahydro-2H,4H-[1,3]dioxolo[4,5-c]oxacyclotetradecin-8-yl]oxy}carbonyl)amino]butyl}piperazin-1-yl)-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (non-preferred name), 16S Ribosomal RNA, ... | | Authors: | Aleksandrova, E.V, Ma, C.-X, Klepacki, D, Alizadeh, F, Vazquez-Laslop, N, Liang, J.-H, Polikanov, Y.S, Mankin, A.S. | | Deposit date: | 2024-01-27 | | Release date: | 2024-08-07 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Macrolones target bacterial ribosomes and DNA gyrase and can evade resistance mechanisms.
Nat.Chem.Biol., 2024
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8VTV
 | | Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with macrolone MCX-91, mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.55A resolution | | Descriptor: | 1-cyclopropyl-7-{7-[({[(3aR,4R,7R,8S,9S,10R,11R,13R,14E,15S,15aR)-10-{[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy}-4-ethyl-11-methoxy-14-(methoxyimino)-3a,7,9,11,13,15-hexamethyl-2,6-dioxododecahydro-2H,4H-[1,3]dioxolo[4,5-c]oxacyclotetradecin-8-yl]oxy}carbonyl)amino]hept-1-yn-1-yl}-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (non-preferred name), 16S Ribosomal RNA, 23S Ribosomal RNA, ... | | Authors: | Aleksandrova, E.V, Ma, C.-X, Klepacki, D, Alizadeh, F, Vazquez-Laslop, N, Liang, J.-H, Polikanov, Y.S, Mankin, A.S. | | Deposit date: | 2024-01-27 | | Release date: | 2024-08-07 | | Method: | X-RAY DIFFRACTION (2.55 Å) | | Cite: | Macrolones target bacterial ribosomes and DNA gyrase and can evade resistance mechanisms.
Nat.Chem.Biol., 2024
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6MJW
 | | human cGAS catalytic domain bound with the inhibitor G150 | | Descriptor: | 1-[9-(6-aminopyridin-3-yl)-6,7-dichloro-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indol-2-yl]-2-hydroxyethan-1-one, Cyclic GMP-AMP synthase, ZINC ION | | Authors: | Lama, L, Adura, C, Xie, W, Tomita, D, Kamei, T, Kuryavyi, V, Gogakos, T, Steinberg, J.I, Miller, M, Ramos-Espiritu, L, Asano, Y, Hashizume, S, Aida, J, Imaeda, T, Okamoto, R, Jennings, A.J, Michinom, M, Kuroita, T, Stamford, A, Gao, P, Meinke, P, Glickman, J.F, Patel, D.J, Tuschl, T. | | Deposit date: | 2018-09-23 | | Release date: | 2019-05-29 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.405 Å) | | Cite: | Development of human cGAS-specific small-molecule inhibitors for repression of dsDNA-triggered interferon expression.
Nat Commun, 10, 2019
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8BTG
 | | Cryo-EM structure of the bacterial replication origin opening basal unwinding system | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, Chromosomal replication initiator protein DnaA, DNA (41-MER), ... | | Authors: | Pelliciari, S, Bodet-Lefevre, S, Murray, H, Ilangovan, A. | | Deposit date: | 2022-11-28 | | Release date: | 2024-02-14 | | Method: | ELECTRON MICROSCOPY (3.2 Å) | | Cite: | The bacterial replication origin BUS promotes nucleobase capture.
Nat Commun, 14, 2023
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6MJU
 | | human cGAS catalytic domain bound with the inhibitor G108 | | Descriptor: | 1-[6,7-dichloro-9-(1H-pyrazol-4-yl)-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indol-2-yl]-2-hydroxyethan-1-one, Cyclic GMP-AMP synthase, ZINC ION | | Authors: | Lama, L, Adura, C, Xie, W, Tomita, D, Kamei, T, Kuryavyi, V, Gogakos, T, Steinberg, J.I, Miller, M, Ramos-Espiritu, L, Asano, Y, Hashizume, S, Aida, J, Imaeda, T, Okamoto, R, Jennings, A.J, Michinom, M, Kuroita, T, Stamford, A, Gao, P, Meinke, P, Glickman, J.F, Patel, D.J, Tuschl, T. | | Deposit date: | 2018-09-22 | | Release date: | 2019-05-29 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | Development of human cGAS-specific small-molecule inhibitors for repression of dsDNA-triggered interferon expression.
Nat Commun, 10, 2019
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6MJX
 | | human cGAS catalytic domain bound with cGAMP | | Descriptor: | Cyclic GMP-AMP synthase, ZINC ION, cGAMP | | Authors: | Lama, L, Adura, C, Xie, W, Tomita, D, Kamei, T, Kuryavyi, V, Gogakos, T, Steinberg, J.I, Miller, M, Ramos-Espiritu, L, Asano, Y, Hashizume, S, Aida, J, Imaeda, T, Okamoto, R, Jennings, A.J, Michinom, M, Kuroita, T, Stamford, A, Gao, P, Meinke, P, Glickman, J.F, Patel, D.J, Tuschl, T. | | Deposit date: | 2018-09-23 | | Release date: | 2019-05-29 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Development of human cGAS-specific small-molecule inhibitors for repression of dsDNA-triggered interferon expression.
Nat Commun, 10, 2019
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1G8N
 | | MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATF5UCGCG):5-FORMYLURIDINE/ ADENOSINE BASE-PAIRS IN B-DNA | | Descriptor: | 5'-D(*CP*GP*CP*GP*AP*AP*TP*(UFR)P*CP*GP*CP*G)-3', MAGNESIUM ION | | Authors: | Tsunoda, M, Karino, N, Ueno, Y, Matsuda, A, Takenaka, A. | | Deposit date: | 2000-11-20 | | Release date: | 2001-02-05 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Crystallization and preliminary X-ray analysis of a DNA dodecamer containing 2'-deoxy-5-formyluridine; what is the role of magnesium cation in crystallization of Dickerson-type DNA dodecamers?
Acta Crystallogr.,Sect.D, 57, 2001
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8EJO
 | | Crystal structure of the homeodomain of Platypus sDUX in complex with DNA | | Descriptor: | 1,2-ETHANEDIOL, DNA (5'-D(*GP*CP*GP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*AP*AP*CP*A)-3'), DNA (5'-D(*TP*GP*TP*TP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*CP*GP*C)-3'), ... | | Authors: | Yin, L, Shi, K, Aihara, H. | | Deposit date: | 2022-09-18 | | Release date: | 2023-09-20 | | Last modified: | 2024-09-18 | | Method: | X-RAY DIFFRACTION (2.67 Å) | | Cite: | Antagonism among DUX family members evolved from an ancestral toxic single homeodomain protein.
Iscience, 26, 2023
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8EJP
 | | Crystal structure of the homeodomain of Platypus sDUX in complex with DNA containing 5-Bromouracil | | Descriptor: | 1,2-ETHANEDIOL, DNA (5'-D(*GP*CP*GP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*AP*AP*CP*A)-3'), DNA (5'-D(*TP*GP*TP*TP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*CP*GP*C)-3'), ... | | Authors: | Yin, L, Shi, K, Aihara, H. | | Deposit date: | 2022-09-18 | | Release date: | 2023-09-20 | | Last modified: | 2024-09-18 | | Method: | X-RAY DIFFRACTION (2.174 Å) | | Cite: | Antagonism among DUX family members evolved from an ancestral toxic single homeodomain protein.
Iscience, 26, 2023
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6CFY
 | | Bosea sp Root 381 apo GapR structure | | Descriptor: | UPF0335 protein ASE63_04290 | | Authors: | Schumacherr, M.A. | | Deposit date: | 2018-02-18 | | Release date: | 2018-09-12 | | Last modified: | 2018-10-17 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | A Bacterial Chromosome Structuring Protein Binds Overtwisted DNA to Stimulate Type II Topoisomerases and Enable DNA Replication.
Cell, 175, 2018
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7DWN
 | | Crystal structure of Vibrio fischeri DarR in complex with DNA reveals the transcriptional activation mechanism of LTTR family members | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Predicted DNA-binding transcriptional regulator | | Authors: | Wang, W.W, Wu, H, He, J.H, Yu, F. | | Deposit date: | 2021-01-17 | | Release date: | 2021-07-07 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.32 Å) | | Cite: | Crystal structure details of Vibrio fischeri DarR and mutant DarR-M202I from LTTR family reveals their activation mechanism.
Int.J.Biol.Macromol., 183, 2021
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7DWO
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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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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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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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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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5ZJ4
 | | Guanine-specific ADP-ribosyltransferase | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, ADP-ribosyltransferase | | Authors: | Yoshida, T, Tsuge, H. | | Deposit date: | 2018-03-19 | | Release date: | 2018-08-08 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.49739277 Å) | | Cite: | Substrate N2atom recognition mechanism in pierisin family DNA-targeting, guanine-specific ADP-ribosyltransferase ScARP.
J. Biol. Chem., 293, 2018
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1G9Y
 | | HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX WITH CALCIUM | | Descriptor: | 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP*GP*C)-3', 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*CP*G)-3', CALCIUM ION, ... | | Authors: | Chevalier, B, Monnat, R.J, Stoddard, B.L. | | Deposit date: | 2000-11-28 | | Release date: | 2001-04-02 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites.
Nat.Struct.Biol., 8, 2001
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8VTU
 | | Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with macrolone MCX-66, mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.40A resolution | | Descriptor: | 1-cyclopropyl-7-[(4-{[3-({(3aR,4R,7R,8S,9S,10R,11R,13R,14E,15S,15aR)-10-{[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy}-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-14-[({3-[5-(methylcarbamoyl)pyridin-3-yl]prop-2-yn-1-yl}oxy)imino]-2,6-dioxododecahydro-2H,4H-[1,3]dioxolo[4,5-c]oxacyclotetradecin-8-yl}oxy)-3-oxopropyl]amino}butyl)amino]-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (non-preferred name), 16S Ribosomal RNA, 23S Ribosomal RNA, ... | | Authors: | Aleksandrova, E.V, Ma, C.-X, Klepacki, D, Alizadeh, F, Vazquez-Laslop, N, Liang, J.-H, Polikanov, Y.S, Mankin, A.S. | | Deposit date: | 2024-01-27 | | Release date: | 2024-08-07 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Macrolones target bacterial ribosomes and DNA gyrase and can evade resistance mechanisms.
Nat.Chem.Biol., 2024
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8VTX
 | | Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in complex with macrolone MCX-128, mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.40A resolution | | Descriptor: | 1-cyclopropyl-7-(4-{4-[({[(3aR,4R,7R,8S,9S,10R,11R,13R,14E,15S,15aR)-10-{[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy}-4-ethyl-11-methoxy-14-(methoxyimino)-3a,7,9,11,13,15-hexamethyl-2,6-dioxododecahydro-2H,4H-[1,3]dioxolo[4,5-c]oxacyclotetradecin-8-yl]oxy}carbonyl)amino]butyl}piperazin-1-yl)-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (non-preferred name), 16S Ribosomal RNA, 23S Ribosomal RNA, ... | | Authors: | Aleksandrova, E.V, Ma, C.-X, Klepacki, D, Alizadeh, F, Vazquez-Laslop, N, Liang, J.-H, Polikanov, Y.S, Mankin, A.S. | | Deposit date: | 2024-01-27 | | Release date: | 2024-08-07 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Macrolones target bacterial ribosomes and DNA gyrase and can evade resistance mechanisms.
Nat.Chem.Biol., 2024
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8VTY
 | | Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with ciprofloxacin and protein Y at 2.60A resolution | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 1-CYCLOPROPYL-6-FLUORO-4-OXO-7-PIPERAZIN-1-YL-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID, 16S Ribosomal RNA, ... | | Authors: | Aleksandrova, E.V, Ma, C.-X, Klepacki, D, Alizadeh, F, Vazquez-Laslop, N, Liang, J.-H, Polikanov, Y.S, Mankin, A.S. | | Deposit date: | 2024-01-27 | | Release date: | 2024-08-07 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Macrolones target bacterial ribosomes and DNA gyrase and can evade resistance mechanisms.
Nat.Chem.Biol., 2024
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5J37
 | | Crystal structure of 60-mer BFDV Capsid Protein in complex with single stranded DNA | | Descriptor: | Beak and feather disease virus capsid protein, PHOSPHATE ION, single stranded DNA | | Authors: | Sarker, S, Raidal, S, Aragao, D, Forwood, J.K. | | Deposit date: | 2016-03-30 | | Release date: | 2016-05-04 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural insights into the assembly and regulation of distinct viral capsid complexes.
Nat Commun, 7, 2016
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5JJ1
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1MO4
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