#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
19C6J|1|A (rep)Group II catalytic intron D1-D4-3Group IIC intron embedded with the TPP riboswitchOceanobacillus iheyensisBacteriaRF02001Group IIC intron embedded with the TPP riboswitchElectron microscopy2.413872024-12-04
29C6I|1|AGroup II catalytic intron D1-D4-3Group IIC IntronOceanobacillus iheyensisBacteriaRF02001Cryo-EM structure of a group IIC intron RNAElectron microscopy2.563932024-12-04
33IGI|1|AGroup II catalytic intron D1-D4-35'-R(*CP*GP*CP*UP*CP*UP*AP*CP*UP*CP*UP*AP*U)-3', Group IIC intronRF02001Tertiary Architecture of the Oceanobacillus Iheyensis Group II IntronX-ray diffraction3.123892009-12-22
48OLV|1|AGroup II catalytic intron D1-D4-3Group IIC intronOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and ARN25850X-ray diffraction2.813942024-06-19
55J02|1|A+ 5J02|1|BGroup II catalytic intron D1-D4-35' EXON ANALOG (5'-R(*CP*UP*GP*UP*UP*AP*(5MU))-3'), GROUP II INTRON LARIATOceanobacillus iheyensisBacteriaRF02001Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+, MG2+ and an inactive 5' exon.X-ray diffraction3.494212016-12-14
64Y1O|1|AGroup II catalytic intron D1-D4-3group II intron, domain 1Oceanobacillus iheyensisBacteriaRF02001Oceanobacillus iheyensis group II intron domain 1X-ray diffraction2.952582015-10-14
74Y1O|1|BGroup II catalytic intron D1-D4-3group II intron, domain 1Oceanobacillus iheyensisBacteriaRF02001Oceanobacillus iheyensis group II intron domain 1X-ray diffraction2.952562015-10-14
84FAR|1|AGroup II catalytic intron D1-D4-3Group IIC intronOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and 5'-exonX-ray diffraction2.863902012-11-14
94E8N|1|AGroup II catalytic intron D1-D4-3Group IIC intronOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of NH4+ and Mg2+X-ray diffraction2.963932012-11-14
106T3S|1|AGroup II catalytic intron D1-D4-3Group IIC Intron RibozymeOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of Na+, Mg2+ and 5'-exonX-ray diffraction3.283932020-05-13
118OLY|1|AGroup II catalytic intron D1-D4-35'-exon, Group IIC intronOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron post first step of splicing in the presence of K+, Mg2+ and intronistat BX-ray diffraction3.113902024-06-19
124FAX|1|AGroup II catalytic intron D1-D4-3Group IIC intronOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Na+ and Mg2+X-ray diffraction3.13922012-11-14
134FAU|1|AGroup II catalytic intron D1-D4-3Group IIC intronOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+ and 5'-exonX-ray diffraction2.873932012-11-14
148OLS|1|AGroup II catalytic intron D1-D4-3Group IIC intronOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and intronistat BX-ray diffraction33902024-06-19
154FAW|1|AGroup II catalytic intron D1-D4-35'-R(*A*UP*UP*UP*AP*UP*UP*A)-3', Group IIC intronOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and a hydrolyzed oligonucleotide fragmentX-ray diffraction2.73902012-11-14
165J01|1|AGroup II catalytic intron D1-D4-3group II intron lariatOceanobacillus iheyensisBacteriaRF02001Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+ and MG2+.X-ray diffraction3.394142016-12-14
174FB0|1|AGroup II catalytic intron D1-D4-3Group IIC intronOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron C377G mutant in a ligand-free state in the presence of K+ and Mg2+X-ray diffraction3.223932012-11-14
184E8Q|1|AGroup II catalytic intron D1-D4-3Group IIC intronOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Tl+ and Mg2+X-ray diffraction2.843932012-11-14
194E8K|1|AGroup II catalytic intron D1-D4-35'-R(*CP*G*AP*UP*UP*UP*AP*UP*UP*A)-3', Group IIC intronOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and a non-hydrolyzed oligonucleotide substrateX-ray diffraction3.033882012-11-14
204E8P|1|AGroup II catalytic intron D1-D4-3Group IIC intronOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Rb+ and Mg2+X-ray diffraction3.283932012-11-14
216T3R|1|AGroup II catalytic intron D1-D4-3Group IIC Intron RibozymeOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of K+, Mg2+ and 5'-exonX-ray diffraction3.573892020-05-13
224E8T|1|AGroup II catalytic intron D1-D4-35'-R(*AP*UP*UP*UP*AP*UP*UP*A)-3', Group IIC intronOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and an oligonucleotide fragment substrate (low energy dataset)X-ray diffraction3.343882012-11-14
238RUI|1|AGroup II catalytic intron D1-D4-3Domains 1-5Oceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and intronistat B after 1h soakingX-ray diffraction3.313902024-06-19
248RUJ|1|AGroup II catalytic intron D1-D4-3Domains 1-5Oceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and ARN25850 after 1h soakingX-ray diffraction3.123902024-06-19
256T3N|1|AGroup II catalytic intron D1-D4-3Group IIC Intron RibozymeOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of Na+, Mg2+ and 5'-exonX-ray diffraction3.223942020-05-13
263EOH|1|AGroup II catalytic intron D1-D4-35'-R(*UP*UP*AP*UP*UP*A)-3', Group IIC intronRF02001Refined group II intron structureX-ray diffraction3.123812008-10-28
278RUM|1|AGroup II catalytic intron D1-D4-3Domains 1-5Oceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+, and intronistat BX-ray diffraction3.623932024-06-19
288RUL|1|AGroup II catalytic intron D1-D4-3Domains 1-5Oceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in the presence of Li+ and Mg2+X-ray diffraction3.623932024-06-19
294FAQ|1|AGroup II catalytic intron D1-D4-3Group IIC intronOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and 5'-exonX-ray diffraction3.113962012-11-14
304Y1N|1|BGroup II catalytic intron D1-D4-3group II intron, domain 1Oceanobacillus iheyensisBacteriaRF02001Oceanobacillus iheyensis group II intron domain 1 with iridium hexamineX-ray diffraction32592015-10-14
314Y1N|1|AGroup II catalytic intron D1-D4-3group II intron, domain 1Oceanobacillus iheyensisBacteriaRF02001Oceanobacillus iheyensis group II intron domain 1 with iridium hexamineX-ray diffraction32492015-10-14
324E8R|1|AGroup II catalytic intron D1-D4-3Group IIC intronOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Cs+ and Mg2+X-ray diffraction3.363932012-11-14
338OLZ|1|AGroup II catalytic intron D1-D4-35'-exon, DOMAINS 1-5Oceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and intronistat B after 2h30 soakingX-ray diffraction3.313902024-06-19
346T3K|1|AGroup II catalytic intron D1-D4-3Group IIC Intron RibozymeOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of K+, Mg2+ and 5'-exonX-ray diffraction3.443902020-05-13
358RUH|1|AGroup II catalytic intron D1-D4-35'-exon, Domains 1-5Oceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and 5'-exonX-ray diffraction4.553902024-06-19
363G78|1|AGroup II catalytic intron D1-D4-3Group II intron, Ligated EXON productOceanobacillus iheyensisBacteriaRF02001Insight into group II intron catalysis from revised crystal structureX-ray diffraction2.83892010-02-16
378RUN|1|AGroup II catalytic intron D1-D4-3Domains 1-5Oceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+, and ARN25850X-ray diffraction3.733932024-06-19
388OLW|1|AGroup II catalytic intron D1-D4-3Group IIC intronOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron before the first step of splicing in the presence of K+, Ca2+ and intronistat BX-ray diffraction43962024-06-19
394E8M|1|AGroup II catalytic intron D1-D4-3Group IIC intronOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Mg2+X-ray diffraction3.53942012-11-14
408RUK|1|AGroup II catalytic intron D1-D4-3Domains 1-5Oceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+, and ARN25850X-ray diffraction4.813882024-06-19
414DS6|1|AGroup II catalytic intron D1-D4-3Mutant Group IIC IntronOceanobacillus iheyensisBacteriaRF02001Crystal structure of a group II intron in the pre-catalytic stateX-ray diffraction3.643932012-04-18
429G4J|1|AGroup II catalytic intron D1-D4-3GROUP IIC INTRONOceanobacillus iheyensisBacteriaRF02001Group II intron assembly intermediate Domain 1 to 3 "Fully open" stateElectron microscopy3.742412025-11-05
433EOG|1|AGroup II catalytic intron D1-D4-35'-R(*UP*UP*AP*UP*UP*A)-3', Group IIC intronRF02001Co-crystallization showing exon recognition by a group II intronX-ray diffraction3.393882008-10-28
443BWP|1|AGroup II catalytic intron D1-D4-3Group IIC intronRF02001Crystal structure of a self-spliced group II intronX-ray diffraction3.13562008-04-15
459G4I|1|AGroup II catalytic intron D1-D4-3GROUP IIC INTRONOceanobacillus iheyensisBacteriaRF02001Group II intron assembly intermediate Domain 1 and 2 "Partly open" stateElectron microscopy4.612732025-11-05
469G4L|1|AGroup II catalytic intron D1-D4-3GROUP IIC INTRONOceanobacillus iheyensisBacteriaRF02001Group II intron assembly intermediate Domain 1 to 3 "Partly open" stateElectron microscopy4.012672025-11-05
479G4V|1|AGroup II catalytic intron D1-D4-3GROUP IIC INTRONOceanobacillus iheyensisBacteriaRF02001Group II intron assembly intermediate Domain 1 and 2 "Fully open" stateElectron microscopy4.692212025-11-05
488OM0|1|AGroup II catalytic intron D1-D4-3Domains 1-5Oceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+ and intronistat BX-ray diffraction3.613902024-06-19
494E8V|1|AGroup II catalytic intron D1-D4-3Group IIC intronOceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Ba2+X-ray diffraction3.993892012-11-14
509G54|1|AGroup II catalytic intron D1-D4-3GROUP IIC INTRONOceanobacillus iheyensisBacteriaRF02001Group II intron assembly intermediate Domain 1, 2, 3 and 4 "Partly open" stateElectron microscopy6.32932025-11-05

Release history

Release4.12
Date2025-11-05

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child

Instances are ordered to put similar structures near each other. Select one instance to see its 3D structure. Selecting two or more instances will show their superposition, but only chains with identical numbers of observed nucleotides will superpose well. Large structures are slow to display; this tool is not designed for that.

#SViewPDBTitleMethodResolution#NTs
14Y1O|1|AOceanobacillus iheyensis group II intron domain 1X-RAY DIFFRACTION2.95258
24Y1N|1|BOceanobacillus iheyensis group II intron domain 1 with iridium hexamineX-RAY DIFFRACTION3259
34Y1N|1|AOceanobacillus iheyensis group II intron domain 1 with iridium hexamineX-RAY DIFFRACTION3249
44Y1O|1|BOceanobacillus iheyensis group II intron domain 1X-RAY DIFFRACTION2.95256
59C6I|1|ACryo-EM structure of a group IIC intron RNAELECTRON MICROSCOPY2.56393
69C6J|1|AGroup IIC intron embedded with the TPP riboswitchELECTRON MICROSCOPY2.41387
74E8V|1|AStructure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Ba2+X-RAY DIFFRACTION3.99389
88OLW|1|AStructure of Oceanobacillus iheyensis group II intron before the first step of splicing in the presence of K+, Ca2+ and intronistat BX-RAY DIFFRACTION4396
94FAQ|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and 5'-exonX-RAY DIFFRACTION3.11396
104E8K|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and a non-hydrolyzed oligonucleotide substrateX-RAY DIFFRACTION3.03388
114E8T|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and an oligonucleotide fragment substrate (low energy dataset)X-RAY DIFFRACTION3.34388
123G78|1|AInsight into group II intron catalysis from revised crystal structureX-RAY DIFFRACTION2.8389
133IGI|1|ATertiary Architecture of the Oceanobacillus Iheyensis Group II IntronX-RAY DIFFRACTION3.12389
148OLZ|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and intronistat B after 2h30 soakingX-RAY DIFFRACTION3.31390
158RUH|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and 5'-exonX-RAY DIFFRACTION4.55390
166T3R|1|AStructure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of K+, Mg2+ and 5'-exonX-RAY DIFFRACTION3.57389
174FAU|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+ and 5'-exonX-RAY DIFFRACTION2.87393
184FAR|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and 5'-exonX-RAY DIFFRACTION2.86390
198OLY|1|AStructure of Oceanobacillus iheyensis group II intron post first step of splicing in the presence of K+, Mg2+ and intronistat BX-RAY DIFFRACTION3.11390
206T3K|1|AStructure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of K+, Mg2+ and 5'-exonX-RAY DIFFRACTION3.44390
218RUN|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+, and ARN25850X-RAY DIFFRACTION3.73393
228RUL|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of Li+ and Mg2+X-RAY DIFFRACTION3.62393
238RUI|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and intronistat B after 1h soakingX-RAY DIFFRACTION3.31390
248OLV|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and ARN25850X-RAY DIFFRACTION2.81394
258OLS|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and intronistat BX-RAY DIFFRACTION3390
264E8M|1|AStructure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Mg2+X-RAY DIFFRACTION3.5394
278RUJ|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and ARN25850 after 1h soakingX-RAY DIFFRACTION3.12390
284FAW|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and a hydrolyzed oligonucleotide fragmentX-RAY DIFFRACTION2.7390
294FB0|1|AStructure of Oceanobacillus iheyensis group II intron C377G mutant in a ligand-free state in the presence of K+ and Mg2+X-RAY DIFFRACTION3.22393
304E8P|1|AStructure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Rb+ and Mg2+X-RAY DIFFRACTION3.28393
314E8Q|1|AStructure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Tl+ and Mg2+X-RAY DIFFRACTION2.84393
324E8N|1|AStructure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of NH4+ and Mg2+X-RAY DIFFRACTION2.96393
334E8R|1|AStructure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Cs+ and Mg2+X-RAY DIFFRACTION3.36393
348OM0|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+ and intronistat BX-RAY DIFFRACTION3.61390
358RUM|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+, and intronistat BX-RAY DIFFRACTION3.62393
364FAX|1|AStructure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Na+ and Mg2+X-RAY DIFFRACTION3.1392
378RUK|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+, and ARN25850X-RAY DIFFRACTION4.81388
386T3S|1|AStructure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of Na+, Mg2+ and 5'-exonX-RAY DIFFRACTION3.28393
396T3N|1|AStructure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of Na+, Mg2+ and 5'-exonX-RAY DIFFRACTION3.22394
404DS6|1|ACrystal structure of a group II intron in the pre-catalytic stateX-RAY DIFFRACTION3.64393
413EOH|1|ARefined group II intron structureX-RAY DIFFRACTION3.12381
423BWP|1|ACrystal structure of a self-spliced group II intronX-RAY DIFFRACTION3.1356
433EOG|1|ACo-crystallization showing exon recognition by a group II intronX-RAY DIFFRACTION3.39388
445J02|1|A+ 5J02|1|BStructure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+, MG2+ and an inactive 5' exon.X-RAY DIFFRACTION3.49421
455J01|1|AStructure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+ and MG2+.X-RAY DIFFRACTION3.39414
469G4L|1|AGroup II intron assembly intermediate Domain 1 to 3 "Partly open" stateELECTRON MICROSCOPY4.01267
479G54|1|AGroup II intron assembly intermediate Domain 1, 2, 3 and 4 "Partly open" stateELECTRON MICROSCOPY6.3293
489G4I|1|AGroup II intron assembly intermediate Domain 1 and 2 "Partly open" stateELECTRON MICROSCOPY4.61273
499G4V|1|AGroup II intron assembly intermediate Domain 1 and 2 "Fully open" stateELECTRON MICROSCOPY4.69221
509G4J|1|AGroup II intron assembly intermediate Domain 1 to 3 "Fully open" stateELECTRON MICROSCOPY3.74241

Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. The ordering in the heat map is the same as in the table. The colorbar ranges from 0 to the maximum observed discrepancy. Click above the diagonal to select a range of structures, below the diagonal to select two structures.


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