#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
29QU7|1|AGroup II catalytic intron D1-D4-3Group IIC IntronOceanobacillus iheyensisBacteriaRF02001Cryo-EM structure of Oceanobacillus iheyensis group II intron domains D1-D5Electron microscopy2.62972026-02-25
39C6I|1|AGroup II catalytic intron D1-D4-3Group IIC IntronOceanobacillus iheyensisBacteriaRF02001Cryo-EM structure of a group IIC intron RNAElectron microscopy2.563932024-12-04
43IGI|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
58OLV|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
65J02|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
74Y1O|1|AGroup II catalytic intron D1-D4-3group II intron, domain 1Oceanobacillus iheyensisBacteriaRF02001Oceanobacillus iheyensis group II intron domain 1X-ray diffraction2.952582015-10-14
84Y1O|1|BGroup II catalytic intron D1-D4-3group II intron, domain 1Oceanobacillus iheyensisBacteriaRF02001Oceanobacillus iheyensis group II intron domain 1X-ray diffraction2.952562015-10-14
94FAR|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
104E8N|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
116T3S|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
128OLY|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
134FAX|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
144FAU|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
158OLS|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
164FAW|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
175J01|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
184FB0|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
194E8Q|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
204E8K|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
214E8P|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
226T3R|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
234E8T|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
248RUI|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
258RUJ|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
266T3N|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
273EOH|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
288RUM|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
298RUL|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
304FAQ|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
314Y1N|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
324Y1N|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
334E8R|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
348OLZ|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
356T3K|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
368RUH|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
373G78|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
388RUN|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
398OLW|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
404E8M|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
419QU6|1|AGroup II catalytic intron D1-D4-3Group IIC Intron, Group IIC Intron 5'-exonOceanobacillus iheyensisBacteriaRF02001Cryo-EM structure of Oceanobacillus iheyensis group II intron domains D1-D5Electron microscopy3.23122026-02-25
428RUK|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
439G4J|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
444DS6|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
459QTJ|1|1Group II catalytic intron D1-D4-3RNA (461-MER)Oceanobacillus iheyensisBacteriaRF02001Structure of Oceanobacillus iheyensis group II intron domains D1-D6Electron microscopy3.794612026-02-18
463EOG|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
473BWP|1|AGroup II catalytic intron D1-D4-3Group IIC intronRF02001Crystal structure of a self-spliced group II intronX-ray diffraction3.13562008-04-15
489G4I|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
499G4L|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
509G4V|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
518OM0|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
524E8V|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
539G54|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
549G56|1|AGroup II catalytic intron D1-D4-3GROUP IIC INTRONOceanobacillus iheyensisBacteriaRF02001Group II intron assembly intermediate Domain 1, 2, 3 and 4 "Fully open" stateElectron microscopy7.542942025-12-17

Release history

Release4.28
Date2026-02-25

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
19QTJ|1|1Structure of Oceanobacillus iheyensis group II intron domains D1-D6ELECTRON MICROSCOPY3.79461
24Y1O|1|AOceanobacillus iheyensis group II intron domain 1X-RAY DIFFRACTION2.95258
34Y1N|1|BOceanobacillus iheyensis group II intron domain 1 with iridium hexamineX-RAY DIFFRACTION3259
44Y1N|1|AOceanobacillus iheyensis group II intron domain 1 with iridium hexamineX-RAY DIFFRACTION3249
54Y1O|1|BOceanobacillus iheyensis group II intron domain 1X-RAY DIFFRACTION2.95256
69C6I|1|ACryo-EM structure of a group IIC intron RNAELECTRON MICROSCOPY2.56393
79C6J|1|AGroup IIC intron embedded with the TPP riboswitchELECTRON MICROSCOPY2.41387
89QU6|1|ACryo-EM structure of Oceanobacillus iheyensis group II intron domains D1-D5ELECTRON MICROSCOPY3.2312
99QU7|1|ACryo-EM structure of Oceanobacillus iheyensis group II intron domains D1-D5ELECTRON MICROSCOPY2.6297
104E8V|1|AStructure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Ba2+X-RAY DIFFRACTION3.99389
118OLW|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
124FAQ|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and 5'-exonX-RAY DIFFRACTION3.11396
134E8K|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and a non-hydrolyzed oligonucleotide substrateX-RAY DIFFRACTION3.03388
144E8T|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
153G78|1|AInsight into group II intron catalysis from revised crystal structureX-RAY DIFFRACTION2.8389
163IGI|1|ATertiary Architecture of the Oceanobacillus Iheyensis Group II IntronX-RAY DIFFRACTION3.12389
178OLZ|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
188RUH|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and 5'-exonX-RAY DIFFRACTION4.55390
194FAU|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+ and 5'-exonX-RAY DIFFRACTION2.87393
206T3R|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
218OLY|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
224FAR|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and 5'-exonX-RAY DIFFRACTION2.86390
236T3K|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
248RUN|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+, and ARN25850X-RAY DIFFRACTION3.73393
258RUL|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of Li+ and Mg2+X-RAY DIFFRACTION3.62393
268RUI|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
278OLV|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and ARN25850X-RAY DIFFRACTION2.81394
288OLS|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and intronistat BX-RAY DIFFRACTION3390
294E8M|1|AStructure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Mg2+X-RAY DIFFRACTION3.5394
308RUJ|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and ARN25850 after 1h soakingX-RAY DIFFRACTION3.12390
314FAW|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and a hydrolyzed oligonucleotide fragmentX-RAY DIFFRACTION2.7390
324FB0|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
334E8N|1|AStructure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of NH4+ and Mg2+X-RAY DIFFRACTION2.96393
344E8Q|1|AStructure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Tl+ and Mg2+X-RAY DIFFRACTION2.84393
354E8P|1|AStructure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Rb+ and Mg2+X-RAY DIFFRACTION3.28393
364E8R|1|AStructure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Cs+ and Mg2+X-RAY DIFFRACTION3.36393
378OM0|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+ and intronistat BX-RAY DIFFRACTION3.61390
388RUM|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+, and intronistat BX-RAY DIFFRACTION3.62393
394FAX|1|AStructure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Na+ and Mg2+X-RAY DIFFRACTION3.1392
408RUK|1|AStructure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+, and ARN25850X-RAY DIFFRACTION4.81388
416T3S|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
426T3N|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
434DS6|1|ACrystal structure of a group II intron in the pre-catalytic stateX-RAY DIFFRACTION3.64393
443EOH|1|ARefined group II intron structureX-RAY DIFFRACTION3.12381
453BWP|1|ACrystal structure of a self-spliced group II intronX-RAY DIFFRACTION3.1356
463EOG|1|ACo-crystallization showing exon recognition by a group II intronX-RAY DIFFRACTION3.39388
475J02|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
485J01|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
499G4L|1|AGroup II intron assembly intermediate Domain 1 to 3 "Partly open" stateELECTRON MICROSCOPY4.01267
509G54|1|AGroup II intron assembly intermediate Domain 1, 2, 3 and 4 "Partly open" stateELECTRON MICROSCOPY6.3293
519G4I|1|AGroup II intron assembly intermediate Domain 1 and 2 "Partly open" stateELECTRON MICROSCOPY4.61273
529G4V|1|AGroup II intron assembly intermediate Domain 1 and 2 "Fully open" stateELECTRON MICROSCOPY4.69221
539G4J|1|AGroup II intron assembly intermediate Domain 1 to 3 "Fully open" stateELECTRON MICROSCOPY3.74241
549G56|1|AGroup II intron assembly intermediate Domain 1, 2, 3 and 4 "Fully open" stateELECTRON MICROSCOPY7.54294

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.


Coloring options:

Copyright 2026 BGSU RNA group. Page generated in 0.0347 s