NR_20.0_35054.7

Members (45)
History
Heat map

#	IFE	Standardized name	Molecule	Organism	Source	Rfam	Title	Method	Res. Å	#NTs	Date
1	3IGI\|1\|A (rep)		5'-R(CPGPCPUPCPUPAPCPUPCPUPAP*U)-3', Group IIC intron				Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron	X-ray diffraction	3.12	389	2009-12-22
2	8OLV\|1\|A	Group II catalytic intron D1-D4-1	Group IIC intron	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and ARN25850	X-ray diffraction	2.81	394	2024-06-19
3	5J02\|1\|A+ 5J02\|1\|B	Group II catalytic intron D1-D4-1	5' EXON ANALOG (5'-R(CPUPGPUPUPAP*(5MU))-3'), GROUP II INTRON LARIAT	Oceanobacillus iheyensis	Bacteria	RF01998	Structure 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 diffraction	3.49	421	2016-12-14
4	4FAX\|1\|A	Group II catalytic intron D1-D4-1	Group IIC intron	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Na+ and Mg2+	X-ray diffraction	3.1	392	2012-11-14
5	4FAR\|1\|A	Group II catalytic intron D1-D4-1	Group IIC intron	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and 5'-exon	X-ray diffraction	2.86	390	2012-11-14
6	8OLS\|1\|A	Group II catalytic intron D1-D4-1	Group IIC intron	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and intronistat B	X-ray diffraction	3	390	2024-06-19
7	4E8N\|1\|A	Group II catalytic intron D1-D4-1	Group IIC intron	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of NH4+ and Mg2+	X-ray diffraction	2.96	393	2012-11-14
8	6T3S\|1\|A	Group II catalytic intron D1-D4-1	Group IIC Intron Ribozyme	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of Na+, Mg2+ and 5'-exon	X-ray diffraction	3.28	393	2020-05-13
9	8OLY\|1\|A	Group II catalytic intron D1-D4-3	5'-exon, Group IIC intron	Oceanobacillus iheyensis	Bacteria	RF02001	Structure of Oceanobacillus iheyensis group II intron post first step of splicing in the presence of K+, Mg2+ and intronistat B	X-ray diffraction	3.11	390	2024-06-19
10	4FAU\|1\|A	Group II catalytic intron D1-D4-1	Group IIC intron	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+ and 5'-exon	X-ray diffraction	2.87	393	2012-11-14
11	8RUI\|1\|A	Group II catalytic intron D1-D4-3	Domains 1-5	Oceanobacillus iheyensis	Bacteria	RF02001	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and intronistat B after 1h soaking	X-ray diffraction	3.31	390	2024-06-19
12	4FB0\|1\|A	Group II catalytic intron D1-D4-1	Group IIC intron	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron C377G mutant in a ligand-free state in the presence of K+ and Mg2+	X-ray diffraction	3.22	393	2012-11-14
13	8RUJ\|1\|A	Group II catalytic intron D1-D4-3	Domains 1-5	Oceanobacillus iheyensis	Bacteria	RF02001	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and ARN25850 after 1h soaking	X-ray diffraction	3.12	390	2024-06-19
14	4E8K\|1\|A	Group II catalytic intron D1-D4-1	5'-R(CPGAPUPUPUPAPUPUPA)-3', Group IIC intron	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and a non-hydrolyzed oligonucleotide substrate	X-ray diffraction	3.03	388	2012-11-14
15	4E8Q\|1\|A	Group II catalytic intron D1-D4-1	Group IIC intron	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Tl+ and Mg2+	X-ray diffraction	2.84	393	2012-11-14
16	4Y1O\|1\|A	Group II catalytic intron D1-D4-3	group II intron, domain 1	Oceanobacillus iheyensis	Bacteria	RF02001	Oceanobacillus iheyensis group II intron domain 1	X-ray diffraction	2.95	258	2015-10-14
17	4Y1O\|1\|B	Group II catalytic intron D1-D4-3	group II intron, domain 1	Oceanobacillus iheyensis	Bacteria	RF02001	Oceanobacillus iheyensis group II intron domain 1	X-ray diffraction	2.95	256	2015-10-14
18	6T3N\|1\|A	Group II catalytic intron D1-D4-1	Group IIC Intron Ribozyme	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of Na+, Mg2+ and 5'-exon	X-ray diffraction	3.22	394	2020-05-13
19	4E8P\|1\|A	Group II catalytic intron D1-D4-1	Group IIC intron	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Rb+ and Mg2+	X-ray diffraction	3.28	393	2012-11-14
20	4E8T\|1\|A	Group II catalytic intron D1-D4-1	5'-R(APUPUPUPAPUPUPA)-3', Group IIC intron	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and an oligonucleotide fragment substrate (low energy dataset)	X-ray diffraction	3.34	388	2012-11-14
21	5J01\|1\|A	Group II catalytic intron D1-D4-1	group II intron lariat	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+ and MG2+.	X-ray diffraction	3.39	414	2016-12-14
22	4FAW\|1\|A	Group II catalytic intron D1-D4-1	5'-R(AUPUPUPAPUPUPA)-3', Group IIC intron	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and a hydrolyzed oligonucleotide fragment	X-ray diffraction	2.7	390	2012-11-14
23	3EOH\|1\|A		5'-R(UPUPAPUPUPA)-3', Group IIC intron				Refined group II intron structure	X-ray diffraction	3.12	381	2008-10-28
24	8RUM\|1\|A	Group II catalytic intron D1-D4-1	Domains 1-5	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+, and intronistat B	X-ray diffraction	3.62	393	2024-06-19
25	8RUL\|1\|A	Group II catalytic intron D1-D4-1	Domains 1-5	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in the presence of Li+ and Mg2+	X-ray diffraction	3.62	393	2024-06-19
26	6T3R\|1\|A	Group II catalytic intron D1-D4-1	Group IIC Intron Ribozyme	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of K+, Mg2+ and 5'-exon	X-ray diffraction	3.57	389	2020-05-13
27	4FAQ\|1\|A	Group II catalytic intron D1-D4-1	Group IIC intron	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and 5'-exon	X-ray diffraction	3.11	396	2012-11-14
28	4E8R\|1\|A	Group II catalytic intron D1-D4-1	Group IIC intron	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Cs+ and Mg2+	X-ray diffraction	3.36	393	2012-11-14
29	8OLZ\|1\|A	Group II catalytic intron D1-D4-3	5'-exon, DOMAINS 1-5	Oceanobacillus iheyensis	Bacteria	RF02001	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and intronistat B after 2h30 soaking	X-ray diffraction	3.31	390	2024-06-19
30	8RUN\|1\|A	Group II catalytic intron D1-D4-1	Domains 1-5	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+, and ARN25850	X-ray diffraction	3.73	393	2024-06-19
31	8RUH\|1\|A	Group II catalytic intron D1-D4-3	5'-exon, Domains 1-5	Oceanobacillus iheyensis	Bacteria	RF02001	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and 5'-exon	X-ray diffraction	4.55	390	2024-06-19
32	8OLW\|1\|A	Group II catalytic intron D1-D4-1	Group IIC intron	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron before the first step of splicing in the presence of K+, Ca2+ and intronistat B	X-ray diffraction	4	396	2024-06-19
33	3G78\|1\|A	Group II catalytic intron D1-D4-1	Group II intron, Ligated EXON product	Oceanobacillus iheyensis	Bacteria	RF01998	Insight into group II intron catalysis from revised crystal structure	X-ray diffraction	2.8	389	2010-02-16
34	4E8M\|1\|A	Group II catalytic intron D1-D4-1	Group IIC intron	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Mg2+	X-ray diffraction	3.5	394	2012-11-14
35	4Y1N\|1\|B	Group II catalytic intron D1-D4-3	group II intron, domain 1	Oceanobacillus iheyensis	Bacteria	RF02001	Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine	X-ray diffraction	3	259	2015-10-14
36	6T3K\|1\|A	Group II catalytic intron D1-D4-1	Group IIC Intron Ribozyme	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of K+, Mg2+ and 5'-exon	X-ray diffraction	3.44	390	2020-05-13
37	4Y1N\|1\|A	Group II catalytic intron D1-D4-3	group II intron, domain 1	Oceanobacillus iheyensis	Bacteria	RF02001	Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine	X-ray diffraction	3	249	2015-10-14
38	8RUK\|1\|A	Group II catalytic intron D1-D4-1	Domains 1-5	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+, and ARN25850	X-ray diffraction	4.81	388	2024-06-19
39	4DS6\|1\|A	Group II catalytic intron D1-D4-1	Mutant Group IIC Intron	Oceanobacillus iheyensis	Bacteria	RF01998	Crystal structure of a group II intron in the pre-catalytic state	X-ray diffraction	3.64	393	2012-04-18
40	3EOG\|1\|A		5'-R(UPUPAPUPUPA)-3', Group IIC intron				Co-crystallization showing exon recognition by a group II intron	X-ray diffraction	3.39	388	2008-10-28
41	8OM0\|1\|A	Group II catalytic intron D1-D4-1	Domains 1-5	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+ and intronistat B	X-ray diffraction	3.61	390	2024-06-19
42	3BWP\|1\|A		Group IIC intron				Crystal structure of a self-spliced group II intron	X-ray diffraction	3.1	356	2008-04-15
43	4E8V\|1\|A	Group II catalytic intron D1-D4-1	Group IIC intron	Oceanobacillus iheyensis	Bacteria	RF01998	Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Ba2+	X-ray diffraction	3.99	389	2012-11-14
44	9C6J\|1\|A	TPP riboswitch (THI element)	Group IIC intron embedded with the TPP riboswitch	Oceanobacillus iheyensis	Bacteria	RF00059	Group IIC intron embedded with the TPP riboswitch	Electron microscopy	2.41	387	2024-12-04
45	9C6I\|1\|A	Group II catalytic intron D1-D4-3	Group IIC Intron	Oceanobacillus iheyensis	Bacteria	RF02001	Cryo-EM structure of a group IIC intron RNA	Electron microscopy	2.56	393	2024-12-04

Release history

Release	3.378	3.379	3.380	3.381
Date	2025-03-13	2025-03-19	2025-03-26	2025-04-02

Parents

This class	Parent classes	Release id	Intersection	Added to this class	Only in parent

Children

This class	Descendant classes	Release id	Intersection	Only in this class	Added 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.

#S	PDB	Title	Method	Resolution	#NTs
1	5J01\|1\|A	Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+ and MG2+.	X-RAY DIFFRACTION	3.39	414
2	5J02\|1\|A+ 5J02\|1\|B	Structure 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 DIFFRACTION	3.49	421
3	3EOG\|1\|A	Co-crystallization showing exon recognition by a group II intron	X-RAY DIFFRACTION	3.39	388
4	3BWP\|1\|A	Crystal structure of a self-spliced group II intron	X-RAY DIFFRACTION	3.1	356
5	3EOH\|1\|A	Refined group II intron structure	X-RAY DIFFRACTION	3.12	381
6	4E8V\|1\|A	Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Ba2+	X-RAY DIFFRACTION	3.99	389
7	8OLW\|1\|A	Structure of Oceanobacillus iheyensis group II intron before the first step of splicing in the presence of K+, Ca2+ and intronistat B	X-RAY DIFFRACTION	4	396
8	4FAQ\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and 5'-exon	X-RAY DIFFRACTION	3.11	396
9	4E8K\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and a non-hydrolyzed oligonucleotide substrate	X-RAY DIFFRACTION	3.03	388
10	4E8T\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and an oligonucleotide fragment substrate (low energy dataset)	X-RAY DIFFRACTION	3.34	388
11	3G78\|1\|A	Insight into group II intron catalysis from revised crystal structure	X-RAY DIFFRACTION	2.8	389
12	3IGI\|1\|A	Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron	X-RAY DIFFRACTION	3.12	389
13	8OLZ\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and intronistat B after 2h30 soaking	X-RAY DIFFRACTION	3.31	390
14	6T3R\|1\|A	Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of K+, Mg2+ and 5'-exon	X-RAY DIFFRACTION	3.57	389
15	8OLY\|1\|A	Structure of Oceanobacillus iheyensis group II intron post first step of splicing in the presence of K+, Mg2+ and intronistat B	X-RAY DIFFRACTION	3.11	390
16	6T3K\|1\|A	Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of K+, Mg2+ and 5'-exon	X-RAY DIFFRACTION	3.44	390
17	4FAR\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and 5'-exon	X-RAY DIFFRACTION	2.86	390
18	4FAU\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+ and 5'-exon	X-RAY DIFFRACTION	2.87	393
19	8RUH\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and 5'-exon	X-RAY DIFFRACTION	4.55	390
20	4FAW\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and a hydrolyzed oligonucleotide fragment	X-RAY DIFFRACTION	2.7	390
21	8RUJ\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and ARN25850 after 1h soaking	X-RAY DIFFRACTION	3.12	390
22	4E8M\|1\|A	Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Mg2+	X-RAY DIFFRACTION	3.5	394
23	8OLS\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and intronistat B	X-RAY DIFFRACTION	3	390
24	8OLV\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and ARN25850	X-RAY DIFFRACTION	2.81	394
25	8RUI\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and intronistat B after 1h soaking	X-RAY DIFFRACTION	3.31	390
26	4FB0\|1\|A	Structure of Oceanobacillus iheyensis group II intron C377G mutant in a ligand-free state in the presence of K+ and Mg2+	X-RAY DIFFRACTION	3.22	393
27	4E8N\|1\|A	Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of NH4+ and Mg2+	X-RAY DIFFRACTION	2.96	393
28	4E8Q\|1\|A	Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Tl+ and Mg2+	X-RAY DIFFRACTION	2.84	393
29	4E8P\|1\|A	Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Rb+ and Mg2+	X-RAY DIFFRACTION	3.28	393
30	4E8R\|1\|A	Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Cs+ and Mg2+	X-RAY DIFFRACTION	3.36	393
31	8RUL\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of Li+ and Mg2+	X-RAY DIFFRACTION	3.62	393
32	8RUN\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+, and ARN25850	X-RAY DIFFRACTION	3.73	393
33	8OM0\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+ and intronistat B	X-RAY DIFFRACTION	3.61	390
34	8RUM\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+, and intronistat B	X-RAY DIFFRACTION	3.62	393
35	4FAX\|1\|A	Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Na+ and Mg2+	X-RAY DIFFRACTION	3.1	392
36	8RUK\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+, and ARN25850	X-RAY DIFFRACTION	4.81	388
37	6T3S\|1\|A	Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of Na+, Mg2+ and 5'-exon	X-RAY DIFFRACTION	3.28	393
38	6T3N\|1\|A	Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of Na+, Mg2+ and 5'-exon	X-RAY DIFFRACTION	3.22	394
39	4DS6\|1\|A	Crystal structure of a group II intron in the pre-catalytic state	X-RAY DIFFRACTION	3.64	393
40	9C6J\|1\|A	Group IIC intron embedded with the TPP riboswitch	ELECTRON MICROSCOPY	2.41	387
41	9C6I\|1\|A	Cryo-EM structure of a group IIC intron RNA	ELECTRON MICROSCOPY	2.56	393
42	4Y1O\|1\|B	Oceanobacillus iheyensis group II intron domain 1	X-RAY DIFFRACTION	2.95	256
43	4Y1N\|1\|A	Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine	X-RAY DIFFRACTION	3	249
44	4Y1N\|1\|B	Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine	X-RAY DIFFRACTION	3	259
45	4Y1O\|1\|A	Oceanobacillus iheyensis group II intron domain 1	X-RAY DIFFRACTION	2.95	258

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: Nucleotide numbers

Equivalence class NR_20.0_35054.7 Current

Release history

Parents

Children