NR_4.0_35054.6

Members (43)
History
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#	IFE	Standardized name	Molecule	Organism	Source	Rfam	Title	Method	Res. Å	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	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	2024-06-19
3	5J02\|1\|A	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	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	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	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	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	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	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	2024-06-19
10	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	2024-06-19
11	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	2012-11-14
12	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	2015-10-14
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	2024-06-19
14	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	2012-11-14
15	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	2015-10-14
16	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	2012-11-14
17	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	2012-11-14
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	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	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	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	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	2012-11-14
23	3EOH\|1\|A		5'-R(UPUPAPUPUPA)-3', Group IIC intron				Refined group II intron structure	X-ray diffraction	3.12	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	2024-06-19
25	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	2020-05-13
26	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	2024-06-19
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	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	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	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	2024-06-19
31	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	2015-10-14
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	2024-06-19
33	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	2015-10-14
34	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	2010-02-16
35	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	2012-11-14
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	2020-05-13
37	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	2012-04-18
38	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	2008-10-28
39	3BWP\|1\|A		Group IIC intron				Crystal structure of a self-spliced group II intron	X-ray diffraction	3.1	2008-04-15
40	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	2024-06-19
41	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	2012-11-14
42	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	2024-12-04
43	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	2024-12-04

Release history

Release	3.364
Date	2024-12-04

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	Length
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	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	414
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	4DS6\|1\|A	Crystal structure of a group II intron in the pre-catalytic state	X-RAY DIFFRACTION	3.64	393
7	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
8	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
9	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
10	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
11	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
12	8RUL\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of Li+ and Mg2+	X-RAY DIFFRACTION	3.62	394
13	8RUN\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+, and ARN25850	X-RAY DIFFRACTION	3.73	393
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	8OLS\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and intronistat B	X-RAY DIFFRACTION	3	390
22	8OLV\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and ARN25850	X-RAY DIFFRACTION	2.81	394
23	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
24	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
25	4FAU\|1\|A	Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+ and 5'-exon	X-RAY DIFFRACTION	2.87	395
26	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
27	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
28	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
29	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
30	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
31	3IGI\|1\|A	Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron	X-RAY DIFFRACTION	3.12	389
32	3G78\|1\|A	Insight into group II intron catalysis from revised crystal structure	X-RAY DIFFRACTION	2.8	389
33	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
34	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
35	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
36	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
37	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
38	9C6J\|1\|A	Group IIC intron embedded with the TPP riboswitch	ELECTRON MICROSCOPY	2.41	495
39	9C6I\|1\|A	Cryo-EM structure of a group IIC intron RNA	ELECTRON MICROSCOPY	2.56	417
40	4Y1O\|1\|B	Oceanobacillus iheyensis group II intron domain 1	X-RAY DIFFRACTION	2.95	256
41	4Y1N\|1\|A	Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine	X-RAY DIFFRACTION	3	249
42	4Y1N\|1\|B	Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine	X-RAY DIFFRACTION	3	259
43	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_4.0_35054.6 Current

Release history

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