NR_3.5_21280.28

Members (42)
History
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#	IFE	Standardized name	Molecule	Organism	Source	Rfam	Title	Method	Res. Å	Date
1	7O7Y\|1\|A2 (rep)	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (high resolution)	Electron microscopy	2.2	2021-06-02
2	7OYD\|1\|9	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b	Electron microscopy	2.3	2022-07-20
3	7O7Z\|1\|A2	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (classified for pseudoknot)	Electron microscopy	2.4	2021-06-02
4	7JQB\|1\|A	Small subunit ribosomal RNA	rRNA	Oryctolagus cuniculus	Eukarya	RF01960	SARS-CoV-2 Nsp1 and rabbit 40S ribosome complex	Electron microscopy	2.7	2020-12-02
5	7ZJW\|1\|S2	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Rabbit 80S ribosome as it decodes the Sec-UGA codon	Electron microscopy	2.8	2022-10-19
6	7UCK\|1\|9	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	80S translation initiation complex with ac4c(-1) mRNA and Harringtonine	Electron microscopy	2.8	2022-06-01
7	6SGC\|1\|A1	Small subunit ribosomal RNA	18S ribosomal RNA	Oryctolagus cuniculus	Eukarya	RF01960	Rabbit 80S ribosome stalled on a poly(A) tail	Electron microscopy	2.8	2019-12-04
8	7TOR\|1\|A18S	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Mammalian 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20	Electron microscopy	2.9	2022-05-25
9	7O80\|1\|A2	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Rabbit 80S ribosome in complex with eRF1 and ABCE1 stalled at the STOP codon in the mutated SARS-CoV-2 slippery site	Electron microscopy	2.9	2021-06-02
10	8P2K\|1\|A2	Small subunit ribosomal RNA	18s rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Ternary complex of translating ribosome, NAC and METAP1	Electron microscopy	2.9	2023-07-19
11	7NWI\|1\|9	Small subunit ribosomal RNA	18S ribosomal RNA	Oryctolagus cuniculus	Eukarya	RF01960	Mammalian pre-termination 80S ribosome with Empty-A site bound by Blasticidin S	Electron microscopy	3.13	2021-07-07
12	6YAL\|1\|2	Small subunit ribosomal RNA	18S ribosomal RNA	Oryctolagus cuniculus	Eukarya	RF01960	Mammalian 48S late-stage initiation complex with beta-globin mRNA	Electron microscopy	3	2020-04-08
13	6R5Q\|1\|K	Small subunit ribosomal RNA	18S ribosomal RNA	Oryctolagus cuniculus	Eukarya	RF01960	Structure of XBP1u-paused ribosome nascent chain complex (post-state)	Electron microscopy	3	2019-07-10
14	7TOQ\|1\|A18S	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Mammalian 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein poly-PR	Electron microscopy	3.1	2022-05-25
15	7ZJX\|1\|S2	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Rabbit 80S ribosome programmed with SECIS and SBP2	Electron microscopy	3.1	2022-09-07
16	7O81\|1\|A2	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Rabbit 80S ribosome colliding in another ribosome stalled by the SARS-CoV-2 pseudoknot	Electron microscopy	3.1	2021-06-02
17	6ZVK\|1\|K3	Small subunit ribosomal RNA	18S RIBOSOMAL RNA	Oryctolagus cuniculus	Eukarya	RF01960	The Halastavi arva virus (HalV) intergenic region IRES promotes translation by the simplest possible initiation mechanism	Electron microscopy	3.49	2020-12-23
18	6P5I\|1\|2	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 1)	Electron microscopy	3.1	2019-09-18
19	6P5K\|1\|2	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 3)	Electron microscopy	3.1	2019-09-18
20	6P5J\|1\|2	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 2)	Electron microscopy	3.1	2019-09-18
21	7UCJ\|1\|9	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Mammalian 80S translation initiation complex with mRNA and Harringtonine	Electron microscopy	3.1	2022-06-01
22	6P4G\|1\|2	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 1)	Electron microscopy	3.1	2019-09-18
23	7MDZ\|1\|9	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	80S rabbit ribosome stalled with benzamide-CHX	Electron microscopy	3.2	2021-09-01
24	6R6P\|1\|K	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Structure of XBP1u-paused ribosome nascent chain complex (rotated state)	Electron microscopy	3.1	2019-07-10
25	6P4H\|1\|2	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 2)	Electron microscopy	3.2	2019-09-18
26	6P5N\|1\|2	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Structure of a mammalian 80S ribosome in complex with a single translocated Israeli Acute Paralysis Virus IRES and eRF1	Electron microscopy	3.2	2019-09-25
27	6D9J\|1\|2	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Mammalian 80S ribosome with a double translocated CrPV-IRES, P-sitetRNA and eRF1.	Electron microscopy	3.2	2018-06-06
28	7JQC\|1\|A	Small subunit ribosomal RNA	rRNA	Oryctolagus cuniculus	Eukarya	RF01960	SARS-CoV-2 Nsp1, CrPV IRES and rabbit 40S ribosome complex	Electron microscopy	3.3	2020-12-02
29	5LZS\|1\|9	Small subunit ribosomal RNA	18S ribosomal RNA	Oryctolagus cuniculus	Eukarya	RF01960	Structure of the mammalian ribosomal elongation complex with aminoacyl-tRNA, eEF1A, and didemnin B	Electron microscopy	3.31	2016-11-30
30	6W2T\|1\|a	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2)	Electron microscopy	3.36	2020-04-22
31	6MTD\|1\|9	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Rabbit 80S ribosome with eEF2 and SERBP1 (unrotated state with 40S head swivel)	Electron microscopy	3.3	2018-11-21
32	5LZV\|1\|9	Small subunit ribosomal RNA	18S ribosomal RNA	Oryctolagus cuniculus	Eukarya	RF01960	Structure of the mammalian ribosomal termination complex with accommodated eRF1(AAQ) and ABCE1.	Electron microscopy	3.35	2016-11-30
33	6D90\|1\|2	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Mammalian 80S ribosome with a double translocated CrPV-IRES, P-site tRNA and eRF1.	Electron microscopy	3.2	2018-06-06
34	7SYS\|1\|2	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Structure of the delta dII IRES eIF2-containing 48S initiation complex, closed conformation. Structure 12(delta dII).	Electron microscopy	3.5	2022-07-27
35	8BTK\|1\|A2	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Structure of the TRAP complex with the Sec translocon and a translating ribosome	Electron microscopy	3.5	2023-05-24
36	6YAN\|1\|2	Small subunit ribosomal RNA	18S ribosomal RNA	Oryctolagus cuniculus	Eukarya	RF01960	Mammalian 48S late-stage translation initiation complex with histone 4 mRNA	Electron microscopy	3.48	2020-04-08
37	6MTC\|1\|9	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Rabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state)	Electron microscopy	3.4	2018-11-21
38	6MTE\|1\|9	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)	Electron microscopy	3.4	2018-11-21
39	6W2S\|1\|A	Small subunit ribosomal RNA	18S rRNA	Oryctolagus cuniculus	Eukarya	RF01960	Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1)	Electron microscopy	3.47	2020-04-22
40	6GZ5\|1\|B1	Small subunit ribosomal RNA	18S ribosomal RNA	Oryctolagus cuniculus	Eukarya	RF01960	tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)	Electron microscopy	3.5	2018-12-05
41	5LZZ\|1\|9	Small subunit ribosomal RNA	18S ribosomal RNA	Oryctolagus cuniculus	Eukarya	RF01960	Structure of the mammalian rescue complex with Pelota and Hbs1l (combined)	Electron microscopy	3.47	2016-11-30
42	3JAH\|1\|9	Small subunit ribosomal RNA	18S ribosomal RNA	Oryctolagus cuniculus	Eukarya	RF01960	Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAG stop codon	Electron microscopy	3.45	2015-08-12

Release history

Release	3.292	3.293	3.294	3.295	3.296	3.297	3.298
Date	2023-07-19	2023-07-26	2023-08-02	2023-08-09	2023-08-16	2023-08-23	2023-08-30

Parents

This class	Parent classes	Release id	Intersection	Added to this class	Only in parent
NR_3.5_21280.28	NR_3.5_21280.27	3.292	(41) 3JAH\|1\|9, 5LZS\|1\|9, 5LZV\|1\|9, 5LZZ\|1\|9, 6D90\|1\|2, 6D9J\|1\|2, 6GZ5\|1\|B1, 6MTC\|1\|9, 6MTD\|1\|9, 6MTE\|1\|9, 6P4G\|1\|2, 6P4H\|1\|2, 6P5I\|1\|2, 6P5J\|1\|2, 6P5K\|1\|2, 6P5N\|1\|2, 6R5Q\|1\|K, 6R6P\|1\|K, 6SGC\|1\|A1, 6W2S\|1\|A, 6W2T\|1\|a, 6YAL\|1\|2, 6YAN\|1\|2, 6ZVK\|1\|K3, 7JQB\|1\|A, 7JQC\|1\|A, 7MDZ\|1\|9, 7NWI\|1\|9, 7O7Y\|1\|A2, 7O7Z\|1\|A2, 7O80\|1\|A2, 7O81\|1\|A2, 7OYD\|1\|9, 7SYS\|1\|2, 7TOQ\|1\|A18S, 7TOR\|1\|A18S, 7UCJ\|1\|9, 7UCK\|1\|9, 7ZJW\|1\|S2, 7ZJX\|1\|S2, 8BTK\|1\|A2	(1) 8P2K\|1\|A2	(0)

Children

This class	Descendant classes	Release id	Intersection	Only in this class	Added to child
NR_3.5_21280.28	NR_3.5_21280.29	3.299	(42) 3JAH\|1\|9, 5LZS\|1\|9, 5LZV\|1\|9, 5LZZ\|1\|9, 6D90\|1\|2, 6D9J\|1\|2, 6GZ5\|1\|B1, 6MTC\|1\|9, 6MTD\|1\|9, 6MTE\|1\|9, 6P4G\|1\|2, 6P4H\|1\|2, 6P5I\|1\|2, 6P5J\|1\|2, 6P5K\|1\|2, 6P5N\|1\|2, 6R5Q\|1\|K, 6R6P\|1\|K, 6SGC\|1\|A1, 6W2S\|1\|A, 6W2T\|1\|a, 6YAL\|1\|2, 6YAN\|1\|2, 6ZVK\|1\|K3, 7JQB\|1\|A, 7JQC\|1\|A, 7MDZ\|1\|9, 7NWI\|1\|9, 7O7Y\|1\|A2, 7O7Z\|1\|A2, 7O80\|1\|A2, 7O81\|1\|A2, 7OYD\|1\|9, 7SYS\|1\|2, 7TOQ\|1\|A18S, 7TOR\|1\|A18S, 7UCJ\|1\|9, 7UCK\|1\|9, 7ZJW\|1\|S2, 7ZJX\|1\|S2, 8BTK\|1\|A2, 8P2K\|1\|A2	(0)	(1) 8BHF\|1\|A3

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	6YAN\|1\|2	Mammalian 48S late-stage translation initiation complex with histone 4 mRNA	ELECTRON MICROSCOPY	3.48	1743
2	6YAL\|1\|2	Mammalian 48S late-stage initiation complex with beta-globin mRNA	ELECTRON MICROSCOPY	3	1743
3	7NWI\|1\|9	Mammalian pre-termination 80S ribosome with Empty-A site bound by Blasticidin S	ELECTRON MICROSCOPY	3.13	1719
4	3JAH\|1\|9	Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAG stop codon	ELECTRON MICROSCOPY	3.45	1719
5	6ZVK\|1\|K3	The Halastavi arva virus (HalV) intergenic region IRES promotes translation by the simplest possible initiation mechanism	ELECTRON MICROSCOPY	3.49	1869
6	6GZ5\|1\|B1	tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)	ELECTRON MICROSCOPY	3.5	1708
7	7O81\|1\|A2	Rabbit 80S ribosome colliding in another ribosome stalled by the SARS-CoV-2 pseudoknot	ELECTRON MICROSCOPY	3.1	1688
8	7ZJW\|1\|S2	Rabbit 80S ribosome as it decodes the Sec-UGA codon	ELECTRON MICROSCOPY	2.8	1689
9	7O80\|1\|A2	Rabbit 80S ribosome in complex with eRF1 and ABCE1 stalled at the STOP codon in the mutated SARS-CoV-2 slippery site	ELECTRON MICROSCOPY	2.9	1688
10	7O7Y\|1\|A2	Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (high resolution)	ELECTRON MICROSCOPY	2.2	1688
11	7O7Z\|1\|A2	Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (classified for pseudoknot)	ELECTRON MICROSCOPY	2.4	1688
12	8BTK\|1\|A2	Structure of the TRAP complex with the Sec translocon and a translating ribosome	ELECTRON MICROSCOPY	3.5	1688
13	8P2K\|1\|A2	Ternary complex of translating ribosome, NAC and METAP1	ELECTRON MICROSCOPY	2.9	1688
14	6P5N\|1\|2	Structure of a mammalian 80S ribosome in complex with a single translocated Israeli Acute Paralysis Virus IRES and eRF1	ELECTRON MICROSCOPY	3.2	1697
15	7JQB\|1\|A	SARS-CoV-2 Nsp1 and rabbit 40S ribosome complex	ELECTRON MICROSCOPY	2.7	1697
16	7TOQ\|1\|A18S	Mammalian 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein poly-PR	ELECTRON MICROSCOPY	3.1	1690
17	6R6P\|1\|K	Structure of XBP1u-paused ribosome nascent chain complex (rotated state)	ELECTRON MICROSCOPY	3.1	1698
18	5LZS\|1\|9	Structure of the mammalian ribosomal elongation complex with aminoacyl-tRNA, eEF1A, and didemnin B	ELECTRON MICROSCOPY	3.31	1697
19	5LZV\|1\|9	Structure of the mammalian ribosomal termination complex with accommodated eRF1(AAQ) and ABCE1.	ELECTRON MICROSCOPY	3.35	1698
20	5LZZ\|1\|9	Structure of the mammalian rescue complex with Pelota and Hbs1l (combined)	ELECTRON MICROSCOPY	3.47	1698
21	6SGC\|1\|A1	Rabbit 80S ribosome stalled on a poly(A) tail	ELECTRON MICROSCOPY	2.8	1697
22	7MDZ\|1\|9	80S rabbit ribosome stalled with benzamide-CHX	ELECTRON MICROSCOPY	3.2	1697
23	6MTC\|1\|9	Rabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state)	ELECTRON MICROSCOPY	3.4	1664
24	6R5Q\|1\|K	Structure of XBP1u-paused ribosome nascent chain complex (post-state)	ELECTRON MICROSCOPY	3	1698
25	7TOR\|1\|A18S	Mammalian 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20	ELECTRON MICROSCOPY	2.9	1691
26	7UCK\|1\|9	80S translation initiation complex with ac4c(-1) mRNA and Harringtonine	ELECTRON MICROSCOPY	2.8	1664
27	7UCJ\|1\|9	Mammalian 80S translation initiation complex with mRNA and Harringtonine	ELECTRON MICROSCOPY	3.1	1664
28	6D90\|1\|2	Mammalian 80S ribosome with a double translocated CrPV-IRES, P-site tRNA and eRF1.	ELECTRON MICROSCOPY	3.2	1697
29	7SYS\|1\|2	Structure of the delta dII IRES eIF2-containing 48S initiation complex, closed conformation. Structure 12(delta dII).	ELECTRON MICROSCOPY	3.5	1697
30	7JQC\|1\|A	SARS-CoV-2 Nsp1, CrPV IRES and rabbit 40S ribosome complex	ELECTRON MICROSCOPY	3.3	1697
31	7ZJX\|1\|S2	Rabbit 80S ribosome programmed with SECIS and SBP2	ELECTRON MICROSCOPY	3.1	1689
32	6P4H\|1\|2	Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 2)	ELECTRON MICROSCOPY	3.2	1697
33	6P4G\|1\|2	Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 1)	ELECTRON MICROSCOPY	3.1	1697
34	6P5K\|1\|2	Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 3)	ELECTRON MICROSCOPY	3.1	1697
35	6P5I\|1\|2	Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 1)	ELECTRON MICROSCOPY	3.1	1697
36	6P5J\|1\|2	Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 2)	ELECTRON MICROSCOPY	3.1	1697
37	7OYD\|1\|9	Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b	ELECTRON MICROSCOPY	2.3	1664
38	6MTE\|1\|9	Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)	ELECTRON MICROSCOPY	3.4	1664
39	6MTD\|1\|9	Rabbit 80S ribosome with eEF2 and SERBP1 (unrotated state with 40S head swivel)	ELECTRON MICROSCOPY	3.3	1692
40	6W2S\|1\|A	Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1)	ELECTRON MICROSCOPY	3.47	1697
41	6W2T\|1\|a	Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2)	ELECTRON MICROSCOPY	3.36	1697
42	6D9J\|1\|2	Mammalian 80S ribosome with a double translocated CrPV-IRES, P-sitetRNA and eRF1.	ELECTRON MICROSCOPY	3.2	1697

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_3.5_21280.28 Obsolete

Release history

Parents

Children