NR_4.0_83593.9

Members (43)
History
Heat map

#	IFE	Standardized name	Molecule	Organism	Source	Rfam	Title	Method	Res. Å	#NTs	Date
1	5AXM\|1\|P (rep)	Transfer RNA	RNA (75-MER)	Saccharomyces cerevisiae	Eukarya	RF00005	Crystal structure of Thg1 like protein (TLP) with tRNA(Phe)	X-ray diffraction	2.21	73	2016-08-03
2	1EVV\|1\|A	Transfer RNA	PHENYLALANINE TRANSFER RNA	Saccharomyces	Eukarya	RF00005	CRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTION	X-ray diffraction	2	76	2000-05-01
3	6XZB\|1\|g2	Transfer RNA	fMet-Phe-tRNA(Phe)	Saccharomyces cerevisiae	Eukarya	RF00005	E. coli 70S ribosome in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet) (focused classification).	Electron microscopy	2.54	76	2020-11-04
4	9YPO\|1\|12	Transfer RNA	MF mRNA, Phe-tRNA	Saccharomyces cerevisiae	Eukarya	RF00005	GTPBP1GCPPhe-tRNA*ribosome in the open state, Structure IIa	Electron microscopy	3	75	2025-12-17
5	8CDR\|1\|Bb	Transfer RNA	Messenger RNA, Transfer RNA Phe	Saccharomyces cerevisiae	Eukarya	RF00005	Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin	Electron microscopy	2.04	76	2023-09-20
6	8CEH\|1\|Bb	Transfer RNA	Messenger RNA, Transfer RNA Phe	Saccharomyces cerevisiae	Eukarya	RF00005	Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin	Electron microscopy	2.05	76	2023-09-20
7	6LVR\|1\|D	Transfer RNA	yeast phenylalanine tRNA	Saccharomyces cerevisiae	Eukarya	RF00005	Crystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNA	X-ray diffraction	2.85	72	2020-08-12
8	5AXN\|1\|P	Transfer RNA	RNA (75-MER)	Saccharomyces cerevisiae	Eukarya	RF00005	Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) and GDPNP	X-ray diffraction	2.7	66	2016-08-03
9	9YPS\|1\|12	Transfer RNA	MF mRNA, Phe-tRNA	Saccharomyces cerevisiae	Eukarya	RF00005	GTPBP1GCPPhe-tRNA*ribosome in the open state, Structure IIb	Electron microscopy	3	75	2025-12-17
10	5M1J\|1\|A3	Transfer RNA	nonstop mRNA, yeast Phe-tRNA-Phe	Saccharomyces cerevisiae	Eukarya	RF00005	Nonstop ribosomal complex bound with Dom34 and Hbs1	Electron microscopy	3.3	76	2017-01-18
11	1OB2\|1\|B	Transfer RNA	TRANSFER-RNA, PHE	Saccharomyces cerevisiae	Eukarya	RF00005	E. coli elongation factor EF-Tu complexed with the antibiotic kirromycin, a GTP analog, and Phe-tRNA	X-ray diffraction	3.35	76	2004-05-27
12	9YPY\|1\|12	Transfer RNA	MF mRNA, Phe-tRNA	Saccharomyces cerevisiae	Eukarya	RF00005	Ribosome with accommodated A-site tRNA, Structure V	Electron microscopy	3	75	2025-12-24
13	9YPV\|1\|12	Transfer RNA	MF mRNA, Phe-tRNA	Saccharomyces cerevisiae	Eukarya	RF00005	GTPBP1GCPPhe-tRNA*ribosome in the open state, Structure IId	Electron microscopy	3	75	2025-12-17
14	6LVR\|1\|B	Transfer RNA	yeast phenylalanine tRNA	Saccharomyces cerevisiae	Eukarya	RF00005	Crystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNA	X-ray diffraction	2.85	72	2020-08-12
15	9YPT\|1\|12	Transfer RNA	MF mRNA, Phe-tRNA	Saccharomyces cerevisiae	Eukarya	RF00005	GTPBP1GCPPhe-tRNA*ribosome in the open state, Structure IIc	Electron microscopy	3.1	75	2025-12-17
16	3WC2\|1\|P	Transfer RNA	76mer-tRNA			RF00005	Crystal structure of C. albicans tRNA(His) guanylyltransferase (Thg1) with a tRNA(Phe)(GUG)	X-ray diffraction	3.64	74	2013-12-18
17	8CF5\|1\|Bb	Transfer RNA	Messenger RNA, Transfer RNA Phe	Saccharomyces cerevisiae	Eukarya	RF00005	Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin	Electron microscopy	2.71	76	2023-09-20
18	9F9S\|1\|DP	Transfer RNA	tRNA	Saccharomyces cerevisiae	Eukarya	RF00005	Yeast SDD1 Disome with Mbf1	Electron microscopy	2.9	76	2024-12-04
19	6GQV\|1\|AY	Transfer RNA	Messenger RNA, Transfer RNA - Phe	Saccharomyces cerevisiae	Eukarya	RF00005	Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP)	Electron microscopy	4	76	2018-07-11
20	6GZ3\|1\|Bw	Transfer RNA	mRNA, pe/E-site-tRNA	Saccharomyces cerevisiae	Eukarya	RF00005	tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1)	Electron microscopy	3.6	76	2018-12-05
21	8CTH\|1\|C	Transfer RNA	Phe-tRNA	Saccharomyces cerevisiae	Eukarya	RF00005	Cryo-EM structure of human METTL1-WDR4-tRNA(Phe) complex	Electron microscopy	3.3	74	2022-12-07
22	6XIR\|1\|AX	Transfer RNA	Transfer RNA	Saccharomyces cerevisiae	Eukarya	RF00005	Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress	Electron microscopy	3.2	73	2020-08-26
23	3WC2\|1\|Q	Transfer RNA	76mer-tRNA			RF00005	Crystal structure of C. albicans tRNA(His) guanylyltransferase (Thg1) with a tRNA(Phe)(GUG)	X-ray diffraction	3.64	73	2013-12-18
24	6GQB\|1\|AX	Transfer RNA	Messenger RNA, Transfer RNA - Phe	Saccharomyces cerevisiae	Eukarya	RF00005	Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin)	Electron microscopy	3.9	76	2018-07-11
25	6GZ5\|1\|Bw	Transfer RNA	E/E-site-tRNA, mRNA	Saccharomyces cerevisiae	Eukarya	RF00005	tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)	Electron microscopy	3.5	76	2018-12-05
26	8CG8\|1\|Bb	Transfer RNA	Messenger RNA, Transfer RNA Phe	Saccharomyces cerevisiae	Eukarya	RF00005	Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin	Electron microscopy	2.57	76	2023-09-20
27	6XIR\|1\|AZ	Transfer RNA	Transfer RNA	Saccharomyces cerevisiae	Eukarya	RF00005	Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress	Electron microscopy	3.2	73	2020-08-26
28	4TNA\|1\|A	Transfer RNA	TRNAPHE	Saccharomyces cerevisiae	Eukarya	RF00005	FURTHER REFINEMENT OF THE STRUCTURE OF YEAST T-RNA-PHE	X-ray diffraction	2.5	76	1978-04-12
29	1EHZ\|1\|A	Transfer RNA	TRANSFER RNA (PHE)	Saccharomyces cerevisiae	Eukarya	RF00005	The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution	X-ray diffraction	1.93	76	2000-10-02
30	8CCS\|1\|Bb	Transfer RNA	Messenger RNA, Transfer RNA Phe	Saccharomyces cerevisiae	Eukarya	RF00005	80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex	Electron microscopy	1.97	76	2023-09-20
31	8CIV\|1\|Bb	Transfer RNA	Messenger RNA, Transfer RNA Phe	Saccharomyces cerevisiae	Eukarya	RF00005	Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin	Electron microscopy	2.47	76	2023-09-20
32	1I9V\|1\|A	Transfer RNA	PHENYLALANINE TRANSFER RNA	Saccharomyces cerevisiae	Eukarya	RF00005	CRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEX	X-ray diffraction	2.6	76	2001-06-04
33	1TN1\|1\|A	Transfer RNA	TRNAPHE	Saccharomyces cerevisiae	Eukarya	RF00005	CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNA	X-ray diffraction	3	76	1987-01-15
34	1TN2\|1\|A	Transfer RNA	TRNAPHE	Saccharomyces cerevisiae	Eukarya	RF00005	CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE T-RNA	X-ray diffraction	3	76	1986-10-24
35	4TRA\|1\|A	Transfer RNA	TRNAPHE	Saccharomyces cerevisiae	Eukarya	RF00005	RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALS	X-ray diffraction	3	76	1987-11-06
36	6TNA\|1\|A	Transfer RNA	TRNAPHE	Saccharomyces cerevisiae	Eukarya	RF00005	CRYSTAL STRUCTURE OF YEAST PHENYLALANINE T-RNA. I.CRYSTALLOGRAPHIC REFINEMENT	X-ray diffraction	2.7	76	1979-01-16
37	1TTT\|1\|F	Transfer RNA	TRANSFER RIBONUCLEIC ACID (YEAST, PHE)			RF00005	Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex	X-ray diffraction	2.7	76	1996-12-23
38	1TTT\|1\|D	Transfer RNA	TRANSFER RIBONUCLEIC ACID (YEAST, PHE)			RF00005	Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex	X-ray diffraction	2.7	76	1996-12-23
39	1TTT\|1\|E	Transfer RNA	TRANSFER RIBONUCLEIC ACID (YEAST, PHE)			RF00005	Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex	X-ray diffraction	2.7	76	1996-12-23
40	6XZ7\|1\|g	Transfer RNA	fMet-Phe-tRNA(Phe)	Saccharomyces cerevisiae	Eukarya	RF00005	E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet).	Electron microscopy	2.1	76	2020-07-22
41	8CDL\|1\|Bb	Transfer RNA	Messenger RNA, Transfer RNA Phe	Saccharomyces cerevisiae	Eukarya	RF00005	80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex	Electron microscopy	2.72	76	2023-09-20
42	1TRA\|1\|A	Transfer RNA	TRNAPHE	Saccharomyces cerevisiae	Eukarya	RF00005	RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES	X-ray diffraction	3	76	1986-07-14
43	8CKU\|1\|Bb	Transfer RNA	Messenger RNA, Transfer RNA Phe	Saccharomyces cerevisiae	Eukarya	RF00005	Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin	Electron microscopy	3.11	76	2023-09-20

Release history

Release	4.19
Date	2025-12-24

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	9YPV\|1\|12	GTPBP1GCPPhe-tRNA*ribosome in the open state, Structure IId	ELECTRON MICROSCOPY	3	75
2	9YPS\|1\|12	GTPBP1GCPPhe-tRNA*ribosome in the open state, Structure IIb	ELECTRON MICROSCOPY	3	75
3	9YPO\|1\|12	GTPBP1GCPPhe-tRNA*ribosome in the open state, Structure IIa	ELECTRON MICROSCOPY	3	75
4	9YPT\|1\|12	GTPBP1GCPPhe-tRNA*ribosome in the open state, Structure IIc	ELECTRON MICROSCOPY	3.1	75
5	1OB2\|1\|B	E. coli elongation factor EF-Tu complexed with the antibiotic kirromycin, a GTP analog, and Phe-tRNA	X-RAY DIFFRACTION	3.35	76
6	1TTT\|1\|E	Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex	X-RAY DIFFRACTION	2.7	76
7	1TTT\|1\|F	Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex	X-RAY DIFFRACTION	2.7	76
8	1TTT\|1\|D	Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex	X-RAY DIFFRACTION	2.7	76
9	3WC2\|1\|Q	Crystal structure of C. albicans tRNA(His) guanylyltransferase (Thg1) with a tRNA(Phe)(GUG)	X-RAY DIFFRACTION	3.64	73
10	3WC2\|1\|P	Crystal structure of C. albicans tRNA(His) guanylyltransferase (Thg1) with a tRNA(Phe)(GUG)	X-RAY DIFFRACTION	3.64	74
11	8CTH\|1\|C	Cryo-EM structure of human METTL1-WDR4-tRNA(Phe) complex	ELECTRON MICROSCOPY	3.3	74
12	1EHZ\|1\|A	The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution	X-RAY DIFFRACTION	1.93	76
13	1TRA\|1\|A	RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES	X-RAY DIFFRACTION	3	76
14	4TNA\|1\|A	FURTHER REFINEMENT OF THE STRUCTURE OF YEAST T-RNA-PHE	X-RAY DIFFRACTION	2.5	76
15	1TN1\|1\|A	CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNA	X-RAY DIFFRACTION	3	76
16	1TN2\|1\|A	CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE T-RNA	X-RAY DIFFRACTION	3	76
17	6TNA\|1\|A	CRYSTAL STRUCTURE OF YEAST PHENYLALANINE T-RNA. I.CRYSTALLOGRAPHIC REFINEMENT	X-RAY DIFFRACTION	2.7	76
18	4TRA\|1\|A	RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALS	X-RAY DIFFRACTION	3	76
19	1I9V\|1\|A	CRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEX	X-RAY DIFFRACTION	2.6	76
20	1EVV\|1\|A	CRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTION	X-RAY DIFFRACTION	2	76
21	5AXM\|1\|P	Crystal structure of Thg1 like protein (TLP) with tRNA(Phe)	X-RAY DIFFRACTION	2.21	73
22	5AXN\|1\|P	Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) and GDPNP	X-RAY DIFFRACTION	2.7	66
23	8CEH\|1\|Bb	Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin	ELECTRON MICROSCOPY	2.05	76
24	8CDR\|1\|Bb	Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin	ELECTRON MICROSCOPY	2.04	76
25	8CIV\|1\|Bb	Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin	ELECTRON MICROSCOPY	2.47	76
26	8CG8\|1\|Bb	Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin	ELECTRON MICROSCOPY	2.57	76
27	8CCS\|1\|Bb	80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex	ELECTRON MICROSCOPY	1.97	76
28	9F9S\|1\|DP	Yeast SDD1 Disome with Mbf1	ELECTRON MICROSCOPY	2.9	76
29	8CDL\|1\|Bb	80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex	ELECTRON MICROSCOPY	2.72	76
30	8CF5\|1\|Bb	Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin	ELECTRON MICROSCOPY	2.71	76
31	8CKU\|1\|Bb	Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin	ELECTRON MICROSCOPY	3.11	76
32	9YPY\|1\|12	Ribosome with accommodated A-site tRNA, Structure V	ELECTRON MICROSCOPY	3	75
33	6XZB\|1\|g2	E. coli 70S ribosome in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet) (focused classification).	ELECTRON MICROSCOPY	2.54	76
34	6XZ7\|1\|g	E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet).	ELECTRON MICROSCOPY	2.1	76
35	5M1J\|1\|A3	Nonstop ribosomal complex bound with Dom34 and Hbs1	ELECTRON MICROSCOPY	3.3	76
36	6LVR\|1\|D	Crystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNA	X-RAY DIFFRACTION	2.85	72
37	6LVR\|1\|B	Crystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNA	X-RAY DIFFRACTION	2.85	72
38	6GZ5\|1\|Bw	tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)	ELECTRON MICROSCOPY	3.5	76
39	6GZ3\|1\|Bw	tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1)	ELECTRON MICROSCOPY	3.6	76
40	6GQB\|1\|AX	Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin)	ELECTRON MICROSCOPY	3.9	76
41	6GQV\|1\|AY	Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP)	ELECTRON MICROSCOPY	4	76
42	6XIR\|1\|AZ	Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress	ELECTRON MICROSCOPY	3.2	73
43	6XIR\|1\|AX	Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress	ELECTRON MICROSCOPY	3.2	73

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_83593.9 Current

Release history

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