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Equivalence class NR_3.5_83593.8 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
15AXM|1|P (rep)Transfer RNARNA (75-MER)Saccharomyces cerevisiaeEukaryaRF00005Crystal structure of Thg1 like protein (TLP) with tRNA(Phe)X-ray diffraction2.21732016-08-03
21EVV|1|ATransfer RNAPHENYLALANINE TRANSFER RNASaccharomycesEukaryaRF00005CRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTIONX-ray diffraction2762000-05-01
36XZB|1|g2Transfer RNAfMet-Phe-tRNA(Phe)Saccharomyces cerevisiaeEukaryaRF00005E. coli 70S ribosome in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet) (focused classification).Electron microscopy2.54762020-11-04
49YPO|1|12Transfer RNAMF mRNA, Phe-tRNASaccharomyces cerevisiaeEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIaElectron microscopy3752025-12-17
58CDR|1|BbTransfer RNAMessenger RNA, Transfer RNA PheSaccharomyces cerevisiaeEukaryaRF00005Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinElectron microscopy2.04762023-09-20
68CEH|1|BbTransfer RNAMessenger RNA, Transfer RNA PheSaccharomyces cerevisiaeEukaryaRF00005Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinElectron microscopy2.05762023-09-20
76LVR|1|DTransfer RNAyeast phenylalanine tRNASaccharomyces cerevisiaeEukaryaRF00005Crystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNAX-ray diffraction2.85722020-08-12
85AXN|1|PTransfer RNARNA (75-MER)Saccharomyces cerevisiaeEukaryaRF00005Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) and GDPNPX-ray diffraction2.7662016-08-03
99YPS|1|12Transfer RNAMF mRNA, Phe-tRNASaccharomyces cerevisiaeEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIbElectron microscopy3752025-12-17
105M1J|1|A3Transfer RNAnonstop mRNA, yeast Phe-tRNA-PheSaccharomyces cerevisiaeEukaryaRF00005Nonstop ribosomal complex bound with Dom34 and Hbs1Electron microscopy3.3762017-01-18
111OB2|1|BTransfer RNATRANSFER-RNA, PHESaccharomyces cerevisiaeEukaryaRF00005E. coli elongation factor EF-Tu complexed with the antibiotic kirromycin, a GTP analog, and Phe-tRNAX-ray diffraction3.35762004-05-27
129YPV|1|12Transfer RNAMF mRNA, Phe-tRNASaccharomyces cerevisiaeEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIdElectron microscopy3752025-12-17
136LVR|1|BTransfer RNAyeast phenylalanine tRNASaccharomyces cerevisiaeEukaryaRF00005Crystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNAX-ray diffraction2.85722020-08-12
149YPT|1|12Transfer RNAMF mRNA, Phe-tRNASaccharomyces cerevisiaeEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIcElectron microscopy3.1752025-12-17
158CF5|1|BbTransfer RNAMessenger RNA, Transfer RNA PheSaccharomyces cerevisiaeEukaryaRF00005Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinElectron microscopy2.71762023-09-20
169F9S|1|DPTransfer RNAtRNASaccharomyces cerevisiaeEukaryaRF00005Yeast SDD1 Disome with Mbf1Electron microscopy2.9762024-12-04
178CTH|1|CTransfer RNAPhe-tRNASaccharomyces cerevisiaeEukaryaRF00005Cryo-EM structure of human METTL1-WDR4-tRNA(Phe) complexElectron microscopy3.3742022-12-07
186XIR|1|AXTransfer RNATransfer RNASaccharomyces cerevisiaeEukaryaRF00005Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative StressElectron microscopy3.2732020-08-26
196GZ5|1|BwTransfer RNAE/E-site-tRNA, mRNASaccharomyces cerevisiaeEukaryaRF00005tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)Electron microscopy3.5762018-12-05
208CG8|1|BbTransfer RNAMessenger RNA, Transfer RNA PheSaccharomyces cerevisiaeEukaryaRF00005Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinElectron microscopy2.57762023-09-20
216XIR|1|AZTransfer RNATransfer RNASaccharomyces cerevisiaeEukaryaRF00005Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative StressElectron microscopy3.2732020-08-26
224TNA|1|ATransfer RNATRNAPHESaccharomyces cerevisiaeEukaryaRF00005FURTHER REFINEMENT OF THE STRUCTURE OF YEAST T-RNA-PHEX-ray diffraction2.5761978-04-12
231EHZ|1|ATransfer RNATRANSFER RNA (PHE)Saccharomyces cerevisiaeEukaryaRF00005The crystal structure of yeast phenylalanine tRNA at 1.93 A resolutionX-ray diffraction1.93762000-10-02
248CCS|1|BbTransfer RNAMessenger RNA, Transfer RNA PheSaccharomyces cerevisiaeEukaryaRF0000580S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complexElectron microscopy1.97762023-09-20
258CIV|1|BbTransfer RNAMessenger RNA, Transfer RNA PheSaccharomyces cerevisiaeEukaryaRF00005Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinElectron microscopy2.47762023-09-20
261I9V|1|ATransfer RNAPHENYLALANINE TRANSFER RNASaccharomyces cerevisiaeEukaryaRF00005CRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEXX-ray diffraction2.6762001-06-04
271TN1|1|ATransfer RNATRNAPHESaccharomyces cerevisiaeEukaryaRF00005CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNAX-ray diffraction3761987-01-15
281TN2|1|ATransfer RNATRNAPHESaccharomyces cerevisiaeEukaryaRF00005CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE T-RNAX-ray diffraction3761986-10-24
294TRA|1|ATransfer RNATRNAPHESaccharomyces cerevisiaeEukaryaRF00005RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALSX-ray diffraction3761987-11-06
306TNA|1|ATransfer RNATRNAPHESaccharomyces cerevisiaeEukaryaRF00005CRYSTAL STRUCTURE OF YEAST PHENYLALANINE T-RNA. I.CRYSTALLOGRAPHIC REFINEMENTX-ray diffraction2.7761979-01-16
311TTT|1|FTransfer RNATRANSFER RIBONUCLEIC ACID (YEAST, PHE)RF00005Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complexX-ray diffraction2.7761996-12-23
321TTT|1|DTransfer RNATRANSFER RIBONUCLEIC ACID (YEAST, PHE)RF00005Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complexX-ray diffraction2.7761996-12-23
331TTT|1|ETransfer RNATRANSFER RIBONUCLEIC ACID (YEAST, PHE)RF00005Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complexX-ray diffraction2.7761996-12-23
346XZ7|1|gTransfer RNAfMet-Phe-tRNA(Phe)Saccharomyces cerevisiaeEukaryaRF00005E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet).Electron microscopy2.1762020-07-22
358CDL|1|BbTransfer RNAMessenger RNA, Transfer RNA PheSaccharomyces cerevisiaeEukaryaRF0000580S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complexElectron microscopy2.72762023-09-20
361TRA|1|ATransfer RNATRNAPHESaccharomyces cerevisiaeEukaryaRF00005RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLESX-ray diffraction3761986-07-14
378CKU|1|BbTransfer RNAMessenger RNA, Transfer RNA PheSaccharomyces cerevisiaeEukaryaRF00005Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarinElectron microscopy3.11762023-09-20

Release history

Release4.18
Date2025-12-17

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

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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
19YPV|1|12GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIdELECTRON MICROSCOPY375
29YPS|1|12GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIbELECTRON MICROSCOPY375
39YPO|1|12GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIaELECTRON MICROSCOPY375
49YPT|1|12GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIcELECTRON MICROSCOPY3.175
51TTT|1|FPhe-tRNA, elongation factoR EF-TU:GDPNP ternary complexX-RAY DIFFRACTION2.776
61TTT|1|EPhe-tRNA, elongation factoR EF-TU:GDPNP ternary complexX-RAY DIFFRACTION2.776
71OB2|1|BE. coli elongation factor EF-Tu complexed with the antibiotic kirromycin, a GTP analog, and Phe-tRNAX-RAY DIFFRACTION3.3576
81TTT|1|DPhe-tRNA, elongation factoR EF-TU:GDPNP ternary complexX-RAY DIFFRACTION2.776
95AXN|1|PCrystal structure of Thg1 like protein (TLP) with tRNA(Phe) and GDPNPX-RAY DIFFRACTION2.766
105AXM|1|PCrystal structure of Thg1 like protein (TLP) with tRNA(Phe)X-RAY DIFFRACTION2.2173
111EVV|1|ACRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTIONX-RAY DIFFRACTION276
121I9V|1|ACRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEXX-RAY DIFFRACTION2.676
134TRA|1|ARESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALSX-RAY DIFFRACTION376
146TNA|1|ACRYSTAL STRUCTURE OF YEAST PHENYLALANINE T-RNA. I.CRYSTALLOGRAPHIC REFINEMENTX-RAY DIFFRACTION2.776
151TN1|1|ACRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNAX-RAY DIFFRACTION376
161TN2|1|ACRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE T-RNAX-RAY DIFFRACTION376
174TNA|1|AFURTHER REFINEMENT OF THE STRUCTURE OF YEAST T-RNA-PHEX-RAY DIFFRACTION2.576
181TRA|1|ARESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLESX-RAY DIFFRACTION376
191EHZ|1|AThe crystal structure of yeast phenylalanine tRNA at 1.93 A resolutionX-RAY DIFFRACTION1.9376
208CTH|1|CCryo-EM structure of human METTL1-WDR4-tRNA(Phe) complexELECTRON MICROSCOPY3.374
218CKU|1|BbTranslocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarinELECTRON MICROSCOPY3.1176
228CF5|1|BbTranslocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinELECTRON MICROSCOPY2.7176
239F9S|1|DPYeast SDD1 Disome with Mbf1ELECTRON MICROSCOPY2.976
248CDL|1|Bb80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complexELECTRON MICROSCOPY2.7276
258CCS|1|Bb80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complexELECTRON MICROSCOPY1.9776
268CIV|1|BbTranslocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinELECTRON MICROSCOPY2.4776
278CG8|1|BbTranslocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinELECTRON MICROSCOPY2.5776
288CEH|1|BbTranslocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinELECTRON MICROSCOPY2.0576
298CDR|1|BbTranslocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinELECTRON MICROSCOPY2.0476
306XZ7|1|gE. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet).ELECTRON MICROSCOPY2.176
316XZB|1|g2E. coli 70S ribosome in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet) (focused classification).ELECTRON MICROSCOPY2.5476
325M1J|1|A3Nonstop ribosomal complex bound with Dom34 and Hbs1ELECTRON MICROSCOPY3.376
336LVR|1|DCrystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNAX-RAY DIFFRACTION2.8572
346LVR|1|BCrystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNAX-RAY DIFFRACTION2.8572
356GZ5|1|BwtRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)ELECTRON MICROSCOPY3.576
366XIR|1|AZCryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative StressELECTRON MICROSCOPY3.273
376XIR|1|AXCryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative StressELECTRON MICROSCOPY3.273

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.


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