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Equivalence class NR_3.5_83593.11 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
49YPG|1|12Transfer RNAMF mRNA, Phe-tRNASaccharomyces cerevisiaeEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the GTPase activation-like state, Structure IIIElectron microscopy3752025-12-31
59YPO|1|12Transfer RNAMF mRNA, Phe-tRNASaccharomyces cerevisiaeEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIaElectron microscopy3752025-12-17
68CDR|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
78CEH|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
86LVR|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
95AXN|1|PTransfer RNARNA (75-MER)Saccharomyces cerevisiaeEukaryaRF00005Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) and GDPNPX-ray diffraction2.7662016-08-03
109YPS|1|12Transfer RNAMF mRNA, Phe-tRNASaccharomyces cerevisiaeEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIbElectron microscopy3752025-12-17
115M1J|1|A3Transfer RNAnonstop mRNA, yeast Phe-tRNA-PheSaccharomyces cerevisiaeEukaryaRF00005Nonstop ribosomal complex bound with Dom34 and Hbs1Electron microscopy3.3762017-01-18
121OB2|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
139YPW|1|12Transfer RNAMF mRNA, Phe-tRNASaccharomyces cerevisiaeEukaryaRF00005GTPBP1*GDP*Phe-tRNA*ribosome in the post-GTP hydrolysis state, Structure IVElectron microscopy2.9752025-12-31
149YPY|1|12Transfer RNAMF mRNA, Phe-tRNASaccharomyces cerevisiaeEukaryaRF00005Ribosome with accommodated A-site tRNA, Structure VElectron microscopy3752025-12-24
159YPV|1|12Transfer RNAMF mRNA, Phe-tRNASaccharomyces cerevisiaeEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIdElectron microscopy3752025-12-17
166LVR|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
179YPT|1|12Transfer RNAMF mRNA, Phe-tRNASaccharomyces cerevisiaeEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIcElectron microscopy3.1752025-12-17
188CF5|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
199Y4G|1|BbTransfer RNAtRNA (77-MER)CtenomyidaeEukaryotaRF00005Structure of tuco-tuco ribosome (rotated, tRNAs, and mRNA)Electron microscopy3.3652026-02-18
209F9S|1|DPTransfer RNAtRNASaccharomyces cerevisiaeEukaryaRF00005Yeast SDD1 Disome with Mbf1Electron microscopy2.9762024-12-04
218CTH|1|CTransfer RNAPhe-tRNASaccharomyces cerevisiaeEukaryaRF00005Cryo-EM structure of human METTL1-WDR4-tRNA(Phe) complexElectron microscopy3.3742022-12-07
226XIR|1|AXTransfer RNATransfer RNASaccharomyces cerevisiaeEukaryaRF00005Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative StressElectron microscopy3.2732020-08-26
236GZ5|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
248CG8|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
256XIR|1|AZTransfer RNATransfer RNASaccharomyces cerevisiaeEukaryaRF00005Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative StressElectron microscopy3.2732020-08-26
264TNA|1|ATransfer RNATRNAPHESaccharomyces cerevisiaeEukaryaRF00005FURTHER REFINEMENT OF THE STRUCTURE OF YEAST T-RNA-PHEX-ray diffraction2.5761978-04-12
271EHZ|1|ATransfer RNATRANSFER RNA (PHE)Saccharomyces cerevisiaeEukaryaRF00005The crystal structure of yeast phenylalanine tRNA at 1.93 A resolutionX-ray diffraction1.93762000-10-02
288CCS|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
298CIV|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
301I9V|1|ATransfer RNAPHENYLALANINE TRANSFER RNASaccharomyces cerevisiaeEukaryaRF00005CRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEXX-ray diffraction2.6762001-06-04
311TN1|1|ATransfer RNATRNAPHESaccharomyces cerevisiaeEukaryaRF00005CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNAX-ray diffraction3761987-01-15
321TN2|1|ATransfer RNATRNAPHESaccharomyces cerevisiaeEukaryaRF00005CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE T-RNAX-ray diffraction3761986-10-24
334TRA|1|ATransfer RNATRNAPHESaccharomyces cerevisiaeEukaryaRF00005RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALSX-ray diffraction3761987-11-06
346TNA|1|ATransfer RNATRNAPHESaccharomyces cerevisiaeEukaryaRF00005CRYSTAL STRUCTURE OF YEAST PHENYLALANINE T-RNA. I.CRYSTALLOGRAPHIC REFINEMENTX-ray diffraction2.7761979-01-16
351TTT|1|FTransfer RNATRANSFER RIBONUCLEIC ACID (YEAST, PHE)RF00005Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complexX-ray diffraction2.7761996-12-23
361TTT|1|DTransfer RNATRANSFER RIBONUCLEIC ACID (YEAST, PHE)RF00005Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complexX-ray diffraction2.7761996-12-23
371TTT|1|ETransfer RNATRANSFER RIBONUCLEIC ACID (YEAST, PHE)RF00005Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complexX-ray diffraction2.7761996-12-23
386XZ7|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
398CDL|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
401TRA|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
418CKU|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

Release4.27
Date2026-02-18

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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
16XIR|1|AXCryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative StressELECTRON MICROSCOPY3.273
26XIR|1|AZCryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative StressELECTRON MICROSCOPY3.273
36GZ5|1|BwtRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)ELECTRON MICROSCOPY3.576
46LVR|1|BCrystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNAX-RAY DIFFRACTION2.8572
56LVR|1|DCrystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNAX-RAY DIFFRACTION2.8572
65M1J|1|A3Nonstop ribosomal complex bound with Dom34 and Hbs1ELECTRON MICROSCOPY3.376
76XZ7|1|gE. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet).ELECTRON MICROSCOPY2.176
86XZB|1|g2E. coli 70S ribosome in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet) (focused classification).ELECTRON MICROSCOPY2.5476
99YPY|1|12Ribosome with accommodated A-site tRNA, Structure VELECTRON MICROSCOPY375
108CG8|1|BbTranslocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinELECTRON MICROSCOPY2.5776
118CEH|1|BbTranslocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinELECTRON MICROSCOPY2.0576
128CDR|1|BbTranslocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinELECTRON MICROSCOPY2.0476
138CIV|1|BbTranslocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinELECTRON MICROSCOPY2.4776
148CCS|1|Bb80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complexELECTRON MICROSCOPY1.9776
159Y4G|1|BbStructure of tuco-tuco ribosome (rotated, tRNAs, and mRNA)ELECTRON MICROSCOPY3.365
168CKU|1|BbTranslocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarinELECTRON MICROSCOPY3.1176
178CF5|1|BbTranslocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinELECTRON MICROSCOPY2.7176
188CDL|1|Bb80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complexELECTRON MICROSCOPY2.7276
199F9S|1|DPYeast SDD1 Disome with Mbf1ELECTRON MICROSCOPY2.976
208CTH|1|CCryo-EM structure of human METTL1-WDR4-tRNA(Phe) complexELECTRON MICROSCOPY3.374
211EHZ|1|AThe crystal structure of yeast phenylalanine tRNA at 1.93 A resolutionX-RAY DIFFRACTION1.9376
221TRA|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
234TNA|1|AFURTHER REFINEMENT OF THE STRUCTURE OF YEAST T-RNA-PHEX-RAY DIFFRACTION2.576
241TN2|1|ACRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE T-RNAX-RAY DIFFRACTION376
251TN1|1|ACRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNAX-RAY DIFFRACTION376
266TNA|1|ACRYSTAL STRUCTURE OF YEAST PHENYLALANINE T-RNA. I.CRYSTALLOGRAPHIC REFINEMENTX-RAY DIFFRACTION2.776
274TRA|1|ARESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALSX-RAY DIFFRACTION376
281I9V|1|ACRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEXX-RAY DIFFRACTION2.676
291EVV|1|ACRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTIONX-RAY DIFFRACTION276
305AXM|1|PCrystal structure of Thg1 like protein (TLP) with tRNA(Phe)X-RAY DIFFRACTION2.2173
315AXN|1|PCrystal structure of Thg1 like protein (TLP) with tRNA(Phe) and GDPNPX-RAY DIFFRACTION2.766
321TTT|1|DPhe-tRNA, elongation factoR EF-TU:GDPNP ternary complexX-RAY DIFFRACTION2.776
331TTT|1|FPhe-tRNA, elongation factoR EF-TU:GDPNP ternary complexX-RAY DIFFRACTION2.776
341TTT|1|EPhe-tRNA, elongation factoR EF-TU:GDPNP ternary complexX-RAY DIFFRACTION2.776
351OB2|1|BE. coli elongation factor EF-Tu complexed with the antibiotic kirromycin, a GTP analog, and Phe-tRNAX-RAY DIFFRACTION3.3576
369YPG|1|12GTPBP1*GCP*Phe-tRNA*ribosome in the GTPase activation-like state, Structure IIIELECTRON MICROSCOPY375
379YPT|1|12GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIcELECTRON MICROSCOPY3.175
389YPV|1|12GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIdELECTRON MICROSCOPY375
399YPS|1|12GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIbELECTRON MICROSCOPY375
409YPO|1|12GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIaELECTRON MICROSCOPY375
419YPW|1|12GTPBP1*GDP*Phe-tRNA*ribosome in the post-GTP hydrolysis state, Structure IVELECTRON MICROSCOPY2.975

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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