RNA 3D Hub //

Equivalence class NR_4.0_83593.6 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
31OB2|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
45AXN|1|PTransfer RNARNA (75-MER)Saccharomyces cerevisiaeEukaryaRF00005Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) and GDPNPX-ray diffraction2.7662016-08-03
56LVR|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
63WC2|1|P76mer-tRNACrystal structure of C. albicans tRNA(His) guanylyltransferase (Thg1) with a tRNA(Phe)(GUG)X-ray diffraction3.64742013-12-18
76LVR|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
83WC2|1|Q76mer-tRNACrystal structure of C. albicans tRNA(His) guanylyltransferase (Thg1) with a tRNA(Phe)(GUG)X-ray diffraction3.64732013-12-18
94TNA|1|ATransfer RNATRNAPHESaccharomyces cerevisiaeEukaryaRF00005FURTHER REFINEMENT OF THE STRUCTURE OF YEAST T-RNA-PHEX-ray diffraction2.5761978-04-12
101EHZ|1|ATransfer RNATRANSFER RNA (PHE)Saccharomyces cerevisiaeEukaryaRF00005The crystal structure of yeast phenylalanine tRNA at 1.93 A resolutionX-ray diffraction1.93762000-10-02
118CCS|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
128CDR|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
138CEH|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
146XZ7|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
158CIV|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
166XZB|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
178CG8|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
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
198CDL|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
201I9V|1|ATransfer RNAPHENYLALANINE TRANSFER RNASaccharomyces cerevisiaeEukaryaRF00005CRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEXX-ray diffraction2.6762001-06-04
219F9S|1|DPTransfer RNAtRNASaccharomyces cerevisiaeEukaryaRF00005Yeast SDD1 Disome with Mbf1Electron microscopy2.9762024-12-04
221TN1|1|ATransfer RNATRNAPHESaccharomyces cerevisiaeEukaryaRF00005CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNAX-ray diffraction3761987-01-15
231TN2|1|ATransfer RNATRNAPHESaccharomyces cerevisiaeEukaryaRF00005CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE T-RNAX-ray diffraction3761986-10-24
248CKU|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
256XIR|1|AZTransfer RNATransfer RNASaccharomyces cerevisiaeEukaryaRF00005Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative StressElectron microscopy3.2732020-08-26
266XIR|1|AXTransfer RNATransfer RNASaccharomyces cerevisiaeEukaryaRF00005Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative StressElectron microscopy3.2732020-08-26
275M1J|1|A3Transfer RNAnonstop mRNA, yeast Phe-tRNA-PheSaccharomyces cerevisiaeEukaryaRF00005Nonstop ribosomal complex bound with Dom34 and Hbs1Electron microscopy3.3762017-01-18
284TRA|1|ATransfer RNATRNAPHESaccharomyces cerevisiaeEukaryaRF00005RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALSX-ray diffraction3761987-11-06
296GZ5|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
308CTH|1|CTransfer RNAPhe-tRNASaccharomyces cerevisiaeEukaryaRF00005Cryo-EM structure of human METTL1-WDR4-tRNA(Phe) complexElectron microscopy3.3742022-12-07
316GZ3|1|BwTransfer RNAmRNA, pe/E-site-tRNASaccharomyces cerevisiaeEukaryaRF00005tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1)Electron microscopy3.6762018-12-05
326TNA|1|ATransfer RNATRNAPHESaccharomyces cerevisiaeEukaryaRF00005CRYSTAL STRUCTURE OF YEAST PHENYLALANINE T-RNA. I.CRYSTALLOGRAPHIC REFINEMENTX-ray diffraction2.7761979-01-16
331TTT|1|FTRANSFER RIBONUCLEIC ACID (YEAST, PHE)Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complexX-ray diffraction2.7761996-12-23
341TTT|1|DTRANSFER RIBONUCLEIC ACID (YEAST, PHE)Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complexX-ray diffraction2.7761996-12-23
351TTT|1|ETRANSFER RIBONUCLEIC ACID (YEAST, PHE)Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complexX-ray diffraction2.7761996-12-23
366GQV|1|AYTransfer RNAMessenger RNA, Transfer RNA - PheSaccharomyces cerevisiaeEukaryaRF00005Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP)Electron microscopy4762018-07-11
376GQB|1|AXTransfer RNAMessenger RNA, Transfer RNA - PheSaccharomyces cerevisiaeEukaryaRF00005Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin)Electron microscopy3.9762018-07-11
381TRA|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

Release history

Release3.3783.3793.3803.381
Date2025-03-132025-03-192025-03-262025-04-02

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

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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
36GQV|1|AYCryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP)ELECTRON MICROSCOPY476
46GQB|1|AXCryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin)ELECTRON MICROSCOPY3.976
56GZ3|1|BwtRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1)ELECTRON MICROSCOPY3.676
66GZ5|1|BwtRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)ELECTRON MICROSCOPY3.576
78CTH|1|CCryo-EM structure of human METTL1-WDR4-tRNA(Phe) complexELECTRON MICROSCOPY3.374
81EHZ|1|AThe crystal structure of yeast phenylalanine tRNA at 1.93 A resolutionX-RAY DIFFRACTION1.9376
91TRA|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
104TNA|1|AFURTHER REFINEMENT OF THE STRUCTURE OF YEAST T-RNA-PHEX-RAY DIFFRACTION2.576
111TN1|1|ACRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNAX-RAY DIFFRACTION376
121TN2|1|ACRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE T-RNAX-RAY DIFFRACTION376
136TNA|1|ACRYSTAL STRUCTURE OF YEAST PHENYLALANINE T-RNA. I.CRYSTALLOGRAPHIC REFINEMENTX-RAY DIFFRACTION2.776
144TRA|1|ARESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALSX-RAY DIFFRACTION376
151I9V|1|ACRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEXX-RAY DIFFRACTION2.676
161EVV|1|ACRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTIONX-RAY DIFFRACTION276
175AXM|1|PCrystal structure of Thg1 like protein (TLP) with tRNA(Phe)X-RAY DIFFRACTION2.2173
185AXN|1|PCrystal structure of Thg1 like protein (TLP) with tRNA(Phe) and GDPNPX-RAY DIFFRACTION2.766
198CKU|1|BbTranslocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarinELECTRON MICROSCOPY3.1176
208CF5|1|BbTranslocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinELECTRON MICROSCOPY2.7176
218CDL|1|Bb80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complexELECTRON MICROSCOPY2.7276
229F9S|1|DPYeast SDD1 Disome with Mbf1ELECTRON MICROSCOPY2.976
238CCS|1|Bb80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complexELECTRON MICROSCOPY1.9776
248CIV|1|BbTranslocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinELECTRON MICROSCOPY2.4776
258CG8|1|BbTranslocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinELECTRON MICROSCOPY2.5776
268CEH|1|BbTranslocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinELECTRON MICROSCOPY2.0576
278CDR|1|BbTranslocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarinELECTRON MICROSCOPY2.0476
286XZ7|1|gE. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet).ELECTRON MICROSCOPY2.176
296XZB|1|g2E. coli 70S ribosome in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet) (focused classification).ELECTRON MICROSCOPY2.5476
305M1J|1|A3Nonstop ribosomal complex bound with Dom34 and Hbs1ELECTRON MICROSCOPY3.376
316LVR|1|DCrystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNAX-RAY DIFFRACTION2.8572
326LVR|1|BCrystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNAX-RAY DIFFRACTION2.8572
331TTT|1|DPhe-tRNA, elongation factoR EF-TU:GDPNP ternary complexX-RAY DIFFRACTION2.776
341TTT|1|FPhe-tRNA, elongation factoR EF-TU:GDPNP ternary complexX-RAY DIFFRACTION2.776
351TTT|1|EPhe-tRNA, elongation factoR EF-TU:GDPNP ternary complexX-RAY DIFFRACTION2.776
361OB2|1|BE. coli elongation factor EF-Tu complexed with the antibiotic kirromycin, a GTP analog, and Phe-tRNAX-RAY DIFFRACTION3.3576
373WC2|1|QCrystal structure of C. albicans tRNA(His) guanylyltransferase (Thg1) with a tRNA(Phe)(GUG)X-RAY DIFFRACTION3.6473
383WC2|1|PCrystal structure of C. albicans tRNA(His) guanylyltransferase (Thg1) with a tRNA(Phe)(GUG)X-RAY DIFFRACTION3.6474

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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