RNA 3D Hub //

Equivalence class NR_20.0_81815.3 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
18T2X|1|tP (rep)Transfer RNAP site tRNASaccharomyces cerevisiaeEukaryaRF00005Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger RNA and eIF5A, PREElectron microscopy2.46752024-12-11
28T2Y|1|tPTransfer RNAP site tRNASaccharomyces cerevisiaeEukaryaRF00005Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, PREElectron microscopy2.2752024-12-11
38T2X|1|tATransfer RNAA site tRNASaccharomyces cerevisiaeEukaryaRF00005Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger RNA and eIF5A, PREElectron microscopy2.46762024-12-11
48T2Y|1|tATransfer RNAA site tRNASaccharomyces cerevisiaeEukaryaRF00005Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, PREElectron microscopy2.2762024-12-11
56TB3|1|nTransfer RNAmRNA, tRNASaccharomyces cerevisiaeEukaryaRF00005yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complexElectron microscopy2.8752020-04-22
68T2Z|1|tPTransfer RNAP site tRNASaccharomyces cerevisiaeEukaryaRF00005Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, POSTElectron microscopy2.4752024-12-11
78K82|1|C5Transfer RNAtRNASaccharomyces cerevisiaeEukaryaRF00005Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNAElectron microscopy3752024-07-10
88T2Z|1|tATransfer RNAA site tRNASaccharomyces cerevisiaeEukaryaRF00005Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, POSTElectron microscopy2.4762024-12-11
96TNU|1|nTransfer RNAmRNA, P-site tRNASaccharomyces cerevisiaeEukaryaRF00005Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs.Electron microscopy3.1752020-04-22
108UT0|1|nTransfer RNAP site initiator tRNASaccharomyces cerevisiaeEukaryaRF00005Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNAElectron microscopy3.22752024-11-06
118UTI|1|nTransfer RNAP site initiator tRNASaccharomyces cerevisiaeEukaryaRF00005Eukaryotic 80S ribosome with Reh1 and A/P site tRNAElectron microscopy3.13752024-11-06
128Z70|1|tTransfer RNAtRNASaccharomyces cerevisiae S288CEukaryaRF00005State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decodingElectron microscopy3.2752024-12-11
137NRC|1|SnTransfer RNARNA (5'-R(P*AP*UP*GP*AP*AP*A)-3'), tRNA (75-MER)Saccharomyces cerevisiae S288CEukaryaRF00005Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5AElectron microscopy3.9752021-05-05
148XU8|1|sTransfer RNAtRNASaccharomyces cerevisiae S288CEukaryaRF00005State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferationElectron microscopy3.4752024-12-11
158CAS|1|1Transfer RNAmRNA, tRNASaccharomyces cerevisiae W303EukaryaRF00005Cryo-EM structure of native Otu2-bound ubiquitinated 48S initiation complex (partial)Electron microscopy3.3752023-05-24
168S8H|1|1Transfer RNAMet-tRNAiSaccharomyces cerevisiae S288CEukaryaRF00005Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-2.2)Electron microscopy4752024-09-11
177B7D|1|SnTransfer RNAmRNA, tRNASaccharomyces cerevisiae S288CEukaryaRF00005Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAsElectron microscopy3.3752021-03-10
188S8G|1|1Transfer RNAMet-tRNAiSaccharomyces cerevisiae S288CEukaryaRF00005Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-2.1)Electron microscopy4752024-09-11
198XU8|1|tTransfer RNAtRNASaccharomyces cerevisiae S288CEukaryaRF00005State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferationElectron microscopy3.4752024-12-11
208YLD|1|tTransfer RNAtRNASaccharomyces cerevisiae S288CEukaryaRF00005State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocationElectron microscopy3.9752024-12-11
218RW1|1|1Transfer RNAMet-tRNAiSaccharomyces cerevisiae S288CEukaryaRF00005Structure of a yeast 48S-AUC preinitiation complex in closed conformationElectron microscopy3.35752024-09-11
226FYX|1|1Transfer RNAmRNA (31-MER), tRNAiSaccharomyces cerevisiaeEukaryaRF00005Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C1)Electron microscopy3.5752018-12-05
238S8D|1|1Transfer RNAMet-tRNAiSaccharomyces cerevisiae S288CEukaryaRF00005Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-2)Electron microscopy3.45752024-09-11
247B7D|1|SmTransfer RNAmRNA, tRNASaccharomyces cerevisiae S288CEukaryaRF00005Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAsElectron microscopy3.3752021-03-10
258S8E|1|1Transfer RNAMet-tRNAiSaccharomyces cerevisiae S288CEukaryaRF00005Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-3.1)Electron microscopy3.85752024-09-11
268S8F|1|1Transfer RNAMet-tRNAiSaccharomyces cerevisiae S288CEukaryaRF00005Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-3.2)Electron microscopy3.95752024-09-11
276FYY|1|1Transfer RNAmRNA (31-MER), tRNAiSaccharomyces cerevisiaeEukaryaRF00005Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C2)Electron microscopy3.02752018-12-05
288YLR|1|uTransfer RNAtRNASaccharomyces cerevisiae S288CEukaryaRF00005State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocationElectron microscopy3.9742024-12-11
298S8I|1|1Transfer RNAMet-tRNAiSaccharomyces cerevisiae S288CEukaryaRF00005Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-eIF1)Electron microscopy4.3752024-09-11
308Z71|1|tTransfer RNAtRNASaccharomyces cerevisiae S288CEukaryaRF00005State 1a (S1a) of yeast 80S ribosome bound to open eEF3 and 2 tRNAs and eEF1A during mRNA decodingElectron microscopy3.6752024-12-11
316GSN|1|1Transfer RNAmRNA, tRNAi (75-MER)Saccharomyces cerevisiaeEukaryaRF00005Structure of a partial yeast 48S preinitiation complex in closed conformationElectron microscopy5.75752019-06-26
326GSM|1|1Transfer RNAMet-tRNAi, mRNA (5'-R(P*AP*AP*U)-3')Saccharomyces cerevisiaeEukaryaRF00005Structure of a partial yeast 48S preinitiation complex in open conformationElectron microscopy5.15752019-07-31
337NRD|1|SnTransfer RNAtRNA (75-MER)Saccharomyces cerevisiae S288CEukaryaRF00005Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNAElectron microscopy4.36752021-04-14
348S8K|1|1Transfer RNAMet-tRNAiSaccharomyces cerevisiae S288CEukaryaRF00005Structure of a yeast 48S-AUC preinitiation complex in swivelled conformation (model py48S-AUC-swiv-eIF1)Electron microscopy4752024-11-06
358YLD|1|sTransfer RNAtRNASaccharomyces cerevisiae S288CEukaryaRF00005State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocationElectron microscopy3.9752024-12-11
366ZU9|1|1Transfer RNAmRNA, tRNASaccharomyces cerevisiaeEukaryaRF00005Structure of a yeast ABCE1-bound 48S initiation complexElectron microscopy6.2752020-10-28
378S8J|1|1Transfer RNAMet-tRNAiSaccharomyces cerevisiae S288CEukaryaRF00005Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-eIF5)Electron microscopy4.7752024-09-11
385OA3|1|1Transfer RNAinitiator Met-tRNA-iSaccharomyces cerevisiaeEukaryaRF00005Human 40S-eIF2D-re-initiation complexElectron microscopy4.2752017-08-09
398YLR|1|tTransfer RNAtRNASaccharomyces cerevisiae S288CEukaryaRF00005State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocationElectron microscopy3.9752024-12-11
403J81|1|1Met-tRNAi, mRNARF00005CryoEM structure of a partial yeast 48S preinitiation complexElectron microscopy4742014-11-05
411YFG|1|ATransfer RNAYEAST INITIATOR TRNASaccharomyces cerevisiaeEukaryaRF00005YEAST INITIATOR TRNAX-ray diffraction3751997-09-03

Release history

Release4.0
Date2025-08-13

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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
13J81|1|1CryoEM structure of a partial yeast 48S preinitiation complexELECTRON MICROSCOPY474
26GSN|1|1Structure of a partial yeast 48S preinitiation complex in closed conformationELECTRON MICROSCOPY5.7575
38S8J|1|1Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-eIF5)ELECTRON MICROSCOPY4.775
48S8F|1|1Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-3.2)ELECTRON MICROSCOPY3.9575
58CAS|1|1Cryo-EM structure of native Otu2-bound ubiquitinated 48S initiation complex (partial)ELECTRON MICROSCOPY3.375
66FYX|1|1Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C1)ELECTRON MICROSCOPY3.575
76ZU9|1|1Structure of a yeast ABCE1-bound 48S initiation complexELECTRON MICROSCOPY6.275
86FYY|1|1Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C2)ELECTRON MICROSCOPY3.0275
98S8G|1|1Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-2.1)ELECTRON MICROSCOPY475
108S8I|1|1Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-eIF1)ELECTRON MICROSCOPY4.375
118S8E|1|1Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-3.1)ELECTRON MICROSCOPY3.8575
128S8D|1|1Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-2)ELECTRON MICROSCOPY3.4575
138RW1|1|1Structure of a yeast 48S-AUC preinitiation complex in closed conformationELECTRON MICROSCOPY3.3575
148S8H|1|1Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-2.2)ELECTRON MICROSCOPY475
158S8K|1|1Structure of a yeast 48S-AUC preinitiation complex in swivelled conformation (model py48S-AUC-swiv-eIF1)ELECTRON MICROSCOPY475
166GSM|1|1Structure of a partial yeast 48S preinitiation complex in open conformationELECTRON MICROSCOPY5.1575
171YFG|1|AYEAST INITIATOR TRNAX-RAY DIFFRACTION375
185OA3|1|1Human 40S-eIF2D-re-initiation complexELECTRON MICROSCOPY4.275
198YLD|1|tState 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocationELECTRON MICROSCOPY3.975
208YLR|1|uState 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocationELECTRON MICROSCOPY3.974
218YLR|1|tState 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocationELECTRON MICROSCOPY3.975
228YLD|1|sState 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocationELECTRON MICROSCOPY3.975
237B7D|1|SmYeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAsELECTRON MICROSCOPY3.375
248XU8|1|sState 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferationELECTRON MICROSCOPY3.475
258XU8|1|tState 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferationELECTRON MICROSCOPY3.475
267B7D|1|SnYeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAsELECTRON MICROSCOPY3.375
278Z70|1|tState 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decodingELECTRON MICROSCOPY3.275
288Z71|1|tState 1a (S1a) of yeast 80S ribosome bound to open eEF3 and 2 tRNAs and eEF1A during mRNA decodingELECTRON MICROSCOPY3.675
298K82|1|C5Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNAELECTRON MICROSCOPY375
306TB3|1|nyeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complexELECTRON MICROSCOPY2.875
317NRD|1|SnStructure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNAELECTRON MICROSCOPY4.3675
328T2Z|1|tPHypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, POSTELECTRON MICROSCOPY2.475
338T2Y|1|tPHypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, PREELECTRON MICROSCOPY2.275
348T2X|1|tPHypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger RNA and eIF5A, PREELECTRON MICROSCOPY2.4675
358UT0|1|nEukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNAELECTRON MICROSCOPY3.2275
367NRC|1|SnStructure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5AELECTRON MICROSCOPY3.975
376TNU|1|nYeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs.ELECTRON MICROSCOPY3.175
388UTI|1|nEukaryotic 80S ribosome with Reh1 and A/P site tRNAELECTRON MICROSCOPY3.1375
398T2X|1|tAHypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger RNA and eIF5A, PREELECTRON MICROSCOPY2.4676
408T2Y|1|tAHypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, PREELECTRON MICROSCOPY2.276
418T2Z|1|tAHypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, POSTELECTRON MICROSCOPY2.476

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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