RNA 3D Hub //

Equivalence class NR_20.0_83098.13 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
18XSX|1|CC (rep)Transfer RNAE-tRNAHomo sapiensEukaryaRF00005Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA, SERBP1 and eEF2Electron microscopy2.4752024-07-10
26ZP4|1|1Transfer RNAtRNAHomo sapiensEukaryaRF00005SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2Electron microscopy2.9752020-07-29
38PPL|1|IwTransfer RNAMet-tRNAi(Met)Homo sapiensEukaryaRF00005MERS-CoV Nsp1 bound to the human 43S pre-initiation complexElectron microscopy2.65752023-10-18
49YPZ|1|13Transfer RNAMet-tRNA, MF mRNAHomo sapiensEukaryaRF00005Vacant ribosome with P-site tRNA, substate 1, Structure IaElectron microscopy2.9742025-12-24
59YQ1|1|13Transfer RNAMet-tRNA, MF mRNAHomo sapiensEukaryaRF00005Vacant ribosome with P-site tRNA, substate 3, Structure IcElectron microscopy2.9742025-12-17
69YQ0|1|13Transfer RNAMet-tRNA, MF mRNAHomo sapiensEukaryaRF00005Vacant ribosome with P-site tRNA, substate 2, Structure IbElectron microscopy2.9742025-12-17
79YPY|1|13Transfer RNAMet-tRNA, MF mRNAHomo sapiensEukaryaRF00005Ribosome with accommodated A-site tRNA, Structure VElectron microscopy3742025-12-24
89SPF|1|EtTransfer RNAE site tRNAHomo sapiensEukaryaRF00005CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINEElectron microscopy2.4542026-01-21
98K2C|1|CCTransfer RNAtRNA-MetHomo sapiensEukaryaRF00005Cryo-EM structure of the human 80S ribosome with TigecyclineElectron microscopy2.4752024-07-10
109SPI|1|EtTransfer RNAE site tRNAHomo sapiensEukaryaRF00005CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING URIDINEElectron microscopy2.4542026-01-21
117QVP|1|B5Transfer RNAmRNA, tRNA P/EHomo sapiensEukaryaRF00005Human collided disome (di-ribosome) stalled on XBP1 mRNAElectron microscopy3752022-10-12
128PJ5|1|wTransfer RNAInitiator Met-tRNA-iHomo sapiensEukaryaRF00005Structure of human 48S translation initiation complex after eIF2 release prior 60S subunit joining (48S-5)Electron microscopy2.9752024-08-14
139YPW|1|13Transfer RNAMet-tRNA, MF mRNAHomo sapiensEukaryaRF00005GTPBP1*GDP*Phe-tRNA*ribosome in the post-GTP hydrolysis state, Structure IVElectron microscopy2.9742025-12-31
149I14|1|B4Transfer RNAP/E tRNAHomo sapiensEukaryaRF00005CRYO-EM STRUCTURE OF HCT15 POLYSOMES IN HYBRID-PRE STATEElectron microscopy3.34752026-01-28
159KRP|1|zyTransfer RNAInitiator Met-tRNA-iHomo sapiensEukaryaRF00005Structure of the HCV IRES-dependent 48S translation initiation complex with eIF5B and eIF3Electron microscopy3.2752025-12-03
167A09|1|fTransfer RNAtRNAHomo sapiensEukaryaRF00005Structure of a human ABCE1-bound 43S pre-initiation complex - State IIIElectron microscopy3.5752020-10-14
178PJ6|1|wTransfer RNAInitiator Met-tRNA-iHomo sapiensEukaryaRF00005Structure of human 48S translation initiation complex with initiator tRNA, eIF1A and eIF3 (off-pathway)Electron microscopy2.9732024-08-14
189YPO|1|13Transfer RNAMet-tRNA, MF mRNAHomo sapiensEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIaElectron microscopy3742025-12-17
196Y57|1|B4Transfer RNAmRNA, P/E tRNAHomo sapiensEukaryaRF00005Structure of human ribosome in hybrid-PRE stateElectron microscopy3.5752020-04-15
208XSZ|1|CCTransfer RNAtRNAHomo sapiensEukaryaRF00005Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA and P-tRNAElectron microscopy3.2752024-07-10
219KN6|1|zyTransfer RNAInitiator Met-tRNA-iHomo sapiensEukaryaRF00005Structure of the HCV IRES-dependent pre-48S translation initiation complex with eIF1A, eIF5B, and eIF3Electron microscopy3.3752025-12-03
229YPG|1|13Transfer RNAMet-tRNA, MF mRNAHomo sapiensEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the GTPase activation-like state, Structure IIIElectron microscopy3742025-12-31
239YPS|1|13Transfer RNAMet-tRNA, MF mRNAHomo sapiensEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIbElectron microscopy3742025-12-17
249YPT|1|13Transfer RNAMet-tRNA, MF mRNAHomo sapiensEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIcElectron microscopy3.1742025-12-17
258PJ4|1|wTransfer RNAInitiator Met-tRNA-iHomo sapiensEukaryaRF00005Structure of human 48S translation initiation complex after eIF5 release (48S-4)Electron microscopy3.2752024-08-14
269RU9|1|EtTransfer RNAE site tRNAHomo sapiensEukaryaRF00005RPS26dC HEK mutant 80S ribosome bound to Kozak mRNA (RPS26dC-Kozak)Electron microscopy2.97752026-06-03
279YPV|1|13Transfer RNAMet-tRNA, MF mRNAHomo sapiensEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIdElectron microscopy3742025-12-17
289RUA|1|S6Transfer RNAE site tRNAHomo sapiensEukaryaRF00005RPS26dC HEK mutant 80S ribosome bound to TISU mRNA (RPS26dC-TISU)Electron microscopy2.9592026-06-03
298PJ1|1|wTransfer RNAInitiator Met-tRNA-iHomo sapiensEukaryaRF00005Structure of human 48S translation initiation complex in open codon scanning state (48S-1)Electron microscopy3.4752024-08-14
309M0P|1|S6Transfer RNAHUMAN INITIATOR MET-TRNA-I|HOMO SAPIENSHomo sapiensEukaryaRF00005Cryo-EM structure of human 80S ribosome in complex with montanineElectron microscopy2.78752026-01-14
314UG0|1|S6Transfer RNAHUMAN INITIATOR MET-TRNA-IHomo sapiensEukaryaRF00005STRUCTURE OF THE HUMAN 80S RIBOSOMEElectron microscopy3.6752015-06-10
329YPZ|1|11Transfer RNAMet-tRNAHomo sapiensEukaryaRF00005Vacant ribosome with P-site tRNA, substate 1, Structure IaElectron microscopy2.9742025-12-24
338PJ2|1|wTransfer RNAInitiator Met-tRNA-iHomo sapiensEukaryaRF00005Structure of human 48S translation initiation complex in AUG recognition state after eIF5-induced GTP hydrolysis by eIF2 (48S-2)Electron microscopy3.4752024-08-14
349YQ1|1|11Transfer RNAMet-tRNAHomo sapiensEukaryaRF00005Vacant ribosome with P-site tRNA, substate 3, Structure IcElectron microscopy2.9742025-12-17
359YQ0|1|11Transfer RNAMet-tRNAHomo sapiensEukaryaRF00005Vacant ribosome with P-site tRNA, substate 2, Structure IbElectron microscopy2.9742025-12-17
369RU8|1|S6Transfer RNAE site tRNAHomo sapiensEukaryaRF00005WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU)Electron microscopy3592026-06-03
377TQL|1|3Transfer RNAHuman Met-tRNAiMetHomo sapiensEukaryaRF00005CryoEM structure of the human 40S small ribosomal subunit in complex with translation initiation factors eIF1A and eIF5B.Electron microscopy3.4752022-04-27
389YPY|1|11Transfer RNAMet-tRNAHomo sapiensEukaryaRF00005Ribosome with accommodated A-site tRNA, Structure VElectron microscopy3742025-12-24
398PJ3|1|wTransfer RNAInitiator Met-tRNA-iHomo sapiensEukaryaRF00005Structure of human 48S translation initiation complex upon transfer of initiator tRNA to eIF5B (48S-3)Electron microscopy3.7752024-08-14
409YPV|1|11Transfer RNAMet-tRNAHomo sapiensEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIdElectron microscopy3742025-12-17
415T2C|1|AnTransfer RNAtRNAHomo sapiensEukaryaRF00005CryoEM structure of the human ribosome at 3.6 Angstrom resolutionElectron microscopy3.6752017-01-25
429YPS|1|11Transfer RNAMet-tRNAHomo sapiensEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIbElectron microscopy3742025-12-17
439YPW|1|11Transfer RNAMet-tRNAHomo sapiensEukaryaRF00005GTPBP1*GDP*Phe-tRNA*ribosome in the post-GTP hydrolysis state, Structure IVElectron microscopy2.9742025-12-31
449YPO|1|11Transfer RNAMet-tRNAHomo sapiensEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIaElectron microscopy3742025-12-17
459YPT|1|11Transfer RNAMet-tRNAHomo sapiensEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIcElectron microscopy3.1742025-12-17
468XSZ|1|CDTransfer RNAtRNAHomo sapiensEukaryaRF00005Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA and P-tRNAElectron microscopy3.2752024-07-10
479YPG|1|11Transfer RNAMet-tRNAHomo sapiensEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the GTPase activation-like state, Structure IIIElectron microscopy3742025-12-31
488XSY|1|CCTransfer RNAE-tRNAHomo sapiensEukaryaRF00005Cryo-EM structure of the human 80S ribosome with Tigecycline, e-tRNA and CCDC124 (40S head Swivelled)Electron microscopy3692024-07-10
496FEC|1|NTransfer RNAMessenger RNA (26-MER), Transfer RNA (75-MER)Homo sapiensEukaryaRF00005Human cap-dependent 48S pre-initiation complexElectron microscopy6.3752018-03-14
504V6X|1|BCTransfer RNAE-tRNAHomo sapiensEukaryaRF00005Structure of the human 80S ribosomeElectron microscopy5752014-07-09
514KZZ|1|jTransfer RNAinitiator Met-RNA-i, mRNAHomo sapiensEukaryaRF00005Rabbit 40S ribosomal subunit in complex with mRNA, initiator tRNA and eIF1AX-ray diffraction7.03752013-07-24
526QZP|1|S6Transfer RNAE site tRNA (75-MER)Homo sapiensEukaryaRF00005High-resolution cryo-EM structure of the human 80S ribosomeElectron microscopy2.9752019-04-24

Release history

Release4.42
Date2026-06-03

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
16QZP|1|S6High-resolution cryo-EM structure of the human 80S ribosomeELECTRON MICROSCOPY2.975
25T2C|1|AnCryoEM structure of the human ribosome at 3.6 Angstrom resolutionELECTRON MICROSCOPY3.675
34UG0|1|S6STRUCTURE OF THE HUMAN 80S RIBOSOMEELECTRON MICROSCOPY3.675
49RU9|1|EtRPS26dC HEK mutant 80S ribosome bound to Kozak mRNA (RPS26dC-Kozak)ELECTRON MICROSCOPY2.9775
59RUA|1|S6RPS26dC HEK mutant 80S ribosome bound to TISU mRNA (RPS26dC-TISU)ELECTRON MICROSCOPY2.959
69RU8|1|S6WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU)ELECTRON MICROSCOPY359
79YQ1|1|11Vacant ribosome with P-site tRNA, substate 3, Structure IcELECTRON MICROSCOPY2.974
89YPZ|1|11Vacant ribosome with P-site tRNA, substate 1, Structure IaELECTRON MICROSCOPY2.974
99YPY|1|11Ribosome with accommodated A-site tRNA, Structure VELECTRON MICROSCOPY374
109YPV|1|11GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIdELECTRON MICROSCOPY374
119YPG|1|11GTPBP1*GCP*Phe-tRNA*ribosome in the GTPase activation-like state, Structure IIIELECTRON MICROSCOPY374
129YPT|1|11GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIcELECTRON MICROSCOPY3.174
139YPO|1|11GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIaELECTRON MICROSCOPY374
149YPW|1|11GTPBP1*GDP*Phe-tRNA*ribosome in the post-GTP hydrolysis state, Structure IVELECTRON MICROSCOPY2.974
159YPS|1|11GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIbELECTRON MICROSCOPY374
169YQ0|1|11Vacant ribosome with P-site tRNA, substate 2, Structure IbELECTRON MICROSCOPY2.974
179SPI|1|EtCRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING URIDINEELECTRON MICROSCOPY2.454
189SPF|1|EtCRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINEELECTRON MICROSCOPY2.454
198XSY|1|CCCryo-EM structure of the human 80S ribosome with Tigecycline, e-tRNA and CCDC124 (40S head Swivelled)ELECTRON MICROSCOPY369
208K2C|1|CCCryo-EM structure of the human 80S ribosome with TigecyclineELECTRON MICROSCOPY2.475
218XSX|1|CCCryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA, SERBP1 and eEF2ELECTRON MICROSCOPY2.475
228XSZ|1|CCCryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA and P-tRNAELECTRON MICROSCOPY3.275
239I14|1|B4CRYO-EM STRUCTURE OF HCT15 POLYSOMES IN HYBRID-PRE STATEELECTRON MICROSCOPY3.3475
246Y57|1|B4Structure of human ribosome in hybrid-PRE stateELECTRON MICROSCOPY3.575
257QVP|1|B5Human collided disome (di-ribosome) stalled on XBP1 mRNAELECTRON MICROSCOPY375
269M0P|1|S6Cryo-EM structure of human 80S ribosome in complex with montanineELECTRON MICROSCOPY2.7875
274V6X|1|BCStructure of the human 80S ribosomeELECTRON MICROSCOPY575
284KZZ|1|jRabbit 40S ribosomal subunit in complex with mRNA, initiator tRNA and eIF1AX-RAY DIFFRACTION7.0375
299YPY|1|13Ribosome with accommodated A-site tRNA, Structure VELECTRON MICROSCOPY374
309YPW|1|13GTPBP1*GDP*Phe-tRNA*ribosome in the post-GTP hydrolysis state, Structure IVELECTRON MICROSCOPY2.974
319YPT|1|13GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIcELECTRON MICROSCOPY3.174
329YPS|1|13GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIbELECTRON MICROSCOPY374
339YPV|1|13GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIdELECTRON MICROSCOPY374
349YPG|1|13GTPBP1*GCP*Phe-tRNA*ribosome in the GTPase activation-like state, Structure IIIELECTRON MICROSCOPY374
359YPO|1|13GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIaELECTRON MICROSCOPY374
369YQ1|1|13Vacant ribosome with P-site tRNA, substate 3, Structure IcELECTRON MICROSCOPY2.974
379YQ0|1|13Vacant ribosome with P-site tRNA, substate 2, Structure IbELECTRON MICROSCOPY2.974
389YPZ|1|13Vacant ribosome with P-site tRNA, substate 1, Structure IaELECTRON MICROSCOPY2.974
398XSZ|1|CDCryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA and P-tRNAELECTRON MICROSCOPY3.275
406FEC|1|NHuman cap-dependent 48S pre-initiation complexELECTRON MICROSCOPY6.375
418PJ6|1|wStructure of human 48S translation initiation complex with initiator tRNA, eIF1A and eIF3 (off-pathway)ELECTRON MICROSCOPY2.973
428PJ2|1|wStructure of human 48S translation initiation complex in AUG recognition state after eIF5-induced GTP hydrolysis by eIF2 (48S-2)ELECTRON MICROSCOPY3.475
437A09|1|fStructure of a human ABCE1-bound 43S pre-initiation complex - State IIIELECTRON MICROSCOPY3.575
446ZP4|1|1SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2ELECTRON MICROSCOPY2.975
458PPL|1|IwMERS-CoV Nsp1 bound to the human 43S pre-initiation complexELECTRON MICROSCOPY2.6575
468PJ1|1|wStructure of human 48S translation initiation complex in open codon scanning state (48S-1)ELECTRON MICROSCOPY3.475
478PJ5|1|wStructure of human 48S translation initiation complex after eIF2 release prior 60S subunit joining (48S-5)ELECTRON MICROSCOPY2.975
488PJ4|1|wStructure of human 48S translation initiation complex after eIF5 release (48S-4)ELECTRON MICROSCOPY3.275
498PJ3|1|wStructure of human 48S translation initiation complex upon transfer of initiator tRNA to eIF5B (48S-3)ELECTRON MICROSCOPY3.775
509KN6|1|zyStructure of the HCV IRES-dependent pre-48S translation initiation complex with eIF1A, eIF5B, and eIF3ELECTRON MICROSCOPY3.375
519KRP|1|zyStructure of the HCV IRES-dependent 48S translation initiation complex with eIF5B and eIF3ELECTRON MICROSCOPY3.275
527TQL|1|3CryoEM structure of the human 40S small ribosomal subunit in complex with translation initiation factors eIF1A and eIF5B.ELECTRON MICROSCOPY3.475

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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